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Gene Dmel\Upf1

General Information
Symbol	Dmel\Upf1	Species	D. melanogaster
Name	Upf1	Annotation symbol	CG1559
Feature type	protein_coding_gene	FlyBase ID	FBgn0030354
Gene Model Status	Current	Stock availability	3 publicly available
Genomic Location
Chromosome (arm)	X	Recombination map
Cytogenetic map	10F4-10F4	Sequence location	X:11,794,029..11,799,404 [-]
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 Upf1 is referred to in FlyBase by the symbol Dmel\Upf1 (CG1559, FBgn0030354). It is a protein_coding_gene from Drosophila melanogaster. Based on sequence similarity, it is predicted to have molecular function: helicase activity. There is experimental evidence that it is involved in the biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; cellular response to hypoxia. 14 alleles are reported. The phenotype of these alleles is annotated with: dorsal appendage. It has 2 annotated transcripts and 2 annotated polypeptides. Protein features are: RNA helicase UPF1, UPF2-interacting domain. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of moderate expression. Peak expression observed within 00-18 hour embryonic stages, during early larval stages, during early pupal stages, in adult female stages. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: adult eye, larval/adult central nervous system, larval/adult salivary gland, larval trachea, adult ovary, adult male reproductive system. Comments on Affy2 ProbeSet: ProbeSet 1623513_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of Upf1. Gene sequence location is X:11794470..11799373.
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.
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FB2013_03	Alleles Upf1[D45B.Scer\UAS] Controlled Vocabulary Terms positive regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Transcripts Upf1-RB Transgenic Constructs P{UAS-Upf1.D45B} Polypeptides Upf1-PB
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 10F4-10F4   Limits computationally determined from genome sequence between P{EP}ATP7EP308 and P{EP}EP1451&P{EP}EP1629
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\Upf1 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 5.51 Low-frequency RNA-Seq exon junction(s) not annotated. Annotated transcripts do not represent all supported alternative splices within 5' UTR.
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Upf1-RA FBtr0073596  NM_132539   5187   1180 Upf1-RB FBtr0342744     4709   1180
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 Upf1-PA   FBpp0073433   129.9   1180   7.34     NP_572767   AAF48115 Upf1-PB   FBpp0309612   129.9   1180   7.34
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • RNA helicase UPF1, UPF2-interacting domain (IPR018999) P-loop containing nucleoside triphosphate hydrolase (IPR027417)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA441347   AA536340   AA941583   AA950499   AE014298 AAF48115   AI110070   AW943020   AY061379 AAL28927   BG632492   BG638122   BG638452   BI353211   BI366995   BI639461   CK132153   CK132223   CK604421   CK604422   CK604815   CK604816   CO188431   CO195839   CO269187   CO277224   CO280589   CO325478   CO339284   CO342352   CO343417   EC057259   EC071183   EC084802   EC220596   EC225597   EC233853   EC248488   EC254295   EC256038   EC256159
UniProtKB/Swiss-Prot	Q9VYS3
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
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
colocalizes_with exon-exon junction complex inferred from direct assay (Guruharsha et al., 2011)
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: adult eye, larval/adult central nervous system, larval/adult salivary gland, larval trachea, adult ovary, adult male reproductive system. [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    128.325 Larval Midgut    62.5 Larval Hindgut    68.5 Larval Malpighian Tubules    72.6 Larval Fat Body    54.1 Larval Salivary Gland    101.9 Larval Trachea    184.35 Larval Carcass    87.75 Adult Head    59.2 Adult Eye    126.45 Adult Brain    122.5 Adult Thoracic-Abdominal Ganglion    103.1 Adult Crop    75.1 Adult Midgut    76 Adult Hindgut    71.9 Adult Malpighian Tubules    30.9 Adult Fat Body    50.8 Adult Salivary Gland    127.4 Adult Heart    79.625 Adult VirginFemale Spermatheca    29.4 Adult InseminatedFemale Spermatheca    31.8 Adult Ovary    136.8 Adult Testis    101.7 Adult Male Accessory Gland    161.9 Adult Carcass    58.3 Expression Level Scale  None   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    128.325 Larval Midgut    62.5 Larval Hindgut    68.5 Larval Malpighian Tubules    72.6 Larval Fat Body    54.1 Larval Salivary Gland    101.9 Larval Trachea    184.35 Larval Carcass    87.75 Adult Head    59.2 Adult Eye    126.45 Adult Brain    122.5 Adult Thoracic-Abdominal Ganglion    103.1 Adult Crop    75.1 Adult Midgut    76 Adult Hindgut    71.9 Adult Malpighian Tubules    30.9 Adult Fat Body    50.8 Adult Salivary Gland    127.4 Adult Heart    79.625 Adult VirginFemale Spermatheca    29.4 Adult InseminatedFemale Spermatheca    31.8 Adult Ovary    136.8 Adult Testis    101.7 Adult Male Accessory Gland    161.9 Adult Carcass    58.3 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    128.325 Larval Midgut    62.5 Larval Hindgut    68.5 Larval Malpighian Tubules    72.6 Larval Fat Body    54.1 Larval Salivary Gland    101.9 Larval Trachea    184.35 Larval Carcass    87.75 Adult Head    59.2 Adult Eye    126.45 Adult Brain    122.5 Adult Thoracic-Abdominal Ganglion    103.1 Adult Crop    75.1 Adult Midgut    76 Adult Hindgut    71.9 Adult Malpighian Tubules    30.9 Adult Fat Body    50.8 Adult Salivary Gland    127.4 Adult Heart    79.625 Adult VirginFemale Spermatheca    29.4 Adult InseminatedFemale Spermatheca    31.8 Adult Ovary    136.8 Adult Testis    101.7 Adult Male Accessory Gland    161.9 Adult Carcass    58.3 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    128.325 Larval Midgut    62.5 Larval Hindgut    68.5 Larval Malpighian Tubules    72.6 Larval Fat Body    54.1 Larval Salivary Gland    101.9 Larval Trachea    184.35 Larval Carcass    87.75 Adult Head    59.2 Adult Eye    126.45 Adult Brain    122.5 Adult Thoracic-Abdominal Ganglion    103.1 Adult Crop    75.1 Adult Midgut    76 Adult Hindgut    71.9 Adult Malpighian Tubules    30.9 Adult Fat Body    50.8 Adult Salivary Gland    127.4 Adult Heart    79.625 Adult VirginFemale Spermatheca    29.4 Adult InseminatedFemale Spermatheca    31.8 Adult Ovary    136.8 Adult Testis    101.7 Adult Male Accessory Gland    161.9 Adult Carcass    58.3 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    128.325 Larval Midgut    62.5 Larval Hindgut    68.5 Larval Malpighian Tubules    72.6 Larval Fat Body    54.1 Larval Salivary Gland    101.9 Larval Trachea    184.35 Larval Carcass    87.75 Adult Head    59.2 Adult Eye    126.45 Adult Brain    122.5 Adult Thoracic-Abdominal Ganglion    103.1 Adult Crop    75.1 Adult Midgut    76 Adult Hindgut    71.9 Adult Malpighian Tubules    30.9 Adult Fat Body    50.8 Adult Salivary Gland    127.4 Adult Heart    79.625 Adult VirginFemale Spermatheca    29.4 Adult InseminatedFemale Spermatheca    31.8 Adult Ovary    136.8 Adult Testis    101.7 Adult Male Accessory Gland    161.9 Adult Carcass    58.3 Expression Level Scale  None   Low   Moderate  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    128.325 Larval Midgut    62.5 Larval Hindgut    68.5 Larval Malpighian Tubules    72.6 Larval Fat Body    54.1 Larval Salivary Gland    101.9 Larval Trachea    184.35 Larval Carcass    87.75 Adult Head    59.2 Adult Eye    126.45 Adult Brain    122.5 Adult Thoracic-Abdominal Ganglion    103.1 Adult Crop    75.1 Adult Midgut    76 Adult Hindgut    71.9 Adult Malpighian Tubules    30.9 Adult Fat Body    50.8 Adult Salivary Gland    127.4 Adult Heart    79.625 Adult VirginFemale Spermatheca    29.4 Adult InseminatedFemale Spermatheca    31.8 Adult Ovary    136.8 Adult Testis    101.7 Adult Male Accessory Gland    161.9 Adult Carcass    58.3 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    128.325 Larval Midgut    62.5 Larval Hindgut    68.5 Larval Malpighian Tubules    72.6 Larval Fat Body    54.1 Larval Salivary Gland    101.9 Larval Trachea    184.35 Larval Carcass    87.75 Adult Head    59.2 Adult Eye    126.45 Adult Brain    122.5 Adult Thoracic-Abdominal Ganglion    103.1 Adult Crop    75.1 Adult Midgut    76 Adult Hindgut    71.9 Adult Malpighian Tubules    30.9 Adult Fat Body    50.8 Adult Salivary Gland    127.4 Adult Heart    79.625 Adult VirginFemale Spermatheca    29.4 Adult InseminatedFemale Spermatheca    31.8 Adult Ovary    136.8 Adult Testis    101.7 Adult Male Accessory Gland    161.9 Adult Carcass    58.3 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    128.325 Larval Midgut    62.5 Larval Hindgut    68.5 Larval Malpighian Tubules    72.6 Larval Fat Body    54.1 Larval Salivary Gland    101.9 Larval Trachea    184.35 Larval Carcass    87.75 Adult Head    59.2 Adult Eye    126.45 Adult Brain    122.5 Adult Thoracic-Abdominal Ganglion    103.1 Adult Crop    75.1 Adult Midgut    76 Adult Hindgut    71.9 Adult Malpighian Tubules    30.9 Adult Fat Body    50.8 Adult Salivary Gland    127.4 Adult Heart    79.625 Adult VirginFemale Spermatheca    29.4 Adult InseminatedFemale Spermatheca    31.8 Adult Ovary    136.8 Adult Testis    101.7 Adult Male Accessory Gland    161.9 Adult Carcass    58.3 Expression Level Scale  None   Low   Moderate   High   Very high  Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut     Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body     Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion     Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body     Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca     Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland     Adult Carcass     FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    59.2   NA  Eye    126.45   NA  Brain    122.5   128.325  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    103.1   NA  Crop    75.1   62.5  Midgut    76   68.5  Hindgut    71.9   72.6  Malpighian Tubules    30.9   54.1  Fat Body    50.8   101.9  Salivary Gland    127.4   NA  Heart    79.625   184.35  Trachea    NA   NA  VirginFemale Spermatheca    29.4   NA  InseminatedFemale Spermatheca    31.8   NA  Ovary    136.8   NA  Testis    101.7   NA  Male Accessory Gland    161.9   87.75  Carcass    58.3 FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
modENCODE Anatomy RNA-Seq
modENCODE Tissue Expression Data (modENCODE_mRNA-Seq_tissues)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    28 central nervous system, larvae L3    20 central nervous system, pupae P8    12 head, virgin 1-day female    10 head, virgin 4-day female    9 head, virgin 20-day female    8 head, mated 1-day female    10 head, mated 4-day female    10 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    14 head, mated 20-day male    13 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    9 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    6 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    6 fat body, white prepupae    11 fat body, pupae P8    10 carcass, larvae L3 wandering    17 carcass, 1-day adult    7 carcass, 4-day adult    10 carcass, 20-day adult    7 ovary, virgin 4-day female    35 ovary, mated 4-day female    41 testis, mated 4-day male    18 accessory gland, mated 4-day male    9 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering  (28) central nervous system, larvae L3    20 central nervous system, pupae P8    12 head, virgin 1-day female    10 head, virgin 4-day female    9 head, virgin 20-day female    8 head, mated 1-day female    10 head, mated 4-day female    10 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    14 head, mated 20-day male    13 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    9 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    6 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    6 fat body, white prepupae    11 fat body, pupae P8    10 carcass, larvae L3 wandering    17 carcass, 1-day adult    7 carcass, 4-day adult    10 carcass, 20-day adult    7 ovary, virgin 4-day female  (35) ovary, mated 4-day female  (41) testis, mated 4-day male    18 accessory gland, mated 4-day male    9 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    28 central nervous system, larvae L3    20 central nervous system, pupae P8    12 head, virgin 1-day female    10 head, virgin 4-day female    9 head, virgin 20-day female    8 head, mated 1-day female    10 head, mated 4-day female    10 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    14 head, mated 20-day male    13 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    9 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    6 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    6 fat body, white prepupae    11 fat body, pupae P8    10 carcass, larvae L3 wandering    17 carcass, 1-day adult    7 carcass, 4-day adult    10 carcass, 20-day adult    7 ovary, virgin 4-day female    35 ovary, mated 4-day female    41 testis, mated 4-day male    18 accessory gland, mated 4-day male    9 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    28 central nervous system, larvae L3    20 central nervous system, pupae P8    12 head, virgin 1-day female    10 head, virgin 4-day female    9 head, virgin 20-day female    8 head, mated 1-day female    10 head, mated 4-day female    10 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    14 head, mated 20-day male    13 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    9 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    6 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    6 fat body, white prepupae    11 fat body, pupae P8    10 carcass, larvae L3 wandering    17 carcass, 1-day adult    7 carcass, 4-day adult    10 carcass, 20-day adult    7 ovary, virgin 4-day female    35 ovary, mated 4-day female    41 testis, mated 4-day male    18 accessory gland, mated 4-day male    9 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    28 central nervous system, larvae L3    20 central nervous system, pupae P8    12 head, virgin 1-day female    10 head, virgin 4-day female    9 head, virgin 20-day female    8 head, mated 1-day female    10 head, mated 4-day female    10 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    14 head, mated 20-day male    13 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    9 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    6 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    6 fat body, white prepupae    11 fat body, pupae P8    10 carcass, larvae L3 wandering    17 carcass, 1-day adult    7 carcass, 4-day adult    10 carcass, 20-day adult    7 ovary, virgin 4-day female    35 ovary, mated 4-day female    41 testis, mated 4-day male    18 accessory gland, mated 4-day male    9 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering  28 central nervous system, larvae L3    20 central nervous system, pupae P8    12 head, virgin 1-day female    10 head, virgin 4-day female    9 head, virgin 20-day female    8 head, mated 1-day female    10 head, mated 4-day female    10 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    14 head, mated 20-day male    13 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    9 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    6 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    6 fat body, white prepupae    11 fat body, pupae P8    10 carcass, larvae L3 wandering    17 carcass, 1-day adult    7 carcass, 4-day adult    10 carcass, 20-day adult    7 ovary, virgin 4-day female  (35) ovary, mated 4-day female  (41) testis, mated 4-day male    18 accessory gland, mated 4-day male    9 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    28 central nervous system, larvae L3    20 central nervous system, pupae P8    12 head, virgin 1-day female    10 head, virgin 4-day female    9 head, virgin 20-day female    8 head, mated 1-day female    10 head, mated 4-day female    10 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    14 head, mated 20-day male    13 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    9 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    6 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    6 fat body, white prepupae    11 fat body, pupae P8    10 carcass, larvae L3 wandering    17 carcass, 1-day adult    7 carcass, 4-day adult    10 carcass, 20-day adult    7 ovary, virgin 4-day female    35 ovary, mated 4-day female    41 testis, mated 4-day male    18 accessory gland, mated 4-day male    9 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    28 central nervous system, larvae L3    20 central nervous system, pupae P8    12 head, virgin 1-day female    10 head, virgin 4-day female    9 head, virgin 20-day female    8 head, mated 1-day female    10 head, mated 4-day female    10 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    14 head, mated 20-day male    13 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    9 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    6 digestive system, 4-day adult    10 digestive system, 20-day adult    8 fat body, larvae L3 wandering    6 fat body, white prepupae    11 fat body, pupae P8    10 carcass, larvae L3 wandering    17 carcass, 1-day adult    7 carcass, 4-day adult    10 carcass, 20-day adult    7 ovary, virgin 4-day female    35 ovary, mated 4-day female    41 testis, mated 4-day male    18 accessory gland, mated 4-day male    9 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Tissue   Expression Level imaginal disc, larvae L3 wandering     central nervous system, larvae L3     central nervous system, pupae P8     head, virgin 1-day female     head, virgin 4-day female     head, virgin 20-day female     head, mated 1-day female     head, mated 4-day female     head, mated 20-day female     head, mated 1-day male     head, mated 4-day male     head, mated 20-day male     salivary gland, larvae L3 wandering     salivary gland, white prepupae     digestive system, larvae L3 wandering     digestive system, 1-day adult     digestive system, 4-day adult     digestive system, 20-day adult     fat body, larvae L3 wandering     fat body, white prepupae     fat body, pupae P8     carcass, larvae L3 wandering     carcass, 1-day adult     carcass, 4-day adult     carcass, 20-day adult     ovary, virgin 4-day female     ovary, mated 4-day female     testis, mated 4-day male     accessory gland, mated 4-day male
modENCODE Development RNA-Seq
modENCODE Temporal Expression Data (modENCODE_mRNA-Seq_U)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of moderate expression. Peak expression observed within 00-18 hour embryonic stages, during early larval stages, during early pupal stages, in adult female 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    33 embryo 02-04hr    13 embryo 04-06hr    33 embryo 06-08hr    33 embryo 08-10hr    27 embryo 10-12hr    25 embryo 12-14hr    18 embryo 14-16hr    18 embryo 16-18hr    14 embryo 18-20hr    12 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    17 larva L2    14 larva L3 12hr old    11 larva L3 puffstage 1-2    9 larva L3 puffstage 3-6    14 larva L3 puffstage 7-9    15 white prepupae new    17 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    16 pupae 3d postWPP    10 pupae 4d postWPP    12 adult male 01day    14 adult male 05day    17 adult male 30day    16 adult female 01day    22 adult female 05day    27 adult female 30day    27 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (33) embryo 02-04hr    13 embryo 04-06hr  (33) embryo 06-08hr  (33) embryo 08-10hr  (27) embryo 10-12hr    25 embryo 12-14hr    18 embryo 14-16hr    18 embryo 16-18hr    14 embryo 18-20hr    12 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    17 larva L2    14 larva L3 12hr old    11 larva L3 puffstage 1-2    9 larva L3 puffstage 3-6    14 larva L3 puffstage 7-9    15 white prepupae new    17 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    16 pupae 3d postWPP    10 pupae 4d postWPP    12 adult male 01day    14 adult male 05day    17 adult male 30day    16 adult female 01day    22 adult female 05day  (27) adult female 30day  (27) Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    33 embryo 02-04hr    13 embryo 04-06hr    33 embryo 06-08hr    33 embryo 08-10hr    27 embryo 10-12hr    25 embryo 12-14hr    18 embryo 14-16hr    18 embryo 16-18hr    14 embryo 18-20hr    12 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    17 larva L2    14 larva L3 12hr old    11 larva L3 puffstage 1-2    9 larva L3 puffstage 3-6    14 larva L3 puffstage 7-9    15 white prepupae new    17 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    16 pupae 3d postWPP    10 pupae 4d postWPP    12 adult male 01day    14 adult male 05day    17 adult male 30day    16 adult female 01day    22 adult female 05day    27 adult female 30day    27 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    33 embryo 02-04hr    13 embryo 04-06hr    33 embryo 06-08hr    33 embryo 08-10hr    27 embryo 10-12hr    25 embryo 12-14hr    18 embryo 14-16hr    18 embryo 16-18hr    14 embryo 18-20hr    12 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    17 larva L2    14 larva L3 12hr old    11 larva L3 puffstage 1-2    9 larva L3 puffstage 3-6    14 larva L3 puffstage 7-9    15 white prepupae new    17 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    16 pupae 3d postWPP    10 pupae 4d postWPP    12 adult male 01day    14 adult male 05day    17 adult male 30day    16 adult female 01day    22 adult female 05day    27 adult female 30day    27 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    33 embryo 02-04hr    13 embryo 04-06hr    33 embryo 06-08hr    33 embryo 08-10hr    27 embryo 10-12hr    25 embryo 12-14hr    18 embryo 14-16hr    18 embryo 16-18hr    14 embryo 18-20hr    12 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    17 larva L2    14 larva L3 12hr old    11 larva L3 puffstage 1-2    9 larva L3 puffstage 3-6    14 larva L3 puffstage 7-9    15 white prepupae new    17 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    16 pupae 3d postWPP    10 pupae 4d postWPP    12 adult male 01day    14 adult male 05day    17 adult male 30day    16 adult female 01day    22 adult female 05day    27 adult female 30day    27 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (33) embryo 02-04hr    13 embryo 04-06hr  (33) embryo 06-08hr  (33) embryo 08-10hr  27 embryo 10-12hr    25 embryo 12-14hr    18 embryo 14-16hr    18 embryo 16-18hr    14 embryo 18-20hr    12 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    17 larva L2    14 larva L3 12hr old    11 larva L3 puffstage 1-2    9 larva L3 puffstage 3-6    14 larva L3 puffstage 7-9    15 white prepupae new    17 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    16 pupae 3d postWPP    10 pupae 4d postWPP    12 adult male 01day    14 adult male 05day    17 adult male 30day    16 adult female 01day    22 adult female 05day  27 adult female 30day  27 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    33 embryo 02-04hr    13 embryo 04-06hr    33 embryo 06-08hr    33 embryo 08-10hr    27 embryo 10-12hr    25 embryo 12-14hr    18 embryo 14-16hr    18 embryo 16-18hr    14 embryo 18-20hr    12 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    17 larva L2    14 larva L3 12hr old    11 larva L3 puffstage 1-2    9 larva L3 puffstage 3-6    14 larva L3 puffstage 7-9    15 white prepupae new    17 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    16 pupae 3d postWPP    10 pupae 4d postWPP    12 adult male 01day    14 adult male 05day    17 adult male 30day    16 adult female 01day    22 adult female 05day    27 adult female 30day    27 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    33 embryo 02-04hr    13 embryo 04-06hr    33 embryo 06-08hr    33 embryo 08-10hr    27 embryo 10-12hr    25 embryo 12-14hr    18 embryo 14-16hr    18 embryo 16-18hr    14 embryo 18-20hr    12 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    17 larva L2    14 larva L3 12hr old    11 larva L3 puffstage 1-2    9 larva L3 puffstage 3-6    14 larva L3 puffstage 7-9    15 white prepupae new    17 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    16 pupae 3d postWPP    10 pupae 4d postWPP    12 adult male 01day    14 adult male 05day    17 adult male 30day    16 adult female 01day    22 adult female 05day    27 adult female 30day    27 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+    34 Schneider line 2 Sg4    35 embryonic 1182-4H    24 embryonic GM2    16 embryonic Kc167    18 embryonic S1    22 embryonic S3    24 leg disc CME L1    32 wing disc CME-W2    26 wing disc ML-DmD8    20 wing disc ML-DmD9    23 wing disc ML-DmD16-c3    30 wing disc ML-DmD21    18 wing disc ML-DmD32    32 haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11    26 antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    20 CNS ML-DmBG1-c1    25 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    24 ovary fGS/OSS    45 ovary OSC    35 ovary OSS    38 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  (34) Schneider line 2 Sg4  (35) embryonic 1182-4H    24 embryonic GM2    16 embryonic Kc167    18 embryonic S1    22 embryonic S3    24 leg disc CME L1  (32) wing disc CME-W2  26 wing disc ML-DmD8    20 wing disc ML-DmD9    23 wing disc ML-DmD16-c3  (30) wing disc ML-DmD21    18 wing disc ML-DmD32  (32) haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11  26 antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    20 CNS ML-DmBG1-c1    25 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    24 ovary fGS/OSS  (45) ovary OSC  (35) ovary OSS  (38) Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    34 Schneider line 2 Sg4    35 embryonic 1182-4H    24 embryonic GM2    16 embryonic Kc167    18 embryonic S1    22 embryonic S3    24 leg disc CME L1    32 wing disc CME-W2    26 wing disc ML-DmD8    20 wing disc ML-DmD9    23 wing disc ML-DmD16-c3    30 wing disc ML-DmD21    18 wing disc ML-DmD32    32 haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11    26 antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    20 CNS ML-DmBG1-c1    25 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    24 ovary fGS/OSS    45 ovary OSC    35 ovary OSS    38 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+    34 Schneider line 2 Sg4    35 embryonic 1182-4H    24 embryonic GM2    16 embryonic Kc167    18 embryonic S1    22 embryonic S3    24 leg disc CME L1    32 wing disc CME-W2    26 wing disc ML-DmD8    20 wing disc ML-DmD9    23 wing disc ML-DmD16-c3    30 wing disc ML-DmD21    18 wing disc ML-DmD32    32 haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11    26 antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    20 CNS ML-DmBG1-c1    25 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    24 ovary fGS/OSS    45 ovary OSC    35 ovary OSS    38 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    34 Schneider line 2 Sg4    35 embryonic 1182-4H    24 embryonic GM2    16 embryonic Kc167    18 embryonic S1    22 embryonic S3    24 leg disc CME L1    32 wing disc CME-W2    26 wing disc ML-DmD8    20 wing disc ML-DmD9    23 wing disc ML-DmD16-c3    30 wing disc ML-DmD21    18 wing disc ML-DmD32    32 haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11    26 antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    20 CNS ML-DmBG1-c1    25 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    24 ovary fGS/OSS    45 ovary OSC    35 ovary OSS    38 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  (34) Schneider line 2 Sg4  (35) embryonic 1182-4H    24 embryonic GM2    16 embryonic Kc167    18 embryonic S1    22 embryonic S3    24 leg disc CME L1  32 wing disc CME-W2  26 wing disc ML-DmD8    20 wing disc ML-DmD9    23 wing disc ML-DmD16-c3  30 wing disc ML-DmD21    18 wing disc ML-DmD32  32 haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11  26 antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    20 CNS ML-DmBG1-c1    25 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    24 ovary fGS/OSS  (45) ovary OSC  (35) ovary OSS  (38) Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    34 Schneider line 2 Sg4    35 embryonic 1182-4H    24 embryonic GM2    16 embryonic Kc167    18 embryonic S1    22 embryonic S3    24 leg disc CME L1    32 wing disc CME-W2    26 wing disc ML-DmD8    20 wing disc ML-DmD9    23 wing disc ML-DmD16-c3    30 wing disc ML-DmD21    18 wing disc ML-DmD32    32 haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11    26 antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    20 CNS ML-DmBG1-c1    25 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    24 ovary fGS/OSS    45 ovary OSC    35 ovary OSS    38 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+    34 Schneider line 2 Sg4    35 embryonic 1182-4H    24 embryonic GM2    16 embryonic Kc167    18 embryonic S1    22 embryonic S3    24 leg disc CME L1    32 wing disc CME-W2    26 wing disc ML-DmD8    20 wing disc ML-DmD9    23 wing disc ML-DmD16-c3    30 wing disc ML-DmD21    18 wing disc ML-DmD32    32 haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11    26 antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    20 CNS ML-DmBG1-c1    25 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    24 ovary fGS/OSS    45 ovary OSC    35 ovary OSS    38 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    14 cold shock, 4-day adult    12 heat shock, 4-day adult    14 Cadmium 50 mM 6 hrs, larvae L3    6 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    15 Cadmium 100 mM 48 hrs, 4-day adult    28 Copper 0.5 mM 12 hrs, larvae L3    12 Copper 15 mM 48 hrs, 4-day adult    34 Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    19 Ethanol 2.5% 3 hrs, larvae L3    27 Ethanol 5% 3 hrs, larvae L3    7 Ethanol 10% 3 hrs, larvae L3    6 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    26 Caffeine 25 mg/ml 48 hrs, 4-day adult    16 Paraquat 5 mM 48 hrs, 4-day adult    24 Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    14 cold shock, 4-day adult    12 heat shock, 4-day adult    14 Cadmium 50 mM 6 hrs, larvae L3    6 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    15 Cadmium 100 mM 48 hrs, 4-day adult  (28) Copper 0.5 mM 12 hrs, larvae L3    12 Copper 15 mM 48 hrs, 4-day adult  (34) Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    19 Ethanol 2.5% 3 hrs, larvae L3  (27) Ethanol 5% 3 hrs, larvae L3    7 Ethanol 10% 3 hrs, larvae L3    6 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult  26 Caffeine 25 mg/ml 48 hrs, 4-day adult    16 Paraquat 5 mM 48 hrs, 4-day adult    24 Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    14 cold shock, 4-day adult    12 heat shock, 4-day adult    14 Cadmium 50 mM 6 hrs, larvae L3    6 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    15 Cadmium 100 mM 48 hrs, 4-day adult    28 Copper 0.5 mM 12 hrs, larvae L3    12 Copper 15 mM 48 hrs, 4-day adult    34 Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    19 Ethanol 2.5% 3 hrs, larvae L3    27 Ethanol 5% 3 hrs, larvae L3    7 Ethanol 10% 3 hrs, larvae L3    6 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    26 Caffeine 25 mg/ml 48 hrs, 4-day adult    16 Paraquat 5 mM 48 hrs, 4-day adult    24 Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    7 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    14 cold shock, 4-day adult    12 heat shock, 4-day adult    14 Cadmium 50 mM 6 hrs, larvae L3    6 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    15 Cadmium 100 mM 48 hrs, 4-day adult    28 Copper 0.5 mM 12 hrs, larvae L3    12 Copper 15 mM 48 hrs, 4-day adult    34 Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    19 Ethanol 2.5% 3 hrs, larvae L3    27 Ethanol 5% 3 hrs, larvae L3    7 Ethanol 10% 3 hrs, larvae L3    6 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    26 Caffeine 25 mg/ml 48 hrs, 4-day adult    16 Paraquat 5 mM 48 hrs, 4-day adult    24 Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    7 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    14 cold shock, 4-day adult    12 heat shock, 4-day adult    14 Cadmium 50 mM 6 hrs, larvae L3    6 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    15 Cadmium 100 mM 48 hrs, 4-day adult    28 Copper 0.5 mM 12 hrs, larvae L3    12 Copper 15 mM 48 hrs, 4-day adult    34 Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    19 Ethanol 2.5% 3 hrs, larvae L3    27 Ethanol 5% 3 hrs, larvae L3    7 Ethanol 10% 3 hrs, larvae L3    6 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    26 Caffeine 25 mg/ml 48 hrs, 4-day adult    16 Paraquat 5 mM 48 hrs, 4-day adult    24 Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    14 cold shock, 4-day adult    12 heat shock, 4-day adult    14 Cadmium 50 mM 6 hrs, larvae L3    6 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    15 Cadmium 100 mM 48 hrs, 4-day adult  28 Copper 0.5 mM 12 hrs, larvae L3    12 Copper 15 mM 48 hrs, 4-day adult  (34) Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    19 Ethanol 2.5% 3 hrs, larvae L3  27 Ethanol 5% 3 hrs, larvae L3    7 Ethanol 10% 3 hrs, larvae L3    6 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult  26 Caffeine 25 mg/ml 48 hrs, 4-day adult    16 Paraquat 5 mM 48 hrs, 4-day adult    24 Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    14 cold shock, 4-day adult    12 heat shock, 4-day adult    14 Cadmium 50 mM 6 hrs, larvae L3    6 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    15 Cadmium 100 mM 48 hrs, 4-day adult    28 Copper 0.5 mM 12 hrs, larvae L3    12 Copper 15 mM 48 hrs, 4-day adult    34 Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    19 Ethanol 2.5% 3 hrs, larvae L3    27 Ethanol 5% 3 hrs, larvae L3    7 Ethanol 10% 3 hrs, larvae L3    6 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    26 Caffeine 25 mg/ml 48 hrs, 4-day adult    16 Paraquat 5 mM 48 hrs, 4-day adult    24 Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    7 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    14 cold shock, 4-day adult    12 heat shock, 4-day adult    14 Cadmium 50 mM 6 hrs, larvae L3    6 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    15 Cadmium 100 mM 48 hrs, 4-day adult    28 Copper 0.5 mM 12 hrs, larvae L3    12 Copper 15 mM 48 hrs, 4-day adult    34 Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    19 Ethanol 2.5% 3 hrs, larvae L3    27 Ethanol 5% 3 hrs, larvae L3    7 Ethanol 10% 3 hrs, larvae L3    6 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    26 Caffeine 25 mg/ml 48 hrs, 4-day adult    16 Paraquat 5 mM 48 hrs, 4-day adult    24 Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    7 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Treatment   Expression Level extended cold, 4-day adult     cold shock, 4-day adult     heat shock, 4-day adult     Cadmium 50 mM 6 hrs, larvae L3     Cadmium 50 mM 12 hrs, larvae L3     Cadmium 50 mM 48 hrs, 4-day adult     Cadmium 100 mM 48 hrs, 4-day adult     Copper 0.5 mM 12 hrs, larvae L3     Copper 15 mM 48 hrs, 4-day adult     Zinc 5 mM 12 hrs, larvae L3     Zinc 4.5 mM 48 hrs, 4-day adult     Ethanol 2.5% 3 hrs, larvae L3     Ethanol 5% 3 hrs, larvae L3     Ethanol 10% 3 hrs, larvae L3     Caffeine 1.5 mg/ml 4 hrs, larvae L3     Caffeine 2.5 mg/ml 48 hrs, 4-day adult     Caffeine 25 mg/ml 48 hrs, 4-day adult     Paraquat 5 mM 48 hrs, 4-day adult     Paraquat 10 mM 48 hrs, 4-day adult     Rotenone 2 μg 12 hrs, larvae L3     Rotenone 8 μg 12 hrs, larvae L3
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010, Graveley et al., 2011) mE2_34_mRNA_expression_cluster_06 mE1_20_mRNA_expression_cluster_09
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0030354 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG1559-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal Upf18-7H Upf114D Upf142 Upf1A92A lethal | embryonic stage | germline clone Upf126A lethal | larval stage Upf126A lethal | male limited | second instar larval stage Upf113D Upf126A lethal | third instar larval stage Upf126A lethal - all die before end of larval stage, with Scer\GAL4Act5C.PI Upf1D45B.Scer\UAS Other Phenotypes Allele mitotic cell cycle defective Upf1dsRNA.cLa Phenotype manifest in Allele adult tracheal system | somatic clone Upf113D Upf126A dorsal appendage Upf113D dorsal appendage | germline clone Upf126A eye | somatic clone Upf113D Upf126A follicle cell | somatic clone Upf113D Upf126A
Classical Alleles ( 8 )
For All Classical Alleles Show
Allele of Upf1 Class Mutagen Stocks Known lesion Upf1G1161 P-element activity 1 -- Upf113D ethyl methanesulfonate 0 Yes Upf114D ethyl methanesulfonate 0 -- Upf125G 0 -- Upf126A ethyl methanesulfonate 0 Yes Upf142 ethyl methanesulfonate 0 -- Upf18-7H ethyl methanesulfonate 0 -- Upf1A92A ethyl methanesulfonate 0 --
Alleles Carried on Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Upf1 Class Mutagen Stocks Known lesion Upf1GL01485 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Upf1Scer\UAS.T:Avic\GFP 1 Yes Upf1D45B.Scer\UAS in vitro construct - regulatory fusion in vitro construct - site directed mutagenesis 0 Yes Upf1dsRNA.cHa in vitro construct - RNAi 0 Yes Upf1dsRNA.cLa in vitro construct - RNAi 0 -- Upf1GD9065 in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes Upf1t15 in vitro construct - genomic fragment 0 Yes
Aneuploid Aberrations
Disrupted in	Df(1)Exel6243 (Ryder, 2004.4.26)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD9065} NA P{TRiP.GL01485} NA P{UASp-GFP.Upf1} NA P{UAS-Upf1.D45B} NA characterization construct P{pot+t15} NA P{pot-CFP.B} NA
Insertions
	Type of insertions Name Expression data insertion of mobile activating element P{EP}Upf1G1161 NA
Gene Ontology: Function, Process & Cellular Component ( 11 unique terms )
Terms Based on Experimental Evidence ( 6 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
cellular response to hypoxia inferred from mutant phenotype (Lee et al., 2008) NOT gene silencing by miRNA inferred from mutant phenotype (Rehwinkel et al., 2005) nuclear-transcribed mRNA catabolic process, nonsense-mediated decay inferred from mutant phenotype (Rehwinkel et al., 2005) positive regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay inferred from mutant phenotype (Micale et al., 2009) NOT RNA interference inferred from mutant phenotype (Rehwinkel et al., 2005)
Cellular Component
CV term Evidence References
colocalizes_with exon-exon junction complex inferred from direct assay (Guruharsha et al., 2011)
Terms Based on Predictions or Assertions ( 6 terms )
Molecular Function
CV term Evidence References
ATP binding inferred from electronic annotation with InterPro:IPR006935, InterPro:IPR018999 (FlyBase Curators et al., 2004-) DNA binding inferred from electronic annotation with InterPro:IPR006935, InterPro:IPR018999 (FlyBase Curators et al., 2004-) helicase activity inferred from sequence or structural similarity with Saccharomyces NAM7 (FlyBase, 1992-) zinc ion binding inferred from electronic annotation with InterPro:IPR018999 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay inferred from sequence or structural similarity with Saccharomyces NAM7 (FlyBase, 1992-) non-traceable author statement (Alonso and Akam, 2002, Swiss-Prot Project Members, 2001.10.16)
Cellular Component
CV term Evidence References
cytoplasm inferred from electronic annotation with InterPro:IPR018999 (FlyBase Curators et al., 2004-) non-traceable author statement (Swiss-Prot Project Members, 2001.10.16)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
Upf1 - Atac1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - BicD experimental knowledge based (Guruharsha et al., 2011) Upf1 - CBP anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG10175 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG10465 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG10483 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG10681 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG10996 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG11594 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG12576 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG12818 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG13567 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG14718 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG14786 experimental knowledge based (Guruharsha et al., 2011) Upf1 - CG1486 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG15096 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG17806 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG2865 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG2921 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG31251 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG31908 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG32649 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG3714 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG4302 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG4847 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG5196 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG5805 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG6123 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG6277 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG6652 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG6686 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG6701 experimental knowledge based (Guruharsha et al., 2011) Upf1 - CG7146 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG7686 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG7829 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG8336 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG8379 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG8939 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CG9114 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CenG1A anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Chi anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Clect27 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - CycG anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - E(spl)m7-HLH anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - EfSec anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - GABPI anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Gad1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Gale anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Gαq anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Hakai anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Hsp70Bb anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Incenp anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Ipk1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Irp-1A anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Lmpt anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Nak anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Nep2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Nf-YB anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - PCID2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Pgam5 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Pof anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Prosβ2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Prp3 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Rab10 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Rab5 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Rab6 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Rbf anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Rcc1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Rcd5 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Rho1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - RnrS anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - RpL35A anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - RpLP0 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - RpS11 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Rpb8 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - SCAR anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Sdc anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Snr1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Syp experimental knowledge based (Guruharsha et al., 2011) Upf1 - TER94 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Tsp anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Ubx anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Upf2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Vha100-2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - Vha100-4 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - alrm anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - ana2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - brk anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - capu anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - cathD anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - crn anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - eIF-2α anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - eIF6 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - gcl anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - hig anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - kst anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - l(1)G0232 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - lin-28 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - mRpL47 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - mRpL48 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - metro anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - mts anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - nito experimental knowledge based (Guruharsha et al., 2011) Upf1 - orb anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - p-cup anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - phtf anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - pigeon anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - rumi anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - sc anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - scat anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - slbo anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - slow anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - sls anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - stv anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - ttm50 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - twe anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - tws anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Upf1 - wee anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23)
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions Upf1 allele Gene References
External Data
Linkouts	DPiM - DPiM, Drosophila Protein interaction Map • FBgn0030354 DroID - A comprehensive database of gene and protein interactions. • FBgn0030354 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 32153
Orthologs
OrthoDB Orthologs (40) - 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 EOG6614PB Dipteran inclusive ortholog search EOG6JQ45H Insect inclusive ortholog search EOG6TX9MQ Arthropod inclusive ortholog search EOG6R228Q Metazoa inclusive ortholog search EOG60SC7F
Orthologs in Drosophila Species (EOG6614PB)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\Upf1     Drosophila simulans   Dsim\GD24645 Y   Drosophila sechellia   Dsec\GM13241 Y   Drosophila erecta   Dere\GG18821 Y   Drosophila yakuba   Dyak\GE17585 Y   Drosophila ananassae   Dana\GF21587 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA29178 Y   Drosophila persimilis   Dper\GL20400 Y   Drosophila willistoni   Dwil\GK25498 Y   Drosophila virilis   Dvir\GJ16782 Y   Drosophila mojavensis   Dmoj\GI14718 Y   Drosophila grimshawi   Dgri\GH11976 Y
Orthologs in non-Drosophila Dipterans (EOG6JQ45H)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL011817   Anopheles gambiae Malaria mosquito  Agam\AGAP001133   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ012300
Orthologs in non-Dipteran Insects (EOG6TX9MQ)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\Upf1   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG001426   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH13335   Atta cephalotes Leafcutter ant  Acep\ACEP26511   Camponotus floridanus Florida carpenter ant  Cflo\CFLO12639   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL22193   Linepithema humile Argentine ant  Lhum\LH19866   Pogonomyrmex barbatus Red harvester ant  Pbar\PB19842   Solenopsis invicta Red fire ant  Sinv\SINV14244   Acyrthosiphon pisum Pea aphid  Apim\ACYPI001512   Acyrthosiphon pisum Pea aphid  Apim\ACYPI008248   Bombyx mori Silkmoth  Bmor\BGIBMGA001540   Pediculus humanus Human body louse  Phum\PHUM244150   Tribolium castaneum Red flour beetle  Tcas\TC000192
Orthologs in non-Insect Arthropods (EOG6R228Q)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\JGI_V11_57163   Ixodes scapularis Deer tick  Isca\ISCW010285
Orthologs in non-Arthropod Metazoa (EOG60SC7F)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Caenorhabditis elegans Nematode  Cele\Y48G8AL.6   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_008761gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_008215gn   Danio rerio Zebrafish  Drer\upf1   Xenopus tropicalis Western clawed frog  Xtro\upf1   Gallus gallus Domestic chicken  Ggal\UPF1   Mus musculus House mouse  Mmus\Upf1   Rattus norvegicus Norway rat  Rnor\ENSRNOG00000020134   Homo sapiens Human  Hsap\ENSG00000005007
Human Orthologs (1)
Gene OMIM HGNC Hsap\ENSG00000005007
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD24645 Drosophila sechellia Dsec\GM13241 Drosophila erecta Dere\GG18821 Drosophila yakuba Dyak\GE17585 Drosophila ananassae Dana\GF21587 Drosophila pseudoobscura pseudoobscura Dpse\GA29178 Drosophila persimilis Dper\GL20400 Drosophila willistoni Dwil\GK25498 Drosophila virilis Dvir\GJ16782 Drosophila mojavensis Dmoj\GI14718 Drosophila grimshawi Dgri\GH11976
Stocks & Reagents
Stocks Listed in FlyBase ( 3 )
Bloomington	24623 w*; P{UASp-GFP.Upf1}2 33539 w* P{EP}Upf1G1161 43144 y1 v1; P{TRiP.GL01485}attP2
Genomic Clones ( 1 )
	BACR12H01 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 32 )
	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	LD30316
Other clones	DPiM_LD30316
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	GM22672 LD16245 LP13450 LP13578 RE52657 SD22039
Other clones	1992 41408 41472 106314 106442 214289.4 214321.13 214383.7 CK01.13C.E2 CK01.123B.F5 EC41059 EK040148 EK093823 EK123421 EK154417 EK196623 EP01516 EP14547 EP16739 GH09524 LD16903 LD25787 UT01174 UT01460
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0030354 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 32153
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments
Other Comments
	dsRNA has been made from templates generated with primers directed against this gene. (Rehwinkel et al., 2005)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_132539 RefSeq (Proteins) • NP_572767 DDBJ / EMBL / GenBank • AA950499 AAF48115 AAL28927 AW943020 AY061379 Entrez Gene - A searchable database of RefSeq genes. • 32153 UniProtKB/Swiss-Prot • Q9VYS3
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • RNA helicase UPF1, UPF2-interacting domain (IPR018999) P-loop containing nucleoside triphosphate hydrolase (IPR027417)
Linkouts
	DPiM - DPiM, Drosophila Protein interaction Map • FBgn0030354 DroID - A comprehensive database of gene and protein interactions. • FBgn0030354 DRSC - Results from RNAi screens. • FBgn0030354 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0030354 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG1559-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0030354 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 32153 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 32153 modMine - Data generated by the modENCODE project. • FBgn0030354
Synonyms & Secondary IDs ( 9 )
Reported As
Symbol Synonym	CG1559 (Gatfield et al., 2003, Alonso and Akam, 2003, Gonzalez et al., 2002, Legube et al., 2006, Hollien and Weissman, 2006, Rehwinkel et al., 2005, Saxton, 2007.7, Greenspan and Clark, 2011, Lee et al., 2008, Ni et al., 2010.12.1) DmUpf1 (Alonso and Akam, 2003) Dm-Upf1 (Alonso and Akam, 2002) smg-2 (Metzstein and Krasnow, 2006) UPF1 (Gatfield and Izaurralde, 2004, Le Hir et al., 2001, Gatfield et al., 2003, Rehwinkel et al., 2005, Hase et al., 2006, Behm-Ansmant et al., 2007, Barbee et al., 2006, Eulalio et al., 2007, Rehwinkel et al., 2005) Upf1 (Hollien and Weissman, 2006, Bokel et al., 2005, Metzstein et al., 2007, Saxton, 2007.7, Metzstein and Krasnow, 2006, Micale et al., 2009, Lee et al., 2008, Roignant and Treisman, 2010, Mourikis et al., 2010, Guruharsha et al., 2011, Gontijo et al., 2011, Saulière et al., 2010, Frizzell et al., 2012, Plocik and Guthrie, 2012) upf1 (Avery et al., 2011, Hansen et al., 2009) Upf1p (Barbee et al., 2006)
Name Synonym	Upf1   up-frameshift suppressor 1 (Metzstein and Krasnow, 2006)
Secondary FlyBase IDs
References ( 48 )
Generate a list of	All references relating to this gene ( 48 )
List References by type	Research paper  ( 27 ) Supplementary material  ( 5 ) Review  ( 2 ) Personal communication to FlyBase  ( 7 ) Abstract  ( 2 ) FlyBase analysis  ( 1 ) Protein sequence record  ( 1 ) Curated genome annotation  ( 2 )
Recent research papers ( 7 )
	Zhang et al., 2013, Mol. Ecol. 22(5): 1400--1415 Natural genetic variation in male reproductive genes contributes to nontransitivity of sperm competitive ability in Drosophila melanogaster. [FBrf0220937] Frizzell et al., 2012, RNA 18(8): 1475--1486 Drosophila mutants show NMD pathway activity is reduced, but not eliminated, in the absence of Smg6. [FBrf0218868] Plocik and Guthrie, 2012, PLoS Genet. 8(3): e1002620 Diverse Forms of RPS9 Splicing Are Part of an Evolving Autoregulatory Circuit. [FBrf0218008] Avery et al., 2011, RNA 17(4): 624--638 Drosophila Upf1 and Upf2 loss of function inhibits cell growth and causes animal death in a Upf3-independent manner. [FBrf0213282] Gontijo et al., 2011, Nat. Commun. 2: 323 Intron retention in the Drosophila melanogaster Rieske iron sulphur protein gene generated a new protein. [FBrf0213743] Greenspan and Clark, 2011, Int. J. Evol. Biol. 2011: 214280 Associations between Variation in X Chromosome Male Reproductive Genes and Sperm Competitive Ability in Drosophila melanogaster. [FBrf0214060] Guruharsha et al., 2011, Cell 147(3): 690--703 A Protein Complex Network of Drosophila melanogaster. [FBrf0216491] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...