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Gene Dmel\Nup54

General Information
Symbol	Dmel\Nup54	Species	D. melanogaster
Name	Nucleoporin 54kD	Annotation symbol	CG8831
Feature type	protein_coding_gene	FlyBase ID	FBgn0033737
Gene Model Status	Current	Stock availability	4 publicly available
Genomic Location
Chromosome (arm)	2R	Recombination map
Cytogenetic map	49A4-49A4	Sequence location	2R:8,315,954..8,318,604 [-]
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 Nucleoporin 54kD is referred to in FlyBase by the symbol Dmel\Nup54 (CG8831, FBgn0033737). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: nucleocytoplasmic transporter activity. There is experimental evidence that it is involved in the biological process: NLS-bearing substrate import into nucleus; protein import into nucleus. 3 alleles are reported. The phenotype of these alleles is annotated with: trichogen cell. It has one annotated transcript and one annotated polypeptide. Protein features are: Nucleoporin Nup54, alpha-helical domain; Nucleoporin Nup54/Nup57/Nup44. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed within 00-06 hour embryonic stages. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: larval central nervous system, larval salivary gland, adult ovary, adult testis. Comments on Affy2 ProbeSet: ProbeSet 1640782_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of Nup54. Gene sequence location is 2R:8315954..8318604.
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 49A4-49A4   Limits computationally determined from genome sequence between P{lacW}l(2)k11404k11404 and P{lacW}fdlk17040
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\Nup54 for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
	Low-frequency RNA-Seq exon junction(s) not annotated. Gene model reviewed during 5.49
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Nup54-RA FBtr0087952  NM_136939   2048   610
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 Nup54-PA   FBpp0087063   64.4   610   8.87     NP_610783   AAF58509
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Nucleoporin Nup54, alpha-helical domain (IPR025712) Nucleoporin Nup54/Nup57/Nup44 (IPR024864)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA264142   AA440760   AA538848   AA802321   AA803470   AA820906   AA950861   AA990808   AE013599 AAF58509   AI061971   AI405307   AI455546   AI456712   AI512200   AI512222   AI512603   AI513498   AI519613   AI519614   AY051713 AAK93137   BF489950   BF492289   BF495132   BF496025   BF496123   BF497352   BF498434   BF500758   BF503458   BF505480   BF505650   BG635597   BI162815   BI173450   BI230361   BI242210   BI242236   BI352581   BI362550   BI370172   BI370431   BI372856   BI375794   BI482239   BI483862   BI578857   BI632159   BI639960   BI640621   BT029947   CO188469   CO267424   CO285971   CO286479   CO315662   CO339182   EC051940   EC054920   EC055270   EC077763   EC195280   EC207339   EC229695   EC260001   EL885501   GH942121   GH945121   GH946469   GH947312   GH947897   GH948962   GH950209   GH952024   GH952043   GH952491   GH957179   GH957595   GH961170   GH963848   GH964321   GH964638   GH966804   GH968272   GH969797   GH971083   GH972839   GH974741   GH978471   GH979368   GH981176   GH982094   GH982229   GH983556   GH984001
UniProtKB/Swiss-Prot	Q9V6B9
UniProtKB/TrEMBL
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 1 -- 3   organism | ubiquitous   (Fisher et al., 2012) Comment:maternally deposited embryonic stage 4 -- 6   organism | ubiquitous   (Fisher et al., 2012) embryonic stage 7 -- 8   antennal anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage central brain anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage dorsal head epidermis anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage visual anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage head mesoderm   (Fisher et al., 2012) organism | ubiquitous   (Fisher et al., 2012) trunk mesoderm   (Fisher et al., 2012) ventral nerve cord primordium   (Fisher et al., 2012) Comment:reported as ventral nerve cord anlage embryonic stage 9 -- 10   central brain primordium   (Fisher et al., 2012) ventral nerve cord primordium   (Fisher et al., 2012) embryonic stage 11 -- 12   anterior midgut primordium   (Fisher et al., 2012) central brain primordium   (Fisher et al., 2012) large intestine primordium   (Fisher et al., 2012) Comment:reported as large intestine specific anlage Malpighian tubule primordium   (Fisher et al., 2012) posterior midgut primordium   (Fisher et al., 2012) ventral nerve cord primordium   (Fisher et al., 2012) embryonic stage 13 -- 16   embryonic brain   (Fisher et al., 2012) embryonic central brain neuron   (Fisher et al., 2012) embryonic Malpighian tubule   (Fisher et al., 2012) embryonic proventriculus   (Fisher et al., 2012) embryonic/larval fat body   (Fisher et al., 2012) embryonic/larval midgut   (Fisher et al., 2012) ventral nerve cord   (Fisher et al., 2012)
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
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 moderate levels in the following post-embryonic organs or tissues: larval central nervous system, larval salivary gland, adult ovary, 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    183.425 Larval Midgut    26.3 Larval Hindgut    56.6 Larval Malpighian Tubules    46.9 Larval Fat Body    71.5 Larval Salivary Gland    103.3 Larval Trachea    77.425 Larval Carcass    55.55 Adult Head    39.9 Adult Eye    52.65 Adult Brain    65.8 Adult Thoracic-Abdominal Ganglion    57.2 Adult Crop    67 Adult Midgut    33.1 Adult Hindgut    40.7 Adult Malpighian Tubules    48.5 Adult Fat Body    32.1 Adult Salivary Gland    59 Adult Heart    35.425 Adult VirginFemale Spermatheca    39.4 Adult InseminatedFemale Spermatheca    41.7 Adult Ovary    335.7 Adult Testis    390.1 Adult Male Accessory Gland    90.9 Adult Carcass    43.1 Expression Level Scale  None   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    183.425 Larval Midgut    26.3 Larval Hindgut    56.6 Larval Malpighian Tubules    46.9 Larval Fat Body    71.5 Larval Salivary Gland    103.3 Larval Trachea    77.425 Larval Carcass    55.55 Adult Head    39.9 Adult Eye    52.65 Adult Brain    65.8 Adult Thoracic-Abdominal Ganglion    57.2 Adult Crop    67 Adult Midgut    33.1 Adult Hindgut    40.7 Adult Malpighian Tubules    48.5 Adult Fat Body    32.1 Adult Salivary Gland    59 Adult Heart    35.425 Adult VirginFemale Spermatheca    39.4 Adult InseminatedFemale Spermatheca    41.7 Adult Ovary    335.7 Adult Testis    390.1 Adult Male Accessory Gland    90.9 Adult Carcass    43.1 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    183.425 Larval Midgut    26.3 Larval Hindgut    56.6 Larval Malpighian Tubules    46.9 Larval Fat Body    71.5 Larval Salivary Gland    103.3 Larval Trachea    77.425 Larval Carcass    55.55 Adult Head    39.9 Adult Eye    52.65 Adult Brain    65.8 Adult Thoracic-Abdominal Ganglion    57.2 Adult Crop    67 Adult Midgut    33.1 Adult Hindgut    40.7 Adult Malpighian Tubules    48.5 Adult Fat Body    32.1 Adult Salivary Gland    59 Adult Heart    35.425 Adult VirginFemale Spermatheca    39.4 Adult InseminatedFemale Spermatheca    41.7 Adult Ovary    335.7 Adult Testis    390.1 Adult Male Accessory Gland    90.9 Adult Carcass    43.1 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    183.425 Larval Midgut    26.3 Larval Hindgut    56.6 Larval Malpighian Tubules    46.9 Larval Fat Body    71.5 Larval Salivary Gland    103.3 Larval Trachea    77.425 Larval Carcass    55.55 Adult Head    39.9 Adult Eye    52.65 Adult Brain    65.8 Adult Thoracic-Abdominal Ganglion    57.2 Adult Crop    67 Adult Midgut    33.1 Adult Hindgut    40.7 Adult Malpighian Tubules    48.5 Adult Fat Body    32.1 Adult Salivary Gland    59 Adult Heart    35.425 Adult VirginFemale Spermatheca    39.4 Adult InseminatedFemale Spermatheca    41.7 Adult Ovary    335.7 Adult Testis    390.1 Adult Male Accessory Gland    90.9 Adult Carcass    43.1 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    183.425 Larval Midgut    26.3 Larval Hindgut    56.6 Larval Malpighian Tubules    46.9 Larval Fat Body    71.5 Larval Salivary Gland    103.3 Larval Trachea    77.425 Larval Carcass    55.55 Adult Head    39.9 Adult Eye    52.65 Adult Brain    65.8 Adult Thoracic-Abdominal Ganglion    57.2 Adult Crop    67 Adult Midgut    33.1 Adult Hindgut    40.7 Adult Malpighian Tubules    48.5 Adult Fat Body    32.1 Adult Salivary Gland    59 Adult Heart    35.425 Adult VirginFemale Spermatheca    39.4 Adult InseminatedFemale Spermatheca    41.7 Adult Ovary    335.7 Adult Testis    390.1 Adult Male Accessory Gland    90.9 Adult Carcass    43.1 Expression Level Scale  None   Low   Moderate   High  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    183.425 Larval Midgut    26.3 Larval Hindgut    56.6 Larval Malpighian Tubules    46.9 Larval Fat Body    71.5 Larval Salivary Gland    103.3 Larval Trachea    77.425 Larval Carcass    55.55 Adult Head    39.9 Adult Eye    52.65 Adult Brain    65.8 Adult Thoracic-Abdominal Ganglion    57.2 Adult Crop    67 Adult Midgut    33.1 Adult Hindgut    40.7 Adult Malpighian Tubules    48.5 Adult Fat Body    32.1 Adult Salivary Gland    59 Adult Heart    35.425 Adult VirginFemale Spermatheca    39.4 Adult InseminatedFemale Spermatheca    41.7 Adult Ovary    335.7 Adult Testis    390.1 Adult Male Accessory Gland    90.9 Adult Carcass    43.1 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    183.425 Larval Midgut    26.3 Larval Hindgut    56.6 Larval Malpighian Tubules    46.9 Larval Fat Body    71.5 Larval Salivary Gland    103.3 Larval Trachea    77.425 Larval Carcass    55.55 Adult Head    39.9 Adult Eye    52.65 Adult Brain    65.8 Adult Thoracic-Abdominal Ganglion    57.2 Adult Crop    67 Adult Midgut    33.1 Adult Hindgut    40.7 Adult Malpighian Tubules    48.5 Adult Fat Body    32.1 Adult Salivary Gland    59 Adult Heart    35.425 Adult VirginFemale Spermatheca    39.4 Adult InseminatedFemale Spermatheca    41.7 Adult Ovary    335.7 Adult Testis    390.1 Adult Male Accessory Gland    90.9 Adult Carcass    43.1 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    183.425 Larval Midgut    26.3 Larval Hindgut    56.6 Larval Malpighian Tubules    46.9 Larval Fat Body    71.5 Larval Salivary Gland    103.3 Larval Trachea    77.425 Larval Carcass    55.55 Adult Head    39.9 Adult Eye    52.65 Adult Brain    65.8 Adult Thoracic-Abdominal Ganglion    57.2 Adult Crop    67 Adult Midgut    33.1 Adult Hindgut    40.7 Adult Malpighian Tubules    48.5 Adult Fat Body    32.1 Adult Salivary Gland    59 Adult Heart    35.425 Adult VirginFemale Spermatheca    39.4 Adult InseminatedFemale Spermatheca    41.7 Adult Ovary    335.7 Adult Testis    390.1 Adult Male Accessory Gland    90.9 Adult Carcass    43.1 Expression Level Scale  None   Low   Moderate   High   Very high  Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut     Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body     Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion     Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body     Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca     Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland     Adult Carcass     FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    no informative data   NA  Eye    52.65   NA  Brain    65.8   183.425  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    57.2   NA  Crop    no informative data   no informative data  Midgut    no informative data   no informative data  Hindgut    no informative data   no informative data  Malpighian Tubules    no informative data   no informative data  Fat Body    no informative data   103.3  Salivary Gland    no informative data   NA  Heart    35.425   77.425  Trachea    NA   NA  VirginFemale Spermatheca    no informative data   NA  InseminatedFemale Spermatheca    no informative data   NA  Ovary    335.7   NA  Testis    390.1   NA  Male Accessory Gland    90.9   no informative data  Carcass    no informative data FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
modENCODE Anatomy RNA-Seq
modENCODE Tissue Expression Data (modENCODE_mRNA-Seq_tissues)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    57 central nervous system, larvae L3    29 central nervous system, pupae P8    10 head, virgin 1-day female    8 head, virgin 4-day female    7 head, virgin 20-day female    7 head, mated 1-day female    6 head, mated 4-day female    7 head, mated 20-day female    7 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    12 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    7 digestive system, 1-day adult    8 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    4 fat body, white prepupae    11 fat body, pupae P8    21 carcass, larvae L3 wandering    19 carcass, 1-day adult    6 carcass, 4-day adult    10 carcass, 20-day adult    9 ovary, virgin 4-day female    97 ovary, mated 4-day female    87 testis, mated 4-day male    116 accessory gland, mated 4-day male    19 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  (57) central nervous system, larvae L3  (29) central nervous system, pupae P8    10 head, virgin 1-day female    8 head, virgin 4-day female    7 head, virgin 20-day female    7 head, mated 1-day female    6 head, mated 4-day female    7 head, mated 20-day female    7 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    12 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    7 digestive system, 1-day adult    8 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    4 fat body, white prepupae    11 fat body, pupae P8    21 carcass, larvae L3 wandering    19 carcass, 1-day adult    6 carcass, 4-day adult    10 carcass, 20-day adult    9 ovary, virgin 4-day female  (97) ovary, mated 4-day female  (87) testis, mated 4-day male  (116) accessory gland, mated 4-day male    19 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    57 central nervous system, larvae L3    29 central nervous system, pupae P8    10 head, virgin 1-day female    8 head, virgin 4-day female    7 head, virgin 20-day female    7 head, mated 1-day female    6 head, mated 4-day female    7 head, mated 20-day female    7 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    12 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    7 digestive system, 1-day adult    8 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    4 fat body, white prepupae    11 fat body, pupae P8    21 carcass, larvae L3 wandering    19 carcass, 1-day adult    6 carcass, 4-day adult    10 carcass, 20-day adult    9 ovary, virgin 4-day female    97 ovary, mated 4-day female    87 testis, mated 4-day male  (116) accessory gland, mated 4-day male    19 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    57 central nervous system, larvae L3    29 central nervous system, pupae P8    10 head, virgin 1-day female    8 head, virgin 4-day female    7 head, virgin 20-day female    7 head, mated 1-day female    6 head, mated 4-day female    7 head, mated 20-day female    7 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    12 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    7 digestive system, 1-day adult    8 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    4 fat body, white prepupae    11 fat body, pupae P8    21 carcass, larvae L3 wandering    19 carcass, 1-day adult    6 carcass, 4-day adult    10 carcass, 20-day adult    9 ovary, virgin 4-day female    97 ovary, mated 4-day female    87 testis, mated 4-day male    116 accessory gland, mated 4-day male    19 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    57 central nervous system, larvae L3    29 central nervous system, pupae P8    10 head, virgin 1-day female    8 head, virgin 4-day female    7 head, virgin 20-day female    7 head, mated 1-day female    6 head, mated 4-day female    7 head, mated 20-day female    7 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    12 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    7 digestive system, 1-day adult    8 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    4 fat body, white prepupae    11 fat body, pupae P8    21 carcass, larvae L3 wandering    19 carcass, 1-day adult    6 carcass, 4-day adult    10 carcass, 20-day adult    9 ovary, virgin 4-day female    97 ovary, mated 4-day female    87 testis, mated 4-day male    116 accessory gland, mated 4-day male    19 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  (57) central nervous system, larvae L3  29 central nervous system, pupae P8    10 head, virgin 1-day female    8 head, virgin 4-day female    7 head, virgin 20-day female    7 head, mated 1-day female    6 head, mated 4-day female    7 head, mated 20-day female    7 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    12 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    7 digestive system, 1-day adult    8 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    4 fat body, white prepupae    11 fat body, pupae P8    21 carcass, larvae L3 wandering    19 carcass, 1-day adult    6 carcass, 4-day adult    10 carcass, 20-day adult    9 ovary, virgin 4-day female  (97) ovary, mated 4-day female  (87) testis, mated 4-day male  (116) accessory gland, mated 4-day male    19 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    57 central nervous system, larvae L3    29 central nervous system, pupae P8    10 head, virgin 1-day female    8 head, virgin 4-day female    7 head, virgin 20-day female    7 head, mated 1-day female    6 head, mated 4-day female    7 head, mated 20-day female    7 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    12 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    7 digestive system, 1-day adult    8 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    4 fat body, white prepupae    11 fat body, pupae P8    21 carcass, larvae L3 wandering    19 carcass, 1-day adult    6 carcass, 4-day adult    10 carcass, 20-day adult    9 ovary, virgin 4-day female    97 ovary, mated 4-day female    87 testis, mated 4-day male  116 accessory gland, mated 4-day male    19 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    57 central nervous system, larvae L3    29 central nervous system, pupae P8    10 head, virgin 1-day female    8 head, virgin 4-day female    7 head, virgin 20-day female    7 head, mated 1-day female    6 head, mated 4-day female    7 head, mated 20-day female    7 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    12 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    7 digestive system, 1-day adult    8 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    4 fat body, white prepupae    11 fat body, pupae P8    21 carcass, larvae L3 wandering    19 carcass, 1-day adult    6 carcass, 4-day adult    10 carcass, 20-day adult    9 ovary, virgin 4-day female    97 ovary, mated 4-day female    87 testis, mated 4-day male    116 accessory gland, mated 4-day male    19 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 moderate 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    69 embryo 02-04hr    59 embryo 04-06hr    36 embryo 06-08hr    30 embryo 08-10hr    23 embryo 10-12hr    17 embryo 12-14hr    13 embryo 14-16hr    14 embryo 16-18hr    16 embryo 18-20hr    19 embryo 20-22hr    12 embryo 22-24hr    11 larva L1    16 larva L2    15 larva L3 12hr old    11 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    12 larva L3 puffstage 7-9    13 white prepupae new    12 white prepupae 12hr    17 white prepupae 24hr    18 pupae 2d postWPP    16 pupae 3d postWPP    12 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    24 adult male 30day    24 adult female 01day    19 adult female 05day    37 adult female 30day    39 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (69) embryo 02-04hr  (59) embryo 04-06hr  (36) embryo 06-08hr  (30) embryo 08-10hr    23 embryo 10-12hr    17 embryo 12-14hr    13 embryo 14-16hr    14 embryo 16-18hr    16 embryo 18-20hr    19 embryo 20-22hr    12 embryo 22-24hr    11 larva L1    16 larva L2    15 larva L3 12hr old    11 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    12 larva L3 puffstage 7-9    13 white prepupae new    12 white prepupae 12hr    17 white prepupae 24hr    18 pupae 2d postWPP    16 pupae 3d postWPP    12 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    24 adult male 30day    24 adult female 01day    19 adult female 05day  (37) adult female 30day  (39) Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    69 embryo 02-04hr    59 embryo 04-06hr    36 embryo 06-08hr    30 embryo 08-10hr    23 embryo 10-12hr    17 embryo 12-14hr    13 embryo 14-16hr    14 embryo 16-18hr    16 embryo 18-20hr    19 embryo 20-22hr    12 embryo 22-24hr    11 larva L1    16 larva L2    15 larva L3 12hr old    11 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    12 larva L3 puffstage 7-9    13 white prepupae new    12 white prepupae 12hr    17 white prepupae 24hr    18 pupae 2d postWPP    16 pupae 3d postWPP    12 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    24 adult male 30day    24 adult female 01day    19 adult female 05day    37 adult female 30day    39 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    69 embryo 02-04hr    59 embryo 04-06hr    36 embryo 06-08hr    30 embryo 08-10hr    23 embryo 10-12hr    17 embryo 12-14hr    13 embryo 14-16hr    14 embryo 16-18hr    16 embryo 18-20hr    19 embryo 20-22hr    12 embryo 22-24hr    11 larva L1    16 larva L2    15 larva L3 12hr old    11 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    12 larva L3 puffstage 7-9    13 white prepupae new    12 white prepupae 12hr    17 white prepupae 24hr    18 pupae 2d postWPP    16 pupae 3d postWPP    12 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    24 adult male 30day    24 adult female 01day    19 adult female 05day    37 adult female 30day    39 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    69 embryo 02-04hr    59 embryo 04-06hr    36 embryo 06-08hr    30 embryo 08-10hr    23 embryo 10-12hr    17 embryo 12-14hr    13 embryo 14-16hr    14 embryo 16-18hr    16 embryo 18-20hr    19 embryo 20-22hr    12 embryo 22-24hr    11 larva L1    16 larva L2    15 larva L3 12hr old    11 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    12 larva L3 puffstage 7-9    13 white prepupae new    12 white prepupae 12hr    17 white prepupae 24hr    18 pupae 2d postWPP    16 pupae 3d postWPP    12 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    24 adult male 30day    24 adult female 01day    19 adult female 05day    37 adult female 30day    39 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (69) embryo 02-04hr  (59) embryo 04-06hr  (36) embryo 06-08hr  30 embryo 08-10hr    23 embryo 10-12hr    17 embryo 12-14hr    13 embryo 14-16hr    14 embryo 16-18hr    16 embryo 18-20hr    19 embryo 20-22hr    12 embryo 22-24hr    11 larva L1    16 larva L2    15 larva L3 12hr old    11 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    12 larva L3 puffstage 7-9    13 white prepupae new    12 white prepupae 12hr    17 white prepupae 24hr    18 pupae 2d postWPP    16 pupae 3d postWPP    12 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    24 adult male 30day    24 adult female 01day    19 adult female 05day  (37) adult female 30day  (39) Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    69 embryo 02-04hr    59 embryo 04-06hr    36 embryo 06-08hr    30 embryo 08-10hr    23 embryo 10-12hr    17 embryo 12-14hr    13 embryo 14-16hr    14 embryo 16-18hr    16 embryo 18-20hr    19 embryo 20-22hr    12 embryo 22-24hr    11 larva L1    16 larva L2    15 larva L3 12hr old    11 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    12 larva L3 puffstage 7-9    13 white prepupae new    12 white prepupae 12hr    17 white prepupae 24hr    18 pupae 2d postWPP    16 pupae 3d postWPP    12 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    24 adult male 30day    24 adult female 01day    19 adult female 05day    37 adult female 30day    39 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    69 embryo 02-04hr    59 embryo 04-06hr    36 embryo 06-08hr    30 embryo 08-10hr    23 embryo 10-12hr    17 embryo 12-14hr    13 embryo 14-16hr    14 embryo 16-18hr    16 embryo 18-20hr    19 embryo 20-22hr    12 embryo 22-24hr    11 larva L1    16 larva L2    15 larva L3 12hr old    11 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    12 larva L3 puffstage 7-9    13 white prepupae new    12 white prepupae 12hr    17 white prepupae 24hr    18 pupae 2d postWPP    16 pupae 3d postWPP    12 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    24 adult male 30day    24 adult female 01day    19 adult female 05day    37 adult female 30day    39 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+    103 Schneider line 2 Sg4    50 embryonic 1182-4H    48 embryonic GM2    43 embryonic Kc167    45 embryonic S1    33 embryonic S3    64 leg disc CME L1    43 wing disc CME-W2    29 wing disc ML-DmD8    38 wing disc ML-DmD9    42 wing disc ML-DmD16-c3    46 wing disc ML-DmD21    59 wing disc ML-DmD32    39 haltere disc ML-DmD17-c3    57 eye-antennal disc ML-DmD11    36 antennal disc ML-DmD20-c5    55 mixed discs ML-DmD4-c1    45 CNS ML-DmBG1-c1    58 CNS ML-DmBG2-c2    34 tumorous blood cells mbn2    26 ovary fGS/OSS    48 ovary OSC    32 ovary OSS    17 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  (103) Schneider line 2 Sg4  (50) embryonic 1182-4H  (48) embryonic GM2  (43) embryonic Kc167  (45) embryonic S1  (33) embryonic S3  (64) leg disc CME L1  (43) wing disc CME-W2  (29) wing disc ML-DmD8  (38) wing disc ML-DmD9  (42) wing disc ML-DmD16-c3  (46) wing disc ML-DmD21  (59) wing disc ML-DmD32  (39) haltere disc ML-DmD17-c3  (57) eye-antennal disc ML-DmD11  (36) antennal disc ML-DmD20-c5  (55) mixed discs ML-DmD4-c1  (45) CNS ML-DmBG1-c1  (58) CNS ML-DmBG2-c2  (34) tumorous blood cells mbn2  26 ovary fGS/OSS  (48) ovary OSC  (32) ovary OSS    17 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+  103 Schneider line 2 Sg4    50 embryonic 1182-4H    48 embryonic GM2    43 embryonic Kc167    45 embryonic S1    33 embryonic S3    64 leg disc CME L1    43 wing disc CME-W2    29 wing disc ML-DmD8    38 wing disc ML-DmD9    42 wing disc ML-DmD16-c3    46 wing disc ML-DmD21    59 wing disc ML-DmD32    39 haltere disc ML-DmD17-c3    57 eye-antennal disc ML-DmD11    36 antennal disc ML-DmD20-c5    55 mixed discs ML-DmD4-c1    45 CNS ML-DmBG1-c1    58 CNS ML-DmBG2-c2    34 tumorous blood cells mbn2    26 ovary fGS/OSS    48 ovary OSC    32 ovary OSS    17 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+    103 Schneider line 2 Sg4    50 embryonic 1182-4H    48 embryonic GM2    43 embryonic Kc167    45 embryonic S1    33 embryonic S3    64 leg disc CME L1    43 wing disc CME-W2    29 wing disc ML-DmD8    38 wing disc ML-DmD9    42 wing disc ML-DmD16-c3    46 wing disc ML-DmD21    59 wing disc ML-DmD32    39 haltere disc ML-DmD17-c3    57 eye-antennal disc ML-DmD11    36 antennal disc ML-DmD20-c5    55 mixed discs ML-DmD4-c1    45 CNS ML-DmBG1-c1    58 CNS ML-DmBG2-c2    34 tumorous blood cells mbn2    26 ovary fGS/OSS    48 ovary OSC    32 ovary OSS    17 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    103 Schneider line 2 Sg4    50 embryonic 1182-4H    48 embryonic GM2    43 embryonic Kc167    45 embryonic S1    33 embryonic S3    64 leg disc CME L1    43 wing disc CME-W2    29 wing disc ML-DmD8    38 wing disc ML-DmD9    42 wing disc ML-DmD16-c3    46 wing disc ML-DmD21    59 wing disc ML-DmD32    39 haltere disc ML-DmD17-c3    57 eye-antennal disc ML-DmD11    36 antennal disc ML-DmD20-c5    55 mixed discs ML-DmD4-c1    45 CNS ML-DmBG1-c1    58 CNS ML-DmBG2-c2    34 tumorous blood cells mbn2    26 ovary fGS/OSS    48 ovary OSC    32 ovary OSS    17 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  (103) Schneider line 2 Sg4  (50) embryonic 1182-4H  (48) embryonic GM2  (43) embryonic Kc167  (45) embryonic S1  (33) embryonic S3  (64) leg disc CME L1  (43) wing disc CME-W2  29 wing disc ML-DmD8  (38) wing disc ML-DmD9  (42) wing disc ML-DmD16-c3  (46) wing disc ML-DmD21  (59) wing disc ML-DmD32  (39) haltere disc ML-DmD17-c3  (57) eye-antennal disc ML-DmD11  (36) antennal disc ML-DmD20-c5  (55) mixed discs ML-DmD4-c1  (45) CNS ML-DmBG1-c1  (58) CNS ML-DmBG2-c2  (34) tumorous blood cells mbn2  26 ovary fGS/OSS  (48) ovary OSC  32 ovary OSS    17 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+  103 Schneider line 2 Sg4    50 embryonic 1182-4H    48 embryonic GM2    43 embryonic Kc167    45 embryonic S1    33 embryonic S3    64 leg disc CME L1    43 wing disc CME-W2    29 wing disc ML-DmD8    38 wing disc ML-DmD9    42 wing disc ML-DmD16-c3    46 wing disc ML-DmD21    59 wing disc ML-DmD32    39 haltere disc ML-DmD17-c3    57 eye-antennal disc ML-DmD11    36 antennal disc ML-DmD20-c5    55 mixed discs ML-DmD4-c1    45 CNS ML-DmBG1-c1    58 CNS ML-DmBG2-c2    34 tumorous blood cells mbn2    26 ovary fGS/OSS    48 ovary OSC    32 ovary OSS    17 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+    103 Schneider line 2 Sg4    50 embryonic 1182-4H    48 embryonic GM2    43 embryonic Kc167    45 embryonic S1    33 embryonic S3    64 leg disc CME L1    43 wing disc CME-W2    29 wing disc ML-DmD8    38 wing disc ML-DmD9    42 wing disc ML-DmD16-c3    46 wing disc ML-DmD21    59 wing disc ML-DmD32    39 haltere disc ML-DmD17-c3    57 eye-antennal disc ML-DmD11    36 antennal disc ML-DmD20-c5    55 mixed discs ML-DmD4-c1    45 CNS ML-DmBG1-c1    58 CNS ML-DmBG2-c2    34 tumorous blood cells mbn2    26 ovary fGS/OSS    48 ovary OSC    32 ovary OSS    17 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    30 cold shock, 4-day adult    16 heat shock, 4-day adult    31 Cadmium 50 mM 6 hrs, larvae L3    12 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult    28 Cadmium 100 mM 48 hrs, 4-day adult    68 Copper 0.5 mM 12 hrs, larvae L3    7 Copper 15 mM 48 hrs, 4-day adult    42 Zinc 5 mM 12 hrs, larvae L3    10 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3    64 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    12 Caffeine 1.5 mg/ml 4 hrs, larvae L3    8 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    60 Caffeine 25 mg/ml 48 hrs, 4-day adult    21 Paraquat 5 mM 48 hrs, 4-day adult    51 Paraquat 10 mM 48 hrs, 4-day adult    50 Rotenone 2 μg 12 hrs, larvae L3    14 Rotenone 8 μg 12 hrs, larvae L3    12 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult  (30) cold shock, 4-day adult    16 heat shock, 4-day adult  (31) Cadmium 50 mM 6 hrs, larvae L3    12 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult  (28) Cadmium 100 mM 48 hrs, 4-day adult  (68) Copper 0.5 mM 12 hrs, larvae L3    7 Copper 15 mM 48 hrs, 4-day adult  (42) Zinc 5 mM 12 hrs, larvae L3    10 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3  (64) Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    12 Caffeine 1.5 mg/ml 4 hrs, larvae L3    8 Caffeine 2.5 mg/ml 48 hrs, 4-day adult  (60) Caffeine 25 mg/ml 48 hrs, 4-day adult    21 Paraquat 5 mM 48 hrs, 4-day adult  (51) Paraquat 10 mM 48 hrs, 4-day adult  (50) Rotenone 2 μg 12 hrs, larvae L3    14 Rotenone 8 μg 12 hrs, larvae L3    12 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    30 cold shock, 4-day adult    16 heat shock, 4-day adult    31 Cadmium 50 mM 6 hrs, larvae L3    12 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult    28 Cadmium 100 mM 48 hrs, 4-day adult    68 Copper 0.5 mM 12 hrs, larvae L3    7 Copper 15 mM 48 hrs, 4-day adult    42 Zinc 5 mM 12 hrs, larvae L3    10 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3    64 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    12 Caffeine 1.5 mg/ml 4 hrs, larvae L3    8 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    60 Caffeine 25 mg/ml 48 hrs, 4-day adult    21 Paraquat 5 mM 48 hrs, 4-day adult    51 Paraquat 10 mM 48 hrs, 4-day adult    50 Rotenone 2 μg 12 hrs, larvae L3    14 Rotenone 8 μg 12 hrs, larvae L3    12 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    30 cold shock, 4-day adult    16 heat shock, 4-day adult    31 Cadmium 50 mM 6 hrs, larvae L3    12 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult    28 Cadmium 100 mM 48 hrs, 4-day adult    68 Copper 0.5 mM 12 hrs, larvae L3    7 Copper 15 mM 48 hrs, 4-day adult    42 Zinc 5 mM 12 hrs, larvae L3    10 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3    64 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    12 Caffeine 1.5 mg/ml 4 hrs, larvae L3    8 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    60 Caffeine 25 mg/ml 48 hrs, 4-day adult    21 Paraquat 5 mM 48 hrs, 4-day adult    51 Paraquat 10 mM 48 hrs, 4-day adult    50 Rotenone 2 μg 12 hrs, larvae L3    14 Rotenone 8 μg 12 hrs, larvae L3    12 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    30 cold shock, 4-day adult    16 heat shock, 4-day adult    31 Cadmium 50 mM 6 hrs, larvae L3    12 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult    28 Cadmium 100 mM 48 hrs, 4-day adult    68 Copper 0.5 mM 12 hrs, larvae L3    7 Copper 15 mM 48 hrs, 4-day adult    42 Zinc 5 mM 12 hrs, larvae L3    10 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3    64 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    12 Caffeine 1.5 mg/ml 4 hrs, larvae L3    8 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    60 Caffeine 25 mg/ml 48 hrs, 4-day adult    21 Paraquat 5 mM 48 hrs, 4-day adult    51 Paraquat 10 mM 48 hrs, 4-day adult    50 Rotenone 2 μg 12 hrs, larvae L3    14 Rotenone 8 μg 12 hrs, larvae L3    12 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  30 cold shock, 4-day adult    16 heat shock, 4-day adult  31 Cadmium 50 mM 6 hrs, larvae L3    12 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult  28 Cadmium 100 mM 48 hrs, 4-day adult  (68) Copper 0.5 mM 12 hrs, larvae L3    7 Copper 15 mM 48 hrs, 4-day adult  (42) Zinc 5 mM 12 hrs, larvae L3    10 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3  (64) Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    12 Caffeine 1.5 mg/ml 4 hrs, larvae L3    8 Caffeine 2.5 mg/ml 48 hrs, 4-day adult  (60) Caffeine 25 mg/ml 48 hrs, 4-day adult    21 Paraquat 5 mM 48 hrs, 4-day adult  (51) Paraquat 10 mM 48 hrs, 4-day adult  (50) Rotenone 2 μg 12 hrs, larvae L3    14 Rotenone 8 μg 12 hrs, larvae L3    12 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    30 cold shock, 4-day adult    16 heat shock, 4-day adult    31 Cadmium 50 mM 6 hrs, larvae L3    12 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult    28 Cadmium 100 mM 48 hrs, 4-day adult    68 Copper 0.5 mM 12 hrs, larvae L3    7 Copper 15 mM 48 hrs, 4-day adult    42 Zinc 5 mM 12 hrs, larvae L3    10 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3    64 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    12 Caffeine 1.5 mg/ml 4 hrs, larvae L3    8 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    60 Caffeine 25 mg/ml 48 hrs, 4-day adult    21 Paraquat 5 mM 48 hrs, 4-day adult    51 Paraquat 10 mM 48 hrs, 4-day adult    50 Rotenone 2 μg 12 hrs, larvae L3    14 Rotenone 8 μg 12 hrs, larvae L3    12 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    30 cold shock, 4-day adult    16 heat shock, 4-day adult    31 Cadmium 50 mM 6 hrs, larvae L3    12 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult    28 Cadmium 100 mM 48 hrs, 4-day adult    68 Copper 0.5 mM 12 hrs, larvae L3    7 Copper 15 mM 48 hrs, 4-day adult    42 Zinc 5 mM 12 hrs, larvae L3    10 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3    64 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    12 Caffeine 1.5 mg/ml 4 hrs, larvae L3    8 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    60 Caffeine 25 mg/ml 48 hrs, 4-day adult    21 Paraquat 5 mM 48 hrs, 4-day adult    51 Paraquat 10 mM 48 hrs, 4-day adult    50 Rotenone 2 μg 12 hrs, larvae L3    14 Rotenone 8 μg 12 hrs, larvae L3    12 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_01 mE1_20_mRNA_expression_cluster_09
External Data & Images
Linkouts	BDGP expression data • LD24841 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0033737 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG8831-RA FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for Nup54 Stages(s) 1-3 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 Nup54GD14041 Other Phenotypes Allele visible, with Scer\GAL4pnr-MD237 Nup54GD14041 Phenotype manifest in Allele trichogen cell, with Scer\GAL4pnr-MD237 Nup54GD14041
Classical Alleles ( 1 )
For All Classical Alleles Show
Allele of Nup54 Class Mutagen Stocks Known lesion Nup54MB03363 1 --
Alleles Carried on Transgenic Constructs ( 2 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Nup54 Class Mutagen Stocks Known lesion Nup54GD14041 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes Nup54KK102105 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes
Aneuploid Aberrations
Disrupted in	Df(2R)Exel6061 (Ryder, 2004.4.26)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data
Insertions
	Type of insertions Name Expression data miscellaneous insertions P{wHy}DG10812 NA insertion of enhancer trap binary system Mi{ET1}Nup54MB03363 No
Gene Ontology: Function, Process & Cellular Component ( 6 unique terms )
Terms Based on Experimental Evidence ( 3 terms )
Molecular Function
CV term Evidence References
nucleocytoplasmic transporter activity inferred from mutant phenotype (Sabri et al., 2007)
Biological Process
CV term Evidence References
NLS-bearing substrate import into nucleus inferred from mutant phenotype (Sabri et al., 2007, Chen and Xu, 2010) protein import into nucleus inferred from mutant phenotype (Sabri et al., 2007)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 4 terms )
Molecular Function
CV term Evidence References
nucleocytoplasmic transporter activity inferred from sequence or structural similarity with UniProtKB:P70582 (assigned by UniProtKB) (Swiss-Prot Project Members, 2004.3.15)
Biological Process
CV term Evidence References
nucleocytoplasmic transport inferred from sequence or structural similarity with UniProtKB:P70582 (assigned by UniProtKB) (Swiss-Prot Project Members, 2004.3.15) protein targeting inferred from sequence or structural similarity with UniProtKB:P70582 (assigned by UniProtKB) (Swiss-Prot Project Members, 2004.3.15)
Cellular Component
CV term Evidence References
nuclear pore inferred from sequence or structural similarity with EMBL:U63840 (FlyBase, 1992-) inferred from sequence or structural similarity with UniProtKB:P70582 (assigned by UniProtKB) (Swiss-Prot Project Members, 2004.3.15)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
Nup54 - Arc1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Nup54 - CG1532 experimental knowledge based, anti tag coimmunoprecipitation, peptide massfingerprinting (Guruharsha et al., 2011, Mintseris et al., 2009.11.23) Nup54 - CG18081 anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based (Mintseris et al., 2009.11.23, Guruharsha et al., 2011) Nup54 - Gale anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Nup54 - RpS12 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Nup54 - RpS21 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Nup54 - Smu1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Nup54 - Treh anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Nup54 - krz experimental knowledge based, anti tag coimmunoprecipitation, peptide massfingerprinting (Guruharsha et al., 2011, Mintseris et al., 2009.11.23)
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions Nup54 allele Gene References
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 62137 DPiM - DPiM, Drosophila Protein interaction Map • FBgn0033737 DroID - A comprehensive database of gene and protein interactions. • FBgn0033737 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 36360
Orthologs
OrthoDB Orthologs (38) - 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 EOG61ZFWS Dipteran inclusive ortholog search EOG6MGSH0 Insect inclusive ortholog search EOG6D7X2N Arthropod inclusive ortholog search EOG6CZ8XT Metazoa inclusive ortholog search EOG69GZ9F
Orthologs in Drosophila Species (EOG61ZFWS)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\Nup54     Drosophila simulans   Dsim\GD25840 Y   Drosophila sechellia   Dsec\GM20361 Y   Drosophila erecta   Dere\GG22579 Y   Drosophila yakuba   Dyak\GE13448 Y   Drosophila ananassae   Dana\GF12062 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA21354 Y   Drosophila persimilis   Dper\GL10909 Y   Drosophila willistoni   Dwil\GK20850 Y   Drosophila virilis   Dvir\GJ22330 Y   Drosophila mojavensis   Dmoj\GI20480 Y   Drosophila grimshawi   Dgri\GH21193 Y
Orthologs in non-Drosophila Dipterans (EOG6MGSH0)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL006544   Anopheles gambiae Malaria mosquito  Agam\AGAP006031   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ010583
Orthologs in non-Dipteran Insects (EOG6D7X2N)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\GB49132   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG003665   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH14867   Atta cephalotes Leafcutter ant  Acep\ACEP18429   Camponotus floridanus Florida carpenter ant  Cflo\CFLO20504   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL15164   Linepithema humile Argentine ant  Lhum\LH10937   Pogonomyrmex barbatus Red harvester ant  Pbar\PB17116   Solenopsis invicta Red fire ant  Sinv\SINV18005   Acyrthosiphon pisum Pea aphid  Apim\ACYPI083890   Acyrthosiphon pisum Pea aphid  Apim\ACYPI069524   Acyrthosiphon pisum Pea aphid  Apim\ACYPI001562   Pediculus humanus Human body louse  Phum\PHUM253150   Tribolium castaneum Red flour beetle  Tcas\TC001231
Orthologs in non-Insect Arthropods (EOG6CZ8XT)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\JGI_V11_306090   Ixodes scapularis Deer tick  Isca\ISCW017334
Orthologs in non-Arthropod Metazoa (EOG69GZ9F)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Caenorhabditis elegans Nematode  Cele\npp-1   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_011789gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_002619gn   Danio rerio Zebrafish  Drer\ENSDARG00000045348   Xenopus tropicalis Western clawed frog  Xtro\nup54   Gallus gallus Domestic chicken  Ggal\NUP54   Rattus norvegicus Norway rat  Rnor\Nup54
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD25840 Drosophila sechellia Dsec\GM20361 Drosophila erecta Dere\GG22579 Drosophila yakuba Dyak\GE13448 Drosophila ananassae Dana\GF12062 Drosophila pseudoobscura pseudoobscura Dpse\GA21354 Drosophila persimilis Dper\GL10909 Drosophila willistoni Dwil\GK20850 Drosophila virilis Dvir\GJ22330 Drosophila mojavensis Dmoj\GI20480 Drosophila grimshawi Dgri\GH21193
Stocks & Reagents
Stocks Listed in FlyBase ( 4 )
Bloomington	23536 w1118; Mi{ET1}Nup54MB03363/SM6a
VDRC	v103724 P{KK102105}VIE-260B v42153 w1118; P{GD14041}v42153 v42154 w1118; P{GD14041}v42154
Genomic Clones ( 2 )
	BACR24H09 BACR37P06 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 91 )
	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	LD24841
Other clones	DPiM_LD24841 IP16983
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	AT03973 AT07715 AT07920 AT09730 AT09840 AT11508 AT12840 AT15780 AT19450 AT26195 AT29202 GH25264 GH26616 GM04201 GM13246 GM19888 LD07769 LD15633 LD18470 LD31012 LD34703 LD35083 LD36828 LD39260 LD39262 LD43960 LD43987 LD44522 RE02051 RE10158 RE16370 RE39486 RE39521 RE47141 RE56590 RE56943 RE60044 RE63667 RE64901 RE66818 RE72788 SD13052 SD22690 SD23556 SD25773
Other clones	157074 214477.29 CK01.50A.C4 CK01.78D.B10 EC051940 EC054920 EC055270 EK040342 EK061329 EK062932 EK150105 EK262128 EP01027 IP16883 RP004055017 RP004064207 RP004143591 RP004149858 RP004150892 RP004175491 RP004193116 RP004203112 RP004203771 RP004209387 RP004210929 RP004219528 RP004223472 RP004224897 RP004233523 RP004234837 RP004251054 RP004259204 RP004260044 RP004357820 RP004391116 RP004417666 RP004436596 RP004457078 RP004475672 RP004500860 RP004505535 RP004511355 RP004537825
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0033737 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 36360
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: Nup54 CG8831 (Gawlinski et al., 2007)
Source for database merge of
Additional comments
Other Comments
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_136939 RefSeq (Proteins) • NP_610783 DDBJ / EMBL / GenBank • AA820906 AAF58509 AAK93137 AI455546 AY051713 Entrez Gene - A searchable database of RefSeq genes. • 36360 UniProtKB/Swiss-Prot • Q9V6B9
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Nucleoporin Nup54, alpha-helical domain (IPR025712) Nucleoporin Nup54/Nup57/Nup44 (IPR024864) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • LD24841
Linkouts
	BioGRID - A database of protein and genetic interactions • 62137 DPiM - DPiM, Drosophila Protein interaction Map • FBgn0033737 DroID - A comprehensive database of gene and protein interactions. • FBgn0033737 DRSC - Results from RNAi screens. • FBgn0033737 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0033737 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG8831-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0033737 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 36360 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 36360 modMine - Data generated by the modENCODE project. • FBgn0033737
Synonyms & Secondary IDs ( 5 )
Reported As
Symbol Synonym	CG8831 (Gawlinski et al., 2007, Keleman et al., 2009.8.5, Sabri et al., 2007) Nup54 (Gawlinski et al., 2007, Sabri et al., 2007, Neumann et al., 2010) nup54 (Sabri et al., 2007, Chen and Xu, 2010)
Name Synonym	Nucleoporin 54   Nucleoporin 54kD
Secondary FlyBase IDs
References ( 24 )
Generate a list of	All references relating to this gene ( 24 )
List References by type	Research paper  ( 4 ) Supplementary material  ( 7 ) Personal communication to FlyBase  ( 7 ) FlyBase analysis  ( 2 ) Protein sequence record  ( 1 ) Website  ( 1 ) Curated genome annotation  ( 2 )
Recent research papers (0)
	All research papers listed in FlyBase were published before 2011 Show research papers ...