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Gene Dmel\RfC38

General Information
Symbol	Dmel\RfC38	Species	D. melanogaster
Name	Replication factor C 38kD subunit	Annotation symbol	CG6258
Feature type	protein_coding_gene	FlyBase ID	FBgn0028700
Gene Model Status	Current	Stock availability	6 publicly available
Genomic Location
Chromosome (arm)	2L	Recombination map
Cytogenetic map	32D4-32D4	Sequence location	2L:11,128,930..11,130,645 [-]
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 Replication factor C 38kD subunit is referred to in FlyBase by the symbol Dmel\RfC38 (CG6258, FBgn0028700). It is a protein_coding_gene from Drosophila melanogaster. Based on sequence similarity, it is predicted to have molecular function: ATPase activity; DNA clamp loader activity. There is experimental evidence that it is involved in the biological process: neurogenesis. 6 alleles are reported. The phenotype of these alleles is annotated with: trichogen cell. It has one annotated transcript and one annotated polypeptide. Protein features are: AAA+ ATPase domain; DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal; Replication factor C, C-terminal domain. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of low expression. Peak expression observed within 00-06 hour embryonic stages. Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: adult ovary. Expression at moderate levels in the following post-embryonic organs or tissues: larval central nervous system, larval hindgut, larval salivary gland, larval trachea, inseminated spermatheca, adult male accessory gland, larval carcass. Comments on Affy2 ProbeSet: ProbeSet 1634081_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of RfC38. Gene sequence location is 2L:11128930..11130645.
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 32D4-32D4   Limits computationally determined from genome sequence between P{EP}ppoEP2478&P{lacW}l(2)k15817k15817 and P{lacW}RfC38k13807 32D4--5 Left limit from in situ hybridisation (FBrf0111489) Right limit from in situ hybridisation (FBrf0111489)
Experimentally Determined Cytological Location
Cytogenetic map Notes References 32D4-32D5   (determined by in situ hybridisation)   (Spradling et al., 1999) 32D4-32D5     (BDGP Project Members, 1994-1999)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\RfC38 for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) RfC38-RA FBtr0080225  NM_135650   1606   356
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 RfC38-PA   FBpp0079812   40.8   356   8.56     NP_609494   AAF53076
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Replication factor C, C-terminal domain (IPR013748) AAA+ ATPase domain (IPR003593) DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal (IPR008921) P-loop containing nucleoside triphosphate hydrolase (IPR027417)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA263648   AA439090   AA439103   AA439110   AA441184   AA539825   AA696631   AA948994   AE014134 AAF53076   AF160912 AAD46852   AI516198   AI520294   AI543847   AI946517   AQ026070   BG639029   BI163384   BI234183   BI237190   BI240530   BI352744   BI364128   BI364374   BI365960   BI375313   BI375877   BI376013   BI376150   BI484713   BI635831   BI639015   BP549727   BP553301   BP553302   CK604766   CK604767   CO284399   CO292076   CO313692   CZ478559   CZ489972   CZ489973   EC073797   EC076684   EC203304   EC235520   EV579407   EV581235   GH751594
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q9U9Q1 Q7KLW6
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
microtubule associated complex inferred from direct assay (Hughes et al., 2008)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
FlyAtlas Anatomical Expression Data (FlyAtlas-RNA.adult) (FlyAtlas-RNA.larva)    Styles Linear Logarithmic Heatmap Back-to-back    Scales gene max expression Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: adult ovary. Expression at moderate levels in the following post-embryonic organs or tissues: larval central nervous system, larval hindgut, larval salivary gland, larval trachea, inseminated spermatheca, 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    444.1 Larval Midgut    61.1 Larval Hindgut    118.8 Larval Malpighian Tubules    76.2 Larval Fat Body    63.9 Larval Salivary Gland    225.5 Larval Trachea    255.45 Larval Carcass    144 Adult Head    57.3 Adult Eye    72.475 Adult Brain    79.7 Adult Thoracic-Abdominal Ganglion    87.9 Adult Crop    74.3 Adult Midgut    65.5 Adult Hindgut    70.2 Adult Malpighian Tubules    83.8 Adult Fat Body    71.7 Adult Salivary Gland    64.3 Adult Heart    58.25 Adult VirginFemale Spermatheca    75.5 Adult InseminatedFemale Spermatheca    109.3 Adult Ovary    741.1 Adult Testis    56.8 Adult Male Accessory Gland    119 Adult Carcass    59.4 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    444.1 Larval Midgut    61.1 Larval Hindgut    118.8 Larval Malpighian Tubules    76.2 Larval Fat Body    63.9 Larval Salivary Gland    225.5 Larval Trachea    255.45 Larval Carcass    144 Adult Head    57.3 Adult Eye    72.475 Adult Brain    79.7 Adult Thoracic-Abdominal Ganglion    87.9 Adult Crop    74.3 Adult Midgut    65.5 Adult Hindgut    70.2 Adult Malpighian Tubules    83.8 Adult Fat Body    71.7 Adult Salivary Gland    64.3 Adult Heart    58.25 Adult VirginFemale Spermatheca    75.5 Adult InseminatedFemale Spermatheca    109.3 Adult Ovary  (741.1) Adult Testis    56.8 Adult Male Accessory Gland    119 Adult Carcass    59.4 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    444.1 Larval Midgut    61.1 Larval Hindgut    118.8 Larval Malpighian Tubules    76.2 Larval Fat Body    63.9 Larval Salivary Gland    225.5 Larval Trachea    255.45 Larval Carcass    144 Adult Head    57.3 Adult Eye    72.475 Adult Brain    79.7 Adult Thoracic-Abdominal Ganglion    87.9 Adult Crop    74.3 Adult Midgut    65.5 Adult Hindgut    70.2 Adult Malpighian Tubules    83.8 Adult Fat Body    71.7 Adult Salivary Gland    64.3 Adult Heart    58.25 Adult VirginFemale Spermatheca    75.5 Adult InseminatedFemale Spermatheca    109.3 Adult Ovary    741.1 Adult Testis    56.8 Adult Male Accessory Gland    119 Adult Carcass    59.4 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    444.1 Larval Midgut    61.1 Larval Hindgut    118.8 Larval Malpighian Tubules    76.2 Larval Fat Body    63.9 Larval Salivary Gland    225.5 Larval Trachea    255.45 Larval Carcass    144 Adult Head    57.3 Adult Eye    72.475 Adult Brain    79.7 Adult Thoracic-Abdominal Ganglion    87.9 Adult Crop    74.3 Adult Midgut    65.5 Adult Hindgut    70.2 Adult Malpighian Tubules    83.8 Adult Fat Body    71.7 Adult Salivary Gland    64.3 Adult Heart    58.25 Adult VirginFemale Spermatheca    75.5 Adult InseminatedFemale Spermatheca    109.3 Adult Ovary    741.1 Adult Testis    56.8 Adult Male Accessory Gland    119 Adult Carcass    59.4 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    444.1 Larval Midgut    61.1 Larval Hindgut    118.8 Larval Malpighian Tubules    76.2 Larval Fat Body    63.9 Larval Salivary Gland    225.5 Larval Trachea    255.45 Larval Carcass    144 Adult Head    57.3 Adult Eye    72.475 Adult Brain    79.7 Adult Thoracic-Abdominal Ganglion    87.9 Adult Crop    74.3 Adult Midgut    65.5 Adult Hindgut    70.2 Adult Malpighian Tubules    83.8 Adult Fat Body    71.7 Adult Salivary Gland    64.3 Adult Heart    58.25 Adult VirginFemale Spermatheca    75.5 Adult InseminatedFemale Spermatheca    109.3 Adult Ovary    741.1 Adult Testis    56.8 Adult Male Accessory Gland    119 Adult Carcass    59.4 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    444.1 Larval Midgut    61.1 Larval Hindgut    118.8 Larval Malpighian Tubules    76.2 Larval Fat Body    63.9 Larval Salivary Gland    225.5 Larval Trachea    255.45 Larval Carcass    144 Adult Head    57.3 Adult Eye    72.475 Adult Brain    79.7 Adult Thoracic-Abdominal Ganglion    87.9 Adult Crop    74.3 Adult Midgut    65.5 Adult Hindgut    70.2 Adult Malpighian Tubules    83.8 Adult Fat Body    71.7 Adult Salivary Gland    64.3 Adult Heart    58.25 Adult VirginFemale Spermatheca    75.5 Adult InseminatedFemale Spermatheca    109.3 Adult Ovary  741.1 Adult Testis    56.8 Adult Male Accessory Gland    119 Adult Carcass    59.4 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    444.1 Larval Midgut    61.1 Larval Hindgut    118.8 Larval Malpighian Tubules    76.2 Larval Fat Body    63.9 Larval Salivary Gland    225.5 Larval Trachea    255.45 Larval Carcass    144 Adult Head    57.3 Adult Eye    72.475 Adult Brain    79.7 Adult Thoracic-Abdominal Ganglion    87.9 Adult Crop    74.3 Adult Midgut    65.5 Adult Hindgut    70.2 Adult Malpighian Tubules    83.8 Adult Fat Body    71.7 Adult Salivary Gland    64.3 Adult Heart    58.25 Adult VirginFemale Spermatheca    75.5 Adult InseminatedFemale Spermatheca    109.3 Adult Ovary    741.1 Adult Testis    56.8 Adult Male Accessory Gland    119 Adult Carcass    59.4 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    444.1 Larval Midgut    61.1 Larval Hindgut    118.8 Larval Malpighian Tubules    76.2 Larval Fat Body    63.9 Larval Salivary Gland    225.5 Larval Trachea    255.45 Larval Carcass    144 Adult Head    57.3 Adult Eye    72.475 Adult Brain    79.7 Adult Thoracic-Abdominal Ganglion    87.9 Adult Crop    74.3 Adult Midgut    65.5 Adult Hindgut    70.2 Adult Malpighian Tubules    83.8 Adult Fat Body    71.7 Adult Salivary Gland    64.3 Adult Heart    58.25 Adult VirginFemale Spermatheca    75.5 Adult InseminatedFemale Spermatheca    109.3 Adult Ovary    741.1 Adult Testis    56.8 Adult Male Accessory Gland    119 Adult Carcass    59.4 Expression Level Scale  None   Low   Moderate   High   Very high  Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut     Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body     Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion     Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body     Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca     Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland     Adult Carcass     FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    57.3   NA  Eye    72.475   NA  Brain    79.7   444.1  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    87.9   NA  Crop    74.3   61.1  Midgut    no informative data   118.8  Hindgut    70.2   76.2  Malpighian Tubules    83.8   no informative data  Fat Body    71.7   225.5  Salivary Gland    no informative data   NA  Heart    58.25   255.45  Trachea    NA   NA  VirginFemale Spermatheca    75.5   NA  InseminatedFemale Spermatheca    109.3   NA  Ovary    741.1   NA  Testis    56.8   NA  Male Accessory Gland    119   144  Carcass    no informative data FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
modENCODE Anatomy RNA-Seq
modENCODE Tissue Expression Data (modENCODE_mRNA-Seq_tissues)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    11 central nervous system, larvae L3    7 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    2 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    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    27 ovary, mated 4-day female    19 testis, mated 4-day male    2 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    11 central nervous system, larvae L3    7 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    2 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    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female  (27) ovary, mated 4-day female    19 testis, mated 4-day male    2 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    11 central nervous system, larvae L3    7 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    2 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    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    27 ovary, mated 4-day female    19 testis, mated 4-day male    2 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Tissue   Expression Level imaginal disc, larvae L3 wandering    11 central nervous system, larvae L3    7 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    2 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    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    27 ovary, mated 4-day female    19 testis, mated 4-day male    2 accessory gland, mated 4-day male    1 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    11 central nervous system, larvae L3    7 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    2 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    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    27 ovary, mated 4-day female    19 testis, mated 4-day male    2 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    11 central nervous system, larvae L3    7 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    2 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    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female  27 ovary, mated 4-day female    19 testis, mated 4-day male    2 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    11 central nervous system, larvae L3    7 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    2 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    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    27 ovary, mated 4-day female    19 testis, mated 4-day male    2 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Tissue   Expression Level imaginal disc, larvae L3 wandering    11 central nervous system, larvae L3    7 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    2 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    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    27 ovary, mated 4-day female    19 testis, mated 4-day male    2 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Tissue   Expression Level imaginal disc, larvae L3 wandering     central nervous system, larvae L3     central nervous system, pupae P8     head, virgin 1-day female     head, virgin 4-day female     head, virgin 20-day female     head, mated 1-day female     head, mated 4-day female     head, mated 20-day female     head, mated 1-day male     head, mated 4-day male     head, mated 20-day male     salivary gland, larvae L3 wandering     salivary gland, white prepupae     digestive system, larvae L3 wandering     digestive system, 1-day adult     digestive system, 4-day adult     digestive system, 20-day adult     fat body, larvae L3 wandering     fat body, white prepupae     fat body, pupae P8     carcass, larvae L3 wandering     carcass, 1-day adult     carcass, 4-day adult     carcass, 20-day adult     ovary, virgin 4-day female     ovary, mated 4-day female     testis, mated 4-day male     accessory gland, mated 4-day male
modENCODE Development RNA-Seq
modENCODE Temporal Expression Data (modENCODE_mRNA-Seq_U)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of low expression. Peak expression observed within 00-06 hour embryonic stages. [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    94 embryo 02-04hr    89 embryo 04-06hr    57 embryo 06-08hr    39 embryo 08-10hr    38 embryo 10-12hr    26 embryo 12-14hr    16 embryo 14-16hr    22 embryo 16-18hr    13 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    9 larva L1    12 larva L2    11 larva L3 12hr old    8 larva L3 puffstage 1-2    10 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    14 white prepupae 12hr    17 white prepupae 24hr    16 pupae 2d postWPP    7 pupae 3d postWPP    4 pupae 4d postWPP    6 adult male 01day    4 adult male 05day    5 adult male 30day    6 adult female 01day    28 adult female 05day    45 adult female 30day    43 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (94) embryo 02-04hr  (89) embryo 04-06hr  (57) embryo 06-08hr  (39) embryo 08-10hr  (38) embryo 10-12hr  26 embryo 12-14hr    16 embryo 14-16hr    22 embryo 16-18hr    13 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    9 larva L1    12 larva L2    11 larva L3 12hr old    8 larva L3 puffstage 1-2    10 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    14 white prepupae 12hr    17 white prepupae 24hr    16 pupae 2d postWPP    7 pupae 3d postWPP    4 pupae 4d postWPP    6 adult male 01day    4 adult male 05day    5 adult male 30day    6 adult female 01day  (28) adult female 05day  (45) adult female 30day  (43) Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    94 embryo 02-04hr    89 embryo 04-06hr    57 embryo 06-08hr    39 embryo 08-10hr    38 embryo 10-12hr    26 embryo 12-14hr    16 embryo 14-16hr    22 embryo 16-18hr    13 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    9 larva L1    12 larva L2    11 larva L3 12hr old    8 larva L3 puffstage 1-2    10 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    14 white prepupae 12hr    17 white prepupae 24hr    16 pupae 2d postWPP    7 pupae 3d postWPP    4 pupae 4d postWPP    6 adult male 01day    4 adult male 05day    5 adult male 30day    6 adult female 01day    28 adult female 05day    45 adult female 30day    43 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    94 embryo 02-04hr    89 embryo 04-06hr    57 embryo 06-08hr    39 embryo 08-10hr    38 embryo 10-12hr    26 embryo 12-14hr    16 embryo 14-16hr    22 embryo 16-18hr    13 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    9 larva L1    12 larva L2    11 larva L3 12hr old    8 larva L3 puffstage 1-2    10 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    14 white prepupae 12hr    17 white prepupae 24hr    16 pupae 2d postWPP    7 pupae 3d postWPP    4 pupae 4d postWPP    6 adult male 01day    4 adult male 05day    5 adult male 30day    6 adult female 01day    28 adult female 05day    45 adult female 30day    43 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    94 embryo 02-04hr    89 embryo 04-06hr    57 embryo 06-08hr    39 embryo 08-10hr    38 embryo 10-12hr    26 embryo 12-14hr    16 embryo 14-16hr    22 embryo 16-18hr    13 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    9 larva L1    12 larva L2    11 larva L3 12hr old    8 larva L3 puffstage 1-2    10 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    14 white prepupae 12hr    17 white prepupae 24hr    16 pupae 2d postWPP    7 pupae 3d postWPP    4 pupae 4d postWPP    6 adult male 01day    4 adult male 05day    5 adult male 30day    6 adult female 01day    28 adult female 05day    45 adult female 30day    43 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (94) embryo 02-04hr  (89) embryo 04-06hr  (57) embryo 06-08hr  (39) embryo 08-10hr  (38) embryo 10-12hr  26 embryo 12-14hr    16 embryo 14-16hr    22 embryo 16-18hr    13 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    9 larva L1    12 larva L2    11 larva L3 12hr old    8 larva L3 puffstage 1-2    10 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    14 white prepupae 12hr    17 white prepupae 24hr    16 pupae 2d postWPP    7 pupae 3d postWPP    4 pupae 4d postWPP    6 adult male 01day    4 adult male 05day    5 adult male 30day    6 adult female 01day  28 adult female 05day  (45) adult female 30day  (43) Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    94 embryo 02-04hr    89 embryo 04-06hr    57 embryo 06-08hr    39 embryo 08-10hr    38 embryo 10-12hr    26 embryo 12-14hr    16 embryo 14-16hr    22 embryo 16-18hr    13 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    9 larva L1    12 larva L2    11 larva L3 12hr old    8 larva L3 puffstage 1-2    10 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    14 white prepupae 12hr    17 white prepupae 24hr    16 pupae 2d postWPP    7 pupae 3d postWPP    4 pupae 4d postWPP    6 adult male 01day    4 adult male 05day    5 adult male 30day    6 adult female 01day    28 adult female 05day    45 adult female 30day    43 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    94 embryo 02-04hr    89 embryo 04-06hr    57 embryo 06-08hr    39 embryo 08-10hr    38 embryo 10-12hr    26 embryo 12-14hr    16 embryo 14-16hr    22 embryo 16-18hr    13 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    9 larva L1    12 larva L2    11 larva L3 12hr old    8 larva L3 puffstage 1-2    10 larva L3 puffstage 3-6    13 larva L3 puffstage 7-9    15 white prepupae new    14 white prepupae 12hr    17 white prepupae 24hr    16 pupae 2d postWPP    7 pupae 3d postWPP    4 pupae 4d postWPP    6 adult male 01day    4 adult male 05day    5 adult male 30day    6 adult female 01day    28 adult female 05day    45 adult female 30day    43 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+    26 Schneider line 2 Sg4    28 embryonic 1182-4H    9 embryonic GM2    9 embryonic Kc167    6 embryonic S1    18 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    12 wing disc ML-DmD8    16 wing disc ML-DmD9    15 wing disc ML-DmD16-c3    16 wing disc ML-DmD21    35 wing disc ML-DmD32    10 haltere disc ML-DmD17-c3    17 eye-antennal disc ML-DmD11    17 antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    14 CNS ML-DmBG2-c2    11 tumorous blood cells mbn2    11 ovary fGS/OSS    17 ovary OSC    10 ovary OSS    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  26 Schneider line 2 Sg4  (28) embryonic 1182-4H    9 embryonic GM2    9 embryonic Kc167    6 embryonic S1    18 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    12 wing disc ML-DmD8    16 wing disc ML-DmD9    15 wing disc ML-DmD16-c3    16 wing disc ML-DmD21  (35) wing disc ML-DmD32    10 haltere disc ML-DmD17-c3    17 eye-antennal disc ML-DmD11    17 antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    14 CNS ML-DmBG2-c2    11 tumorous blood cells mbn2    11 ovary fGS/OSS    17 ovary OSC    10 ovary OSS    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    26 Schneider line 2 Sg4    28 embryonic 1182-4H    9 embryonic GM2    9 embryonic Kc167    6 embryonic S1    18 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    12 wing disc ML-DmD8    16 wing disc ML-DmD9    15 wing disc ML-DmD16-c3    16 wing disc ML-DmD21    35 wing disc ML-DmD32    10 haltere disc ML-DmD17-c3    17 eye-antennal disc ML-DmD11    17 antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    14 CNS ML-DmBG2-c2    11 tumorous blood cells mbn2    11 ovary fGS/OSS    17 ovary OSC    10 ovary OSS    7 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+    26 Schneider line 2 Sg4    28 embryonic 1182-4H    9 embryonic GM2    9 embryonic Kc167    6 embryonic S1    18 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    12 wing disc ML-DmD8    16 wing disc ML-DmD9    15 wing disc ML-DmD16-c3    16 wing disc ML-DmD21    35 wing disc ML-DmD32    10 haltere disc ML-DmD17-c3    17 eye-antennal disc ML-DmD11    17 antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    14 CNS ML-DmBG2-c2    11 tumorous blood cells mbn2    11 ovary fGS/OSS    17 ovary OSC    10 ovary OSS    7 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    26 Schneider line 2 Sg4    28 embryonic 1182-4H    9 embryonic GM2    9 embryonic Kc167    6 embryonic S1    18 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    12 wing disc ML-DmD8    16 wing disc ML-DmD9    15 wing disc ML-DmD16-c3    16 wing disc ML-DmD21    35 wing disc ML-DmD32    10 haltere disc ML-DmD17-c3    17 eye-antennal disc ML-DmD11    17 antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    14 CNS ML-DmBG2-c2    11 tumorous blood cells mbn2    11 ovary fGS/OSS    17 ovary OSC    10 ovary OSS    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  26 Schneider line 2 Sg4  28 embryonic 1182-4H    9 embryonic GM2    9 embryonic Kc167    6 embryonic S1    18 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    12 wing disc ML-DmD8    16 wing disc ML-DmD9    15 wing disc ML-DmD16-c3    16 wing disc ML-DmD21  (35) wing disc ML-DmD32    10 haltere disc ML-DmD17-c3    17 eye-antennal disc ML-DmD11    17 antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    14 CNS ML-DmBG2-c2    11 tumorous blood cells mbn2    11 ovary fGS/OSS    17 ovary OSC    10 ovary OSS    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    26 Schneider line 2 Sg4    28 embryonic 1182-4H    9 embryonic GM2    9 embryonic Kc167    6 embryonic S1    18 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    12 wing disc ML-DmD8    16 wing disc ML-DmD9    15 wing disc ML-DmD16-c3    16 wing disc ML-DmD21    35 wing disc ML-DmD32    10 haltere disc ML-DmD17-c3    17 eye-antennal disc ML-DmD11    17 antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    14 CNS ML-DmBG2-c2    11 tumorous blood cells mbn2    11 ovary fGS/OSS    17 ovary OSC    10 ovary OSS    7 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+    26 Schneider line 2 Sg4    28 embryonic 1182-4H    9 embryonic GM2    9 embryonic Kc167    6 embryonic S1    18 embryonic S3    15 leg disc CME L1    17 wing disc CME-W2    12 wing disc ML-DmD8    16 wing disc ML-DmD9    15 wing disc ML-DmD16-c3    16 wing disc ML-DmD21    35 wing disc ML-DmD32    10 haltere disc ML-DmD17-c3    17 eye-antennal disc ML-DmD11    17 antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    14 CNS ML-DmBG2-c2    11 tumorous blood cells mbn2    11 ovary fGS/OSS    17 ovary OSC    10 ovary OSS    7 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    5 cold shock, 4-day adult    3 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    15 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    26 Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    14 Caffeine 25 mg/ml 48 hrs, 4-day adult    5 Paraquat 5 mM 48 hrs, 4-day adult    11 Paraquat 10 mM 48 hrs, 4-day adult    16 Rotenone 2 μg 12 hrs, larvae L3    8 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    5 cold shock, 4-day adult    3 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    15 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3  26 Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    14 Caffeine 25 mg/ml 48 hrs, 4-day adult    5 Paraquat 5 mM 48 hrs, 4-day adult    11 Paraquat 10 mM 48 hrs, 4-day adult    16 Rotenone 2 μg 12 hrs, larvae L3    8 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    5 cold shock, 4-day adult    3 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    15 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    26 Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    14 Caffeine 25 mg/ml 48 hrs, 4-day adult    5 Paraquat 5 mM 48 hrs, 4-day adult    11 Paraquat 10 mM 48 hrs, 4-day adult    16 Rotenone 2 μg 12 hrs, larvae L3    8 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    5 cold shock, 4-day adult    3 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    15 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    26 Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    14 Caffeine 25 mg/ml 48 hrs, 4-day adult    5 Paraquat 5 mM 48 hrs, 4-day adult    11 Paraquat 10 mM 48 hrs, 4-day adult    16 Rotenone 2 μg 12 hrs, larvae L3    8 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    5 cold shock, 4-day adult    3 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    15 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    26 Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    14 Caffeine 25 mg/ml 48 hrs, 4-day adult    5 Paraquat 5 mM 48 hrs, 4-day adult    11 Paraquat 10 mM 48 hrs, 4-day adult    16 Rotenone 2 μg 12 hrs, larvae L3    8 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    5 cold shock, 4-day adult    3 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    15 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3  26 Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    14 Caffeine 25 mg/ml 48 hrs, 4-day adult    5 Paraquat 5 mM 48 hrs, 4-day adult    11 Paraquat 10 mM 48 hrs, 4-day adult    16 Rotenone 2 μg 12 hrs, larvae L3    8 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    5 cold shock, 4-day adult    3 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    15 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    26 Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    14 Caffeine 25 mg/ml 48 hrs, 4-day adult    5 Paraquat 5 mM 48 hrs, 4-day adult    11 Paraquat 10 mM 48 hrs, 4-day adult    16 Rotenone 2 μg 12 hrs, larvae L3    8 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    5 cold shock, 4-day adult    3 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    15 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    26 Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    14 Caffeine 25 mg/ml 48 hrs, 4-day adult    5 Paraquat 5 mM 48 hrs, 4-day adult    11 Paraquat 10 mM 48 hrs, 4-day adult    16 Rotenone 2 μg 12 hrs, larvae L3    8 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_13 mE1_20_mRNA_expression_cluster_04
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0028700 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG6258-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal RfC38GD4101 lethal | recessive RfC38k13807 viable, with Scer\GAL4pnr-MD237 RfC38GD4101 Other Phenotypes Allele neuroanatomy defective | larval stage RfC38GD4101 visible, with Scer\GAL4pnr-MD237 RfC38GD4101 Phenotype manifest in Allele embryonic/larval neuroblast | larval stage RfC38GD4101 ganglion mother cell | larval stage RfC38GD4101 trichogen cell, with Scer\GAL4pnr-MD237 RfC38GD4101
Classical Alleles ( 3 )
For All Classical Alleles Show
Allele of RfC38 Class Mutagen Stocks Known lesion RfC38k13807 P-element activity 2 -- RfC38e00704 piggyBac transposase 1 -- RfC38f07177 piggyBac transposase 1 --
Alleles Carried on Transgenic Constructs ( 3 )
For All Alleles Carried on Transgenic Constructs Show
Allele of RfC38 Class Mutagen Stocks Known lesion RfC38GD4101 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes RfC389 in vitro construct - genomic fragment 0 Yes RfC38NIG.6258R in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Not disrupted in	Df(2L)BSC242 (Maehara et al., 2012) Df(2L)EP372M190 (Maehara et al., 2012) Df(2L)EP372M201 (Maehara et al., 2012) Df(2L)EP372M203 (Maehara et al., 2012) Df(2L)EP372M219 (Maehara et al., 2012) Df(2L)Prl (Spradling et al., 1999, BDGP Project Members, 1994-1999)
Disrupted in	Df(2L)Exel6027 (Ryder, 2004.4.26)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD4101} NA P{NIG.6258R} NA characterization construct P{Nup160+t9} NA
Insertions
	Type of insertions Name Expression data insertion of enhancer trap P{lacW}RfC38k13807 No miscellaneous insertions PBac{RB}RfC38e00704 NA PBac{WH}RfC38f07177 NA
Gene Ontology: Function, Process & Cellular Component ( 7 unique terms )
Terms Based on Experimental Evidence ( 2 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
neurogenesis inferred from mutant phenotype (Neumüller et al., 2011)
Cellular Component
CV term Evidence References
microtubule associated complex inferred from direct assay (Hughes et al., 2008)
Terms Based on Predictions or Assertions ( 5 terms )
Molecular Function
CV term Evidence References
ATPase activity inferred from sequence or structural similarity with Saccharomyces RFC5 (FlyBase, 1992-) DNA clamp loader activity inferred from sequence or structural similarity with Saccharomyces RFC5 (FlyBase, 1992-) nucleotide binding inferred from electronic annotation with InterPro:IPR003593 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
DNA replication inferred from electronic annotation with InterPro:IPR008921, InterPro:IPR019483 (FlyBase Curators et al., 2004-)
Cellular Component
CV term Evidence References
DNA replication factor C complex inferred from sequence or structural similarity with Saccharomyces RFC5 (FlyBase, 1992-)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
RfC38 - CG15047 experimental knowledge based (Guruharsha et al., 2011) RfC38 - CG16817 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) RfC38 - CG3165 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) RfC38 - CG31675 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) RfC38 - CG3548 experimental knowledge based (Guruharsha et al., 2011) RfC38 - CG5196 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) RfC38 - CG5846 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) RfC38 - CG5961 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) RfC38 - CG8142 experimental knowledge based (Guruharsha et al., 2011) RfC38 - Crk anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) RfC38 - D1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) RfC38 - Gnf1 experimental knowledge based (Guruharsha et al., 2011) RfC38 - Irbp experimental knowledge based (Guruharsha et al., 2011) RfC38 - Kr-h1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) RfC38 - Ku80 experimental knowledge based (Guruharsha et al., 2011) RfC38 - Parp experimental knowledge based (Guruharsha et al., 2011) RfC38 - Stat92E anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) RfC38 - hbn anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) RfC38 - lack anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) RfC38 - vri anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) RfC38 - βggt-II 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 RfC38 allele Gene References RfC38k13807 cutlet (Jaffe and Jongens, 2001)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 60612 DroID - A comprehensive database of gene and protein interactions. • FBgn0028700 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 34550
Orthologs
OrthoDB Orthologs (38) - based on analysis using Dmel annotation version 5.41
OrthoDB Ortholog Groups
	OrthoDB orthology group searches (Waterhouse et al., 2011, Nucleic Acids Res. 39(Database issue): D283--D288) Drosophila inclusive ortholog search EOG6FBJCW Dipteran inclusive ortholog search EOG6VT65W Insect inclusive ortholog search EOG63R2HB Arthropod inclusive ortholog search EOG644J20 Metazoa inclusive ortholog search EOG6V4G2J
Orthologs in Drosophila Species (EOG6FBJCW)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\RfC38     Drosophila simulans   Dsim\GD22189 Y   Drosophila sechellia   Dsec\GM11127 Y   Drosophila erecta   Dere\GG10322 Y   Drosophila yakuba   Dyak\GE12972 Y   Drosophila ananassae   Dana\GF14225 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA19473 Y   Drosophila persimilis   Dper\GL18586 Y   Drosophila willistoni   Dwil\GK15241 Y   Drosophila virilis   Dvir\GJ14536 Y   Drosophila mojavensis   Dmoj\GI18150 Y   Drosophila grimshawi   Dgri\GH10966 Y
Orthologs in non-Drosophila Dipterans (EOG6VT65W)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL007581   Anopheles gambiae Malaria mosquito  Agam\AGAP009047   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ801697
Orthologs in non-Dipteran Insects (EOG63R2HB)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\RfC38   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG012946   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH19693   Atta cephalotes Leafcutter ant  Acep\ACEP13702   Camponotus floridanus Florida carpenter ant  Cflo\CFLO23257   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL21767   Linepithema humile Argentine ant  Lhum\LH14864   Pogonomyrmex barbatus Red harvester ant  Pbar\PB23894   Solenopsis invicta Red fire ant  Sinv\SINV21626   Acyrthosiphon pisum Pea aphid  Apim\ACYPI001146   Bombyx mori Silkmoth  Bmor\BGIBMGA011461   Pediculus humanus Human body louse  Phum\PHUM253510   Tribolium castaneum Red flour beetle  Tcas\TC006622
Orthologs in non-Insect Arthropods (EOG644J20)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\srv-27   Ixodes scapularis Deer tick  Isca\ISCW003705
Orthologs in non-Arthropod Metazoa (EOG6V4G2J)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Caenorhabditis elegans Nematode  Cele\rfc-3   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_004468gn   Danio rerio Zebrafish  Drer\rfc3   Xenopus tropicalis Western clawed frog  Xtro\rfc3   Gallus gallus Domestic chicken  Ggal\RFC3   Mus musculus House mouse  Mmus\Rfc3   Rattus norvegicus Norway rat  Rnor\Rfc3   Homo sapiens Human  Hsap\RFC3
Human Orthologs (1)
Gene OMIM HGNC Hsap\RFC3
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD22189 Drosophila sechellia Dsec\GM11127 Drosophila erecta Dere\GG10322 Drosophila yakuba Dyak\GE12972 Drosophila ananassae Dana\GF14225 Drosophila pseudoobscura pseudoobscura Dpse\GA19473 Drosophila persimilis Dper\GL18586 Drosophila willistoni Dwil\GK15241 Drosophila virilis Dvir\GJ14536 Drosophila mojavensis Dmoj\GI18150 Drosophila grimshawi Dgri\GH10966
Stocks & Reagents
Stocks Listed in FlyBase ( 6 )
Bloomington	11109 y1 w67c23; P{lacW}RfC38k13807/CyO
Harvard	- PBac{RB}RfC38e00704 - PBac{WH}RfC38f07177
Kyoto	111333 yd2 w1118 P{ey-FLP.N}2 P{GMR-lacZ.C(38.1)}TPN1; P{lacW}RfC38k13807 P{neoFRT}40A/CyO y+
VDRC	v12618 w1118; P{GD4101}v12618 v12620 w1118; P{GD4101}v12620/TM3
Genomic Clones ( 2 )
	BACR09F02 BACR20O15 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 40 )
	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	LD06837
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	GM08039 GM20577 LD13549 LD13565 LD13576 LD16086 LD19089 LD27721 LD40413 LD45506 RE02765 RE29841 RE33372 RE37383 RE49180 RE49467 RE51367 RE63087 RE63777 RE63933 RE64083 RE67855 SD17338 SD21444
Other clones	51527 71143 107882 125654 bs27c11 Dmel_dig_016024_0619_3353 Dmel_dig_019235_0614_2947 EK165957 EK199129 EK233747 FGM103B05 FGM223F12 LD41983 RP003116831 UT01435
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0028700 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 34550
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: BcDNA:LD06837 CG6258 (Gong, 1999.11)
Source for database merge of	Source for merge of: RfC38 CG6258 (FlyBase, 1996-)
Additional comments
Other Comments
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_135650 RefSeq (Proteins) • NP_609494 DDBJ / EMBL / GenBank • AA263648 AA439090 AAD46852 AAF53076 AF160912 AI516198 AI946517 AQ026070 CZ478559 CZ489972 CZ489973 Entrez Gene - A searchable database of RefSeq genes. • 34550 UniProtKB/TrEMBL • Q7KLW6 Q9U9Q1
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Replication factor C, C-terminal domain (IPR013748) AAA+ ATPase domain (IPR003593) DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal (IPR008921) P-loop containing nucleoside triphosphate hydrolase (IPR027417)
Linkouts
	BioGRID - A database of protein and genetic interactions • 60612 DroID - A comprehensive database of gene and protein interactions. • FBgn0028700 DRSC - Results from RNAi screens. • FBgn0028700 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0028700 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG6258-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0028700 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 34550 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 34550 modMine - Data generated by the modENCODE project. • FBgn0028700
Synonyms & Secondary IDs ( 10 )
Reported As
Symbol Synonym	BcDNA:LD06837 (Giot et al., 2003, ) CG6258 (Oliver, 2001.8.16, Whitfield, 2000.5.17, Jin et al., 2001, Krause et al., 2001, Hughes et al., 2008, Lowery et al., 2010) DmRFC5 (Krause et al., 2001) l(2)k13807 (Beaton, 2000.1.31) l(2)rfc38 (Jaffe and Jongens, 2001) n(2)k13807 (Spradling, 1999.12.9) Rfc38 (Spradling et al., 1999) RfC38 (Cayirlioglu et al., 2003, Maehara et al., 2012, Tang and Presgraves, 2009, Buch et al., 2008, Sawamura et al., 2010, Fisher et al., 2008, Érdi et al., 2012, Japanese National Institute of Genetics, 2012.5.21, Antao et al., 2012)
Name Synonym	DNA replication factor, 38k subunit (Spradling et al., 1999) Replication factor C 38kD subunit (Spradling et al., 1999)
Secondary FlyBase IDs
	FBgn0027894
References ( 38 )
Generate a list of	All references relating to this gene ( 38 )
List References by type	Research paper  ( 14 ) Supplementary material  ( 6 ) Personal communication to FlyBase  ( 12 ) FlyBase analysis  ( 2 ) Stock list  ( 1 ) Curated genome annotation  ( 3 )
Recent research papers ( 3 )
	Antao et al., 2012, Mol. Cell. Biol. 32(12): 2170--2182 Protein Landscape at Drosophila melanogaster Telomere-Associated Sequence Repeats. [FBrf0218429] Maehara et al., 2012, Genes & Genet. Systems 87(2): 99--106 Genetic dissection of Nucleoporin 160 (Nup160), a gene involved in multiple phenotypes of reproductive isolation in Drosophila. [FBrf0218968] Érdi et al., 2012, Autophagy 8(7): 1124--1135 Loss of the starvation-induced gene Rack1 leads to glycogen deficiency and impaired autophagic responses in Drosophila. [FBrf0219844] Show all research papers ...