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Gene Dmel\Rrp40

General Information
Symbol	Dmel\Rrp40	Species	D. melanogaster
Name		Annotation symbol	CG31938
Feature type	protein_coding_gene	FlyBase ID	FBgn0260648
Gene Model Status	Current	Stock availability	2 publicly available
Also Known As	dRrp40
Genomic Location
Chromosome (arm)	2L	Recombination map
Cytogenetic map	22B1-22B1	Sequence location	2L:1,728,732..1,729,575 [+]
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	This gene is referred to in FlyBase by the symbol Dmel\Rrp40 (CG31938, FBgn0260648). It is a protein_coding_gene from Drosophila melanogaster. Based on sequence similarity, it is predicted to have molecular function: 3'-5'-exoribonuclease activity. There is experimental evidence that it is involved in the biological process: regulation of gene expression. 2 alleles are reported. The phenotype of these alleles is annotated with: mesothoracic tergum. It has one annotated transcript and one annotated polypeptide. Protein features are: Exosome complex RNA-binding protein 1/RRP40/RRP4; RNA-binding domain, S1. 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, in adult female stages. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: larval central nervous system, adult fat body, larval salivary gland, larval trachea, adult female reproductive system, adult male accessory gland, larval carcass. Comments on Affy2 ProbeSet: ProbeSet 1637923_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of Rrp40. Gene sequence location is 2L:1728732..1729575.
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 22B1-22B1   Limits computationally determined from genome sequence between P{PZ}l(2)0411104111 and P{lacW}CG17646k11021
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\Rrp40 for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
	Gene model reviewed during 5.46
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Rrp40-RA FBtr0077883  NM_164435   844   232
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 Rrp40-PA   FBpp0077551   25.0   232   8.46     NP_722725   AAN10459
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Exosome complex RNA-binding protein 1/RRP40/RRP4 (IPR026699) RNA-binding domain, S1 (IPR022967)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014134 AAN10459   BT023807   EV598976
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q8IPX7
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
cytoplasm inferred from direct assay (Graham et al., 2006) nuclear exosome (RNase complex) inferred from direct assay (Andrulis et al., 2002)
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, adult fat body, larval salivary gland, larval trachea, adult female reproductive system, adult male accessory gland, larval carcass. [download data (TSV)] Guide to FlyAtlas expression level colors   No expression (0 - 9.999)   Low expression (10 - 99.999)   Moderate expression (100 - 499.999)   High level expression (500 - 999.999)   Very high expression (>999.999) Linear, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    189.925 Larval Midgut    58 Larval Hindgut    74.6 Larval Malpighian Tubules    53.2 Larval Fat Body    60.1 Larval Salivary Gland    163.9 Larval Trachea    139.775 Larval Carcass    133.05 Adult Head    66.6 Adult Eye    43.15 Adult Brain    40.8 Adult Thoracic-Abdominal Ganglion    41.7 Adult Crop    80.2 Adult Midgut    98.6 Adult Hindgut    67.8 Adult Malpighian Tubules    81.9 Adult Fat Body    102.6 Adult Salivary Gland    67.9 Adult Heart    69.5 Adult VirginFemale Spermatheca    140.3 Adult InseminatedFemale Spermatheca    136.1 Adult Ovary    176 Adult Testis    23.2 Adult Male Accessory Gland    118.4 Adult Carcass    79.3 Expression Level Scale  None   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    189.925 Larval Midgut    58 Larval Hindgut    74.6 Larval Malpighian Tubules    53.2 Larval Fat Body    60.1 Larval Salivary Gland    163.9 Larval Trachea    139.775 Larval Carcass    133.05 Adult Head    66.6 Adult Eye    43.15 Adult Brain    40.8 Adult Thoracic-Abdominal Ganglion    41.7 Adult Crop    80.2 Adult Midgut    98.6 Adult Hindgut    67.8 Adult Malpighian Tubules    81.9 Adult Fat Body    102.6 Adult Salivary Gland    67.9 Adult Heart    69.5 Adult VirginFemale Spermatheca    140.3 Adult InseminatedFemale Spermatheca    136.1 Adult Ovary    176 Adult Testis    23.2 Adult Male Accessory Gland    118.4 Adult Carcass    79.3 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    189.925 Larval Midgut    58 Larval Hindgut    74.6 Larval Malpighian Tubules    53.2 Larval Fat Body    60.1 Larval Salivary Gland    163.9 Larval Trachea    139.775 Larval Carcass    133.05 Adult Head    66.6 Adult Eye    43.15 Adult Brain    40.8 Adult Thoracic-Abdominal Ganglion    41.7 Adult Crop    80.2 Adult Midgut    98.6 Adult Hindgut    67.8 Adult Malpighian Tubules    81.9 Adult Fat Body    102.6 Adult Salivary Gland    67.9 Adult Heart    69.5 Adult VirginFemale Spermatheca    140.3 Adult InseminatedFemale Spermatheca    136.1 Adult Ovary    176 Adult Testis    23.2 Adult Male Accessory Gland    118.4 Adult Carcass    79.3 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    189.925 Larval Midgut    58 Larval Hindgut    74.6 Larval Malpighian Tubules    53.2 Larval Fat Body    60.1 Larval Salivary Gland    163.9 Larval Trachea    139.775 Larval Carcass    133.05 Adult Head    66.6 Adult Eye    43.15 Adult Brain    40.8 Adult Thoracic-Abdominal Ganglion    41.7 Adult Crop    80.2 Adult Midgut    98.6 Adult Hindgut    67.8 Adult Malpighian Tubules    81.9 Adult Fat Body    102.6 Adult Salivary Gland    67.9 Adult Heart    69.5 Adult VirginFemale Spermatheca    140.3 Adult InseminatedFemale Spermatheca    136.1 Adult Ovary    176 Adult Testis    23.2 Adult Male Accessory Gland    118.4 Adult Carcass    79.3 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    189.925 Larval Midgut    58 Larval Hindgut    74.6 Larval Malpighian Tubules    53.2 Larval Fat Body    60.1 Larval Salivary Gland    163.9 Larval Trachea    139.775 Larval Carcass    133.05 Adult Head    66.6 Adult Eye    43.15 Adult Brain    40.8 Adult Thoracic-Abdominal Ganglion    41.7 Adult Crop    80.2 Adult Midgut    98.6 Adult Hindgut    67.8 Adult Malpighian Tubules    81.9 Adult Fat Body    102.6 Adult Salivary Gland    67.9 Adult Heart    69.5 Adult VirginFemale Spermatheca    140.3 Adult InseminatedFemale Spermatheca    136.1 Adult Ovary    176 Adult Testis    23.2 Adult Male Accessory Gland    118.4 Adult Carcass    79.3 Expression Level Scale  None   Low   Moderate  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    189.925 Larval Midgut    58 Larval Hindgut    74.6 Larval Malpighian Tubules    53.2 Larval Fat Body    60.1 Larval Salivary Gland    163.9 Larval Trachea    139.775 Larval Carcass    133.05 Adult Head    66.6 Adult Eye    43.15 Adult Brain    40.8 Adult Thoracic-Abdominal Ganglion    41.7 Adult Crop    80.2 Adult Midgut    98.6 Adult Hindgut    67.8 Adult Malpighian Tubules    81.9 Adult Fat Body    102.6 Adult Salivary Gland    67.9 Adult Heart    69.5 Adult VirginFemale Spermatheca    140.3 Adult InseminatedFemale Spermatheca    136.1 Adult Ovary    176 Adult Testis    23.2 Adult Male Accessory Gland    118.4 Adult Carcass    79.3 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    189.925 Larval Midgut    58 Larval Hindgut    74.6 Larval Malpighian Tubules    53.2 Larval Fat Body    60.1 Larval Salivary Gland    163.9 Larval Trachea    139.775 Larval Carcass    133.05 Adult Head    66.6 Adult Eye    43.15 Adult Brain    40.8 Adult Thoracic-Abdominal Ganglion    41.7 Adult Crop    80.2 Adult Midgut    98.6 Adult Hindgut    67.8 Adult Malpighian Tubules    81.9 Adult Fat Body    102.6 Adult Salivary Gland    67.9 Adult Heart    69.5 Adult VirginFemale Spermatheca    140.3 Adult InseminatedFemale Spermatheca    136.1 Adult Ovary    176 Adult Testis    23.2 Adult Male Accessory Gland    118.4 Adult Carcass    79.3 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    189.925 Larval Midgut    58 Larval Hindgut    74.6 Larval Malpighian Tubules    53.2 Larval Fat Body    60.1 Larval Salivary Gland    163.9 Larval Trachea    139.775 Larval Carcass    133.05 Adult Head    66.6 Adult Eye    43.15 Adult Brain    40.8 Adult Thoracic-Abdominal Ganglion    41.7 Adult Crop    80.2 Adult Midgut    98.6 Adult Hindgut    67.8 Adult Malpighian Tubules    81.9 Adult Fat Body    102.6 Adult Salivary Gland    67.9 Adult Heart    69.5 Adult VirginFemale Spermatheca    140.3 Adult InseminatedFemale Spermatheca    136.1 Adult Ovary    176 Adult Testis    23.2 Adult Male Accessory Gland    118.4 Adult Carcass    79.3 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    66.6   NA  Eye    43.15   NA  Brain    40.8   189.925  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    41.7   NA  Crop    80.2   58  Midgut    98.6   74.6  Hindgut    67.8   53.2  Malpighian Tubules    81.9   60.1  Fat Body    102.6   163.9  Salivary Gland    no informative data   NA  Heart    69.5   139.775  Trachea    NA   NA  VirginFemale Spermatheca    140.3   NA  InseminatedFemale Spermatheca    136.1   NA  Ovary    176   NA  Testis    23.2   NA  Male Accessory Gland    118.4   133.05  Carcass    79.3 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    7 central nervous system, larvae L3    6 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    1 head, mated 4-day female    2 head, mated 20-day female    2 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    3 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    4 fat body, larvae L3 wandering    1 fat body, white prepupae    1 fat body, pupae P8    0 carcass, larvae L3 wandering    5 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    9 ovary, mated 4-day female    5 testis, mated 4-day male    3 accessory gland, mated 4-day male    2 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    7 central nervous system, larvae L3    6 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    1 head, mated 4-day female    2 head, mated 20-day female    2 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    3 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    4 fat body, larvae L3 wandering    1 fat body, white prepupae    1 fat body, pupae P8    0 carcass, larvae L3 wandering    5 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    9 ovary, mated 4-day female    5 testis, mated 4-day male    3 accessory gland, mated 4-day male    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    7 central nervous system, larvae L3    6 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    1 head, mated 4-day female    2 head, mated 20-day female    2 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    3 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    4 fat body, larvae L3 wandering    1 fat body, white prepupae    1 fat body, pupae P8    0 carcass, larvae L3 wandering    5 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    9 ovary, mated 4-day female    5 testis, mated 4-day male    3 accessory gland, mated 4-day male    2 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    7 central nervous system, larvae L3    6 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    1 head, mated 4-day female    2 head, mated 20-day female    2 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    3 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    4 fat body, larvae L3 wandering    1 fat body, white prepupae    1 fat body, pupae P8    0 carcass, larvae L3 wandering    5 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    9 ovary, mated 4-day female    5 testis, mated 4-day male    3 accessory gland, mated 4-day male    2 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    7 central nervous system, larvae L3    6 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    1 head, mated 4-day female    2 head, mated 20-day female    2 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    3 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    4 fat body, larvae L3 wandering    1 fat body, white prepupae    1 fat body, pupae P8    0 carcass, larvae L3 wandering    5 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    9 ovary, mated 4-day female    5 testis, mated 4-day male    3 accessory gland, mated 4-day male    2 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    7 central nervous system, larvae L3    6 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    1 head, mated 4-day female    2 head, mated 20-day female    2 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    3 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    4 fat body, larvae L3 wandering    1 fat body, white prepupae    1 fat body, pupae P8    0 carcass, larvae L3 wandering    5 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    9 ovary, mated 4-day female    5 testis, mated 4-day male    3 accessory gland, mated 4-day male    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    7 central nervous system, larvae L3    6 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    1 head, mated 4-day female    2 head, mated 20-day female    2 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    3 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    4 fat body, larvae L3 wandering    1 fat body, white prepupae    1 fat body, pupae P8    0 carcass, larvae L3 wandering    5 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    9 ovary, mated 4-day female    5 testis, mated 4-day male    3 accessory gland, mated 4-day male    2 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    7 central nervous system, larvae L3    6 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    1 head, mated 4-day female    2 head, mated 20-day female    2 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    3 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    4 fat body, larvae L3 wandering    1 fat body, white prepupae    1 fat body, pupae P8    0 carcass, larvae L3 wandering    5 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    9 ovary, mated 4-day female    5 testis, mated 4-day male    3 accessory gland, mated 4-day male    2 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, 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    28 embryo 02-04hr    23 embryo 04-06hr    44 embryo 06-08hr    42 embryo 08-10hr    35 embryo 10-12hr    30 embryo 12-14hr    20 embryo 14-16hr    12 embryo 16-18hr    8 embryo 18-20hr    11 embryo 20-22hr    18 embryo 22-24hr    15 larva L1    36 larva L2    26 larva L3 12hr old    19 larva L3 puffstage 1-2    12 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    13 white prepupae 12hr    11 white prepupae 24hr    15 pupae 2d postWPP    9 pupae 3d postWPP    6 pupae 4d postWPP    8 adult male 01day    6 adult male 05day    9 adult male 30day    8 adult female 01day    19 adult female 05day    26 adult female 30day    30 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (28) embryo 02-04hr    23 embryo 04-06hr  (44) embryo 06-08hr  (42) embryo 08-10hr  (35) embryo 10-12hr  (30) embryo 12-14hr    20 embryo 14-16hr    12 embryo 16-18hr    8 embryo 18-20hr    11 embryo 20-22hr    18 embryo 22-24hr    15 larva L1  (36) larva L2  26 larva L3 12hr old    19 larva L3 puffstage 1-2    12 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    13 white prepupae 12hr    11 white prepupae 24hr    15 pupae 2d postWPP    9 pupae 3d postWPP    6 pupae 4d postWPP    8 adult male 01day    6 adult male 05day    9 adult male 30day    8 adult female 01day    19 adult female 05day  26 adult female 30day  (30) Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    28 embryo 02-04hr    23 embryo 04-06hr    44 embryo 06-08hr    42 embryo 08-10hr    35 embryo 10-12hr    30 embryo 12-14hr    20 embryo 14-16hr    12 embryo 16-18hr    8 embryo 18-20hr    11 embryo 20-22hr    18 embryo 22-24hr    15 larva L1    36 larva L2    26 larva L3 12hr old    19 larva L3 puffstage 1-2    12 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    13 white prepupae 12hr    11 white prepupae 24hr    15 pupae 2d postWPP    9 pupae 3d postWPP    6 pupae 4d postWPP    8 adult male 01day    6 adult male 05day    9 adult male 30day    8 adult female 01day    19 adult female 05day    26 adult female 30day    30 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    28 embryo 02-04hr    23 embryo 04-06hr    44 embryo 06-08hr    42 embryo 08-10hr    35 embryo 10-12hr    30 embryo 12-14hr    20 embryo 14-16hr    12 embryo 16-18hr    8 embryo 18-20hr    11 embryo 20-22hr    18 embryo 22-24hr    15 larva L1    36 larva L2    26 larva L3 12hr old    19 larva L3 puffstage 1-2    12 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    13 white prepupae 12hr    11 white prepupae 24hr    15 pupae 2d postWPP    9 pupae 3d postWPP    6 pupae 4d postWPP    8 adult male 01day    6 adult male 05day    9 adult male 30day    8 adult female 01day    19 adult female 05day    26 adult female 30day    30 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    28 embryo 02-04hr    23 embryo 04-06hr    44 embryo 06-08hr    42 embryo 08-10hr    35 embryo 10-12hr    30 embryo 12-14hr    20 embryo 14-16hr    12 embryo 16-18hr    8 embryo 18-20hr    11 embryo 20-22hr    18 embryo 22-24hr    15 larva L1    36 larva L2    26 larva L3 12hr old    19 larva L3 puffstage 1-2    12 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    13 white prepupae 12hr    11 white prepupae 24hr    15 pupae 2d postWPP    9 pupae 3d postWPP    6 pupae 4d postWPP    8 adult male 01day    6 adult male 05day    9 adult male 30day    8 adult female 01day    19 adult female 05day    26 adult female 30day    30 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  28 embryo 02-04hr    23 embryo 04-06hr  (44) embryo 06-08hr  (42) embryo 08-10hr  (35) embryo 10-12hr  30 embryo 12-14hr    20 embryo 14-16hr    12 embryo 16-18hr    8 embryo 18-20hr    11 embryo 20-22hr    18 embryo 22-24hr    15 larva L1  (36) larva L2  26 larva L3 12hr old    19 larva L3 puffstage 1-2    12 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    13 white prepupae 12hr    11 white prepupae 24hr    15 pupae 2d postWPP    9 pupae 3d postWPP    6 pupae 4d postWPP    8 adult male 01day    6 adult male 05day    9 adult male 30day    8 adult female 01day    19 adult female 05day  26 adult female 30day  30 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    28 embryo 02-04hr    23 embryo 04-06hr    44 embryo 06-08hr    42 embryo 08-10hr    35 embryo 10-12hr    30 embryo 12-14hr    20 embryo 14-16hr    12 embryo 16-18hr    8 embryo 18-20hr    11 embryo 20-22hr    18 embryo 22-24hr    15 larva L1    36 larva L2    26 larva L3 12hr old    19 larva L3 puffstage 1-2    12 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    13 white prepupae 12hr    11 white prepupae 24hr    15 pupae 2d postWPP    9 pupae 3d postWPP    6 pupae 4d postWPP    8 adult male 01day    6 adult male 05day    9 adult male 30day    8 adult female 01day    19 adult female 05day    26 adult female 30day    30 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    28 embryo 02-04hr    23 embryo 04-06hr    44 embryo 06-08hr    42 embryo 08-10hr    35 embryo 10-12hr    30 embryo 12-14hr    20 embryo 14-16hr    12 embryo 16-18hr    8 embryo 18-20hr    11 embryo 20-22hr    18 embryo 22-24hr    15 larva L1    36 larva L2    26 larva L3 12hr old    19 larva L3 puffstage 1-2    12 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    13 white prepupae 12hr    11 white prepupae 24hr    15 pupae 2d postWPP    9 pupae 3d postWPP    6 pupae 4d postWPP    8 adult male 01day    6 adult male 05day    9 adult male 30day    8 adult female 01day    19 adult female 05day    26 adult female 30day    30 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+    32 Schneider line 2 Sg4    26 embryonic 1182-4H    12 embryonic GM2    9 embryonic Kc167    7 embryonic S1    14 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    11 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    22 wing disc ML-DmD32    8 haltere disc ML-DmD17-c3    14 eye-antennal disc ML-DmD11    9 antennal disc ML-DmD20-c5    16 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    14 tumorous blood cells mbn2    8 ovary fGS/OSS    5 ovary OSC    4 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  (32) Schneider line 2 Sg4  26 embryonic 1182-4H    12 embryonic GM2    9 embryonic Kc167    7 embryonic S1    14 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    11 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    22 wing disc ML-DmD32    8 haltere disc ML-DmD17-c3    14 eye-antennal disc ML-DmD11    9 antennal disc ML-DmD20-c5    16 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    14 tumorous blood cells mbn2    8 ovary fGS/OSS    5 ovary OSC    4 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    32 Schneider line 2 Sg4    26 embryonic 1182-4H    12 embryonic GM2    9 embryonic Kc167    7 embryonic S1    14 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    11 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    22 wing disc ML-DmD32    8 haltere disc ML-DmD17-c3    14 eye-antennal disc ML-DmD11    9 antennal disc ML-DmD20-c5    16 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    14 tumorous blood cells mbn2    8 ovary fGS/OSS    5 ovary OSC    4 ovary OSS    4 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+    32 Schneider line 2 Sg4    26 embryonic 1182-4H    12 embryonic GM2    9 embryonic Kc167    7 embryonic S1    14 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    11 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    22 wing disc ML-DmD32    8 haltere disc ML-DmD17-c3    14 eye-antennal disc ML-DmD11    9 antennal disc ML-DmD20-c5    16 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    14 tumorous blood cells mbn2    8 ovary fGS/OSS    5 ovary OSC    4 ovary OSS    4 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    32 Schneider line 2 Sg4    26 embryonic 1182-4H    12 embryonic GM2    9 embryonic Kc167    7 embryonic S1    14 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    11 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    22 wing disc ML-DmD32    8 haltere disc ML-DmD17-c3    14 eye-antennal disc ML-DmD11    9 antennal disc ML-DmD20-c5    16 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    14 tumorous blood cells mbn2    8 ovary fGS/OSS    5 ovary OSC    4 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  32 Schneider line 2 Sg4  26 embryonic 1182-4H    12 embryonic GM2    9 embryonic Kc167    7 embryonic S1    14 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    11 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    22 wing disc ML-DmD32    8 haltere disc ML-DmD17-c3    14 eye-antennal disc ML-DmD11    9 antennal disc ML-DmD20-c5    16 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    14 tumorous blood cells mbn2    8 ovary fGS/OSS    5 ovary OSC    4 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    32 Schneider line 2 Sg4    26 embryonic 1182-4H    12 embryonic GM2    9 embryonic Kc167    7 embryonic S1    14 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    11 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    22 wing disc ML-DmD32    8 haltere disc ML-DmD17-c3    14 eye-antennal disc ML-DmD11    9 antennal disc ML-DmD20-c5    16 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    14 tumorous blood cells mbn2    8 ovary fGS/OSS    5 ovary OSC    4 ovary OSS    4 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+    32 Schneider line 2 Sg4    26 embryonic 1182-4H    12 embryonic GM2    9 embryonic Kc167    7 embryonic S1    14 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    11 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    22 wing disc ML-DmD32    8 haltere disc ML-DmD17-c3    14 eye-antennal disc ML-DmD11    9 antennal disc ML-DmD20-c5    16 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    14 tumorous blood cells mbn2    8 ovary fGS/OSS    5 ovary OSC    4 ovary OSS    4 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    4 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    4 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    3 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    9 Rotenone 8 μg 12 hrs, larvae L3    10 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    4 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    4 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    3 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    9 Rotenone 8 μg 12 hrs, larvae L3    10 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    4 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    4 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    3 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    9 Rotenone 8 μg 12 hrs, larvae L3    10 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    4 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    4 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    3 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    9 Rotenone 8 μg 12 hrs, larvae L3    10 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    4 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    4 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    3 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    9 Rotenone 8 μg 12 hrs, larvae L3    10 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    4 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    4 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    3 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    9 Rotenone 8 μg 12 hrs, larvae L3    10 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    4 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    4 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    3 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    9 Rotenone 8 μg 12 hrs, larvae L3    10 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    4 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    4 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    3 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    9 Rotenone 8 μg 12 hrs, larvae L3    10 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_08 mE1_20_mRNA_expression_cluster_04
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0260648
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele viable, with Scer\GAL4pnr-MD237 Rrp40GD10414 Other Phenotypes Allele visible, with Scer\GAL4pnr-MD237 Rrp40GD10414 Phenotype manifest in Allele mesothoracic tergum, with Scer\GAL4pnr-MD237 Rrp40GD10414
Classical Alleles ( 1 )
For All Classical Alleles Show
Allele of Rrp40 Class Mutagen Stocks Known lesion Rrp40G5958 P-element activity 1 --
Alleles Carried on Transgenic Constructs ( 1 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Rrp40 Class Mutagen Stocks Known lesion Rrp40GD10414 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes
Aneuploid Aberrations
Disrupted in	Df(2L)Exel6005 (Ryder, 2004.4.26) Df(2L)Exel7007 (Ryder, 2004.4.26)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data
Insertions
	Type of insertions Name Expression data insertion of enhancer trap P{lacW}l(2)SH0241SH0241 No insertion of mobile activating element P{EP}EnoG5958 NA
Gene Ontology: Function, Process & Cellular Component ( 7 unique terms )
Terms Based on Experimental Evidence ( 3 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
regulation of gene expression inferred from mutant phenotype (Kiss and Andrulis, 2010)
Cellular Component
CV term Evidence References
cytoplasm inferred from direct assay (Graham et al., 2006) nuclear exosome (RNase complex) inferred from direct assay (Andrulis et al., 2002)
Terms Based on Predictions or Assertions ( 5 terms )
Molecular Function
CV term Evidence References
3'-5'-exoribonuclease activity inferred from sequence or structural similarity with UniProtKB:Q9NQT5 (FlyBase Genome Annotators, 2004) RNA binding inferred from electronic annotation with InterPro:IPR026699 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
rRNA processing inferred from sequence or structural similarity with UniProtKB:Q9NQT5 (FlyBase Genome Annotators, 2004)
Cellular Component
CV term Evidence References
exosome (RNase complex) inferred from sequence or structural similarity with UniProtKB:Q9NQT5 (FlyBase Genome Annotators, 2004) nuclear exosome (RNase complex) inferred from sequence or structural similarity with Saccharomyces RRP40 (Andrulis et al., 2002)
Sequence Ontology: Class of Gene
	gene   nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
Rrp40 - AR-2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Aats-met anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Baldspot anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - BubR1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG10139 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG10465 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG10889 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG1092 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG10934 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG11594 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG12519 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG12818 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG12869 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG13865 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG14500 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG15220 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG16817 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG1902 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG2921 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG2931 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG30411 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG31810 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG32137 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG32278 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG32812 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG3689 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG3793 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG3919 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG3995 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG4302 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG4415 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG4610 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG4619 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG4973 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG5482 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG5886 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG5989 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG6796 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG7272 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG7339 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG7429 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG7686 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG8026 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG8360 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG8671 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG8993 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG9090 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG9281 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CG9947 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - CR18854 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Cbl anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Cchl anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Cct5 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Cdc27 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Chmp1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Clect27 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Crk anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Csl4 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Dip3 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Dok anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - EndoG anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Ets96B anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - GABPI anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Golgin84 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Hakai anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - ImpL2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Jra anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Mcm5 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Mcm7 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Mhc anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Mnn1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Mpp6 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Mtr3 experimental knowledge based, anti tag coimmunoprecipitation, peptide massfingerprinting (Guruharsha et al., 2011, Mintseris et al., 2009.11.23) Rrp40 - ND42 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Obp19c anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Opbp anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Pitslre anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Pka-C1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Pof anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Pten anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Rab11 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - RasGAP1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - RhoGDI anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Rpb8 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Rrp4 experimental knowledge based (Guruharsha et al., 2011) Rrp40 - Rrp42 experimental knowledge based (Guruharsha et al., 2011) Rrp40 - Rrp46 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - SNCF anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Sbp2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Ski6 experimental knowledge based (Guruharsha et al., 2011) Rrp40 - Stat92E anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Su(var)2-10 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Syb anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Tbp anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Ufd1-like anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - Vps25 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - WASp anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - ana2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - bap anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - caup anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - coro anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - elB anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - fzy anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - grk anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - grp anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - hyx anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - ihog anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - inaC anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - l(1)G0469 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - lkb1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - mTerf5 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - msl-3 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - qua anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - spz3 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - ste24a anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - stops anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - thoc5 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - tor anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rrp40 - ttm50 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 Rrp40 allele Gene References
External Data
Linkouts	DPiM - DPiM, Drosophila Protein interaction Map • FBgn0260648 DroID - A comprehensive database of gene and protein interactions. • FBgn0260648 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 319033
Orthologs
OrthoDB Orthologs (41) - 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 EOG66MC4W Dipteran inclusive ortholog search EOG634WG2 Insect inclusive ortholog search EOG6ZGN8G Arthropod inclusive ortholog search EOG6NVX2F Metazoa inclusive ortholog search EOG6P32WJ
Orthologs in Drosophila Species (EOG66MC4W)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\Rrp40     Drosophila simulans   Dsim\GD23107 Y   Drosophila sechellia   Dsec\GM16829 Y   Drosophila erecta   Dere\GG24804 Y   Drosophila yakuba   Dyak\GE17692 Y   Drosophila ananassae   Dana\GF14006 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA16580 Y   Drosophila persimilis   Dper\GL19652 Y   Drosophila willistoni   Dwil\GK18349 Y   Drosophila willistoni   Dwil\GK20196     Drosophila virilis   Dvir\GJ22758 Y   Drosophila mojavensis   Dmoj\GI17269 Y   Drosophila grimshawi   Dgri\GH25200 Y
Orthologs in non-Drosophila Dipterans (EOG634WG2)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL014498   Aedes aegypti Yellow fever mosquito  Aaeg\AAEL013103   Anopheles gambiae Malaria mosquito  Agam\AGAP010247   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ802372
Orthologs in non-Dipteran Insects (EOG6ZGN8G)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\Rrp40   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG002742   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH15265   Atta cephalotes Leafcutter ant  Acep\ACEP16628   Camponotus floridanus Florida carpenter ant  Cflo\CFLO20855   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL15903   Linepithema humile Argentine ant  Lhum\LH12820   Pogonomyrmex barbatus Red harvester ant  Pbar\PB12610   Solenopsis invicta Red fire ant  Sinv\SINV22579   Acyrthosiphon pisum Pea aphid  Apim\ACYPI56194   Bombyx mori Silkmoth  Bmor\BGIBMGA009893   Pediculus humanus Human body louse  Phum\PHUM438090   Tribolium castaneum Red flour beetle  Tcas\TC005405
Orthologs in non-Insect Arthropods (EOG6NVX2F)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\accD   Daphnia pulex Water flea  Dpux\Zfp53
Orthologs in non-Arthropod Metazoa (EOG6P32WJ)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Caenorhabditis elegans Nematode  Cele\exos-3   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_026932gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_014762gn   Danio rerio Zebrafish  Drer\exosc3   Xenopus tropicalis Western clawed frog  Xtro\exosc3   Gallus gallus Domestic chicken  Ggal\EXOSC3   Mus musculus House mouse  Mmus\Exosc3   Rattus norvegicus Norway rat  Rnor\ENSRNOG00000012409   Homo sapiens Human  Hsap\EXOSC3
Human Orthologs (1)
Gene OMIM HGNC Hsap\EXOSC3
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD23107 Drosophila sechellia Dsec\GM16829 Drosophila erecta Dere\GG24804 Drosophila yakuba Dyak\GE17692 Drosophila ananassae Dana\GF14006 Drosophila pseudoobscura pseudoobscura Dpse\GA16580 Drosophila persimilis Dper\GL19652 Drosophila willistoni Dwil\GK18349 Drosophila virilis Dvir\GJ22758 Drosophila mojavensis Dmoj\GI17269 Drosophila grimshawi Dgri\GH25200
Stocks & Reagents
Stocks Listed in FlyBase ( 2 )
Bloomington	28470 y1 w*; P{EP}EnoG5958 Rrp40G5958/CyO
VDRC	v40306 w1118; P{GD10414}v40306
Genomic Clones ( 2 )
	BACR19B15 BACR25P15 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 3 )
	Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.
cDNA Clones, Fully Sequenced
BDGP DGC clones	RE44908
Other clones	DPiM_RE44908
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones	Dmel_neb_015509_0917_0764
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0260648 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 319033
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: Rrp40 CG31938 (Graham et al., 2006)
Additional comments
Other Comments
	Identification: as a protein that copurifies with Spt6 protein. (Andrulis et al., 2002) New annotation (CG31938) in release 3 of the genome annotation. (FlyBase Genome Annotators, 2002-2003)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_164435 RefSeq (Proteins) • NP_722725 DDBJ / EMBL / GenBank • AAN10459 Entrez Gene - A searchable database of RefSeq genes. • 319033 UniProtKB/TrEMBL • Q8IPX7
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Exosome complex RNA-binding protein 1/RRP40/RRP4 (IPR026699) RNA-binding domain, S1 (IPR022967)
Linkouts
	DPiM - DPiM, Drosophila Protein interaction Map • FBgn0260648 DroID - A comprehensive database of gene and protein interactions. • FBgn0260648 DRSC - Results from RNAi screens. • FBgn0260648 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0260648 FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0260648 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 319033 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 319033 modMine - Data generated by the modENCODE project. • FBgn0260648
Synonyms & Secondary IDs ( 3 )
Reported As
Symbol Synonym	CG31938 (Graham et al., 2006, Hödl and Basler, 2009) dRrp40 (Graham et al., 2009, Andrulis et al., 2002, Graham et al., 2006, Mamolen et al., 2010) Rrp40 (Guo et al., 2011, Graham et al., 2009, Kiss and Andrulis, 2010, Saulière et al., 2010, Kiss et al., 2012)
Name Synonym	CG31938   Rrp40
Secondary FlyBase IDs
	FBgn0051938 FBgn0064224
References ( 25 )
Generate a list of	All references relating to this gene ( 25 )
List References by type	Research paper  ( 12 ) Supplementary material  ( 5 ) Personal communication to FlyBase  ( 5 ) FlyBase analysis  ( 3 )
Recent research papers ( 3 )
	Lim et al., 2013, Nucleic Acids Res. 41(5): 2963--2980 Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila. [FBrf0221054] Kiss et al., 2012, Biochem. Biophys. Res. Commun. 423(3): 461--466 Dis3- and exosome subunit-responsive 3' mRNA instability elements. [FBrf0219677] Guo et al., 2011, Mol. Cell. Biol. 31(4): 639--651 Poly(A) Signals Located near the 5' End of Genes Are Silenced by a General Mechanism That Prevents Premature 3'-End Processing. [FBrf0212905] Show all research papers ...