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Gene Dmel\faf

General Information
Symbol	Dmel\faf	Species	D. melanogaster
Name	fat facets	Annotation symbol	CG1945
Feature type	protein_coding_gene	FlyBase ID	FBgn0005632
Gene Model Status	Current	Stock availability	18 publicly available
Genomic Location
Chromosome (arm)	3R	Recombination map
Cytogenetic map	100D2-100D2	Sequence location	3R:27,602,742..27,616,403 [+]
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 fat facets is referred to in FlyBase by the symbol Dmel\faf (CG1945, FBgn0005632). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: protein binding. There is experimental evidence that it is involved in the biological process: mystery cell differentiation; protein deubiquitination; compound eye development; dorsal/ventral axis specification; embryo development; cellularization; nuclear migration; ubiquitin-dependent protein catabolic process. 58 alleles are reported. The phenotypes of these alleles are annotated with: organ system subdivision; organ system; external compound sense organ; peripheral nervous system; synapse; adult segment; thoracic segment; extended germ band embryo; eo support cell; rhabdomere R7; cytoplasmic part; spiracle. It has 7 annotated transcripts and 7 annotated polypeptides. Protein features are: Armadillo-type fold; Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2; Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed within 00-06 hour embryonic stages. Summary of FlyAtlas Anatomical Expression Data: Two or more Affy2 ProbeSets identify exons of this gene. This is a summary of the tissue expression peaks exhibited in at least one of these ProbeSets. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, larval/adult central nervous system, adult crop, larval/adult midgut, larval/adult hindgut, larval/adult Malpighian tubules, adult heart, larval fat body, larval/adult salivary gland, larval trachea, adult ovary, adult male accessory gland. Gene sequence location is 3R:27602742..27616403.
User Contributed Data
	Beta version, feedback welcome
External Summaries
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2013_03
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 100D2-100D2   Limits computationally determined from genome sequence between P{EP}pygoEP1076 and P{PZ}ttk02667&P{lacW}ttkj6C7
Experimentally Determined Cytological Location
Cytogenetic map Notes References 100D1-100D3   (determined by in situ hybridisation)   (Abdelilah-Seyfried et al., 2000) 100E-100E     (Fischer-Vize, 1993.1.22) 100E-100E     (Fischer-Vize, 1993.1.22) 100E-100E   (determined by in situ hybridisation)   (Fischer-Vize et al., 1992)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\faf 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 5.49 Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters. Low-frequency RNA-Seq exon junction(s) not annotated. DGC clone appears problematic: BcDNA:RE01547 appears 3' truncated and incomplete. DGC clone LD22582 appears problematic: incomplete CDS
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) faf-RA FBtr0085843  NM_079873   9194   2778 faf-RC FBtr0085844  NM_170576   8682   2711 faf-RD FBtr0307547  NM_001260458   9163   2773 faf-RE FBtr0307548  NM_001260459   9411   2761 faf-RG FBtr0307550  NM_001260461   9837   2773 faf-RH FBtr0339188     9179   2773 faf-RI FBtr0339189     9379   2761
Additional Transcript Data & Comments
Reported size (kB)	8.9, 8.5 (compiled cDNA) (Fischer-Vize et al., 1992)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein faf-PA   FBpp0085202   311.1   2778   5.95     NP_524612   AAF57198 faf-PC   FBpp0085203   304.1   2711   6.02     NP_733455   AAN14291 faf-PD   FBpp0300199   310.6   2773   5.95     NP_001247387   AFH06704 faf-PE   FBpp0300200   309.9   2761   6.22     NP_001247388   AFH06705 faf-PG   FBpp0300202   310.6   2773   5.95     NP_001247390   AFH06707 faf-PH   FBpp0308326   310.6   2773   5.95       faf-PI   FBpp0308327   309.9   2761   6.22
Additional Polypeptide Data & Comments
Reported size (kDa)	2747, 2711 (aa); 300 (kD predicted) (Fischer-Vize et al., 1992)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (IPR018200) Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (IPR001394) Armadillo-type fold (IPR016024) MEROPS - An information resource for peptidases and the proteins that inhibit them • C19.007
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA141072   AA141197   AA391465   AA697811   AA698697   AA816323   AA816411   AA817335   AE014297 AAF57198   AE014297 AAN14291   AF145677 AAD38652   AE014297 AFH06704   AE014297 AFH06705   AE014297 AFH06707   AI297542   AI455285   AI512532   AI513421   AI516418   AQ025072   AQ254727   AY075439   BG636462   BG639134   BI162152   BI581005   BI581006   BI581044   BI581391   BI582005   BI582204   BI611794   BI614620   BI623462   BI628999   BT011433   BT011436   BT122191   CO181014   CO192823   CO267180   CO295737   CO306620   CO318547   CO328703   CO334151   CO341360   CZ467486   CZ470631   CZ471337   CZ471338   EC066839   EC074578   EC079097   EC198470   EC221462   EC238953   EC251365   EC257816   EC259369   EL875379   EL875380   EL884222   ES695822   GH942635   GH942954   GH944382   GH952053   GH953890   GH961803   GH962191   GH963359   GH967197   GH967459   GH968817   GH973116   L04958 AAF01346   L04959 AAF01345   L04960 AAF01347   L04960 AAF01348
UniProtKB/Swiss-Prot	P55824
UniProtKB/TrEMBL
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
No Assay Recorded Stage Tissue/Position (including subcellular localization) Reference adult stage & oogenesis   germarium   (Fischer-Vize et al., 1992) nurse cell   (Fischer-Vize et al., 1992) in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 1 -- 3   organism   (Fisher et al., 2012) Comment:maternally deposited embryonic stage 4 -- 6   organism   (Fisher et al., 2012) embryonic stage 13 -- 16   embryonic brain   (Fisher et al., 2012) embryonic/larval midgut   (Fisher et al., 2012) ventral nerve cord   (Fisher et al., 2012)
Additional Descriptive Data
	faf transcripts are detected in the germarium and in the egg chambers at subsequent stages of oogenesis. faf transcripts are observed in nurse cells and unlike faf protein, do not localize to the posterior of the oocyte at stage S10. The probe used does not distinguish between the two faf transcripts. (Fischer-Vize et al., 1992)
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference larval stage   eye-antennal disc   (Fischer-Vize et al., 1992) embryonic/larval fat body   (Fischer-Vize et al., 1992) embryonic/larval digestive system   (Fischer-Vize et al., 1992) oogenesis & larval stage   ovary   (Fischer-Vize et al., 1992) larval stage & spermatogenesis   testis   (Fischer-Vize et al., 1992) third instar larval stage   morphogenetic furrow | anterior to   (Fischer-Vize et al., 1992) adult stage & oogenesis   nurse cell   (Fischer-Vize et al., 1992) adult stage & oogenesis stage S10   oocyte | posterior   (Fischer-Vize et al., 1992) adult stageoogenesis stage S10 -- S14   oocyte | posterior   (Fischer-Vize et al., 1992) spermatogenesis & adult stage   testis   (Fischer-Vize et al., 1992) oogenesis   egg chamber   (Fischer-Vize et al., 1992)
Additional Descriptive Data
	faf protein distribution was deduced from the localization of a faf-:-Ecol\lacZ fusion protein. faf protein is detected in eye imaginal discs ahead of the morphogenetic furrow and at a lower level behind the furrow but not in the furrow. It is also observed in other imaginal discs, fat body, gut, larval ovary and testis, and adult male sex organs. faf protein is detected in ovaries in the germarium and at all subsequent stages of oogenesis. Staining is restricted to the nurse cells until stage S10 when it becomes apparent at the oocyte posterior pole. Posterior localization of faf is dependent on osk. (Fischer-Vize et al., 1992) faf protein distribution was deduced from the localization of a faf-:-Ecol\lacZ fusion protein. faf protein is detected in eye imaginal discs ahead of and behind the morphogenetic furrow but not in the furrow. It is also observed in other imaginal discs, fat body, gut, larval ovary and testis, and adult male sex organs. faf protein is detected in ovaries in the germarium and at all subsequent stages of oogenesis. Staining is restricted to the nurse cells until stage S10 when it becomes apparent at the oocyte posterior pole. Posterior localization of faf is dependent on osk. (Fischer-Vize et al., 1992)
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
cytoplasm inferred from direct assay (Fischer-Vize et al., 1992)
Expression Deduced from Reporters
Reporter: P{faf-lacZ.F} Stage Tissue/Position (including subcellular localization) Reference third instar larval stage   embryonic/larval fat body   (Fischer-Vize et al., 1992) embryonic/larval digestive system   (Fischer-Vize et al., 1992) morphogenetic furrow | anterior to   (Fischer-Vize et al., 1992) imaginal disc   (Fischer-Vize et al., 1992) oogenesis & third instar larval stage   ovary   (Fischer-Vize et al., 1992) third instar larval stage & spermatogenesis   testis   (Fischer-Vize et al., 1992) oogenesis & adult stage | female   ovary   (Fischer-Vize et al., 1992) spermatogenesis & adult stage   testis   (Fischer-Vize et al., 1992) Reporter: P{faf-lacZ.nls} Stage Tissue/Position (including subcellular localization) Reference third instar larval stage   cone cell   (Fischer-Vize et al., 1992) eye-antennal disc   (Fischer-Vize et al., 1992) photoreceptor cell   (Fischer-Vize et al., 1992)
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: Two or more Affy2 ProbeSets identify exons of this gene. This is a summary of the tissue expression peaks exhibited in at least one of these ProbeSets. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, larval/adult central nervous system, adult crop, larval/adult midgut, larval/adult hindgut, larval/adult Malpighian tubules, adult heart, larval fat body, larval/adult salivary gland, larval trachea, adult ovary, adult male accessory gland. [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) 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 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    24 central nervous system, larvae L3    38 central nervous system, pupae P8    39 head, virgin 1-day female    21 head, virgin 4-day female    20 head, virgin 20-day female    18 head, mated 1-day female    19 head, mated 4-day female    18 head, mated 20-day female    17 head, mated 1-day male    28 head, mated 4-day male    28 head, mated 20-day male    31 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    11 digestive system, 1-day adult    13 digestive system, 4-day adult    16 digestive system, 20-day adult    17 fat body, larvae L3 wandering    12 fat body, white prepupae    19 fat body, pupae P8    11 carcass, larvae L3 wandering    24 carcass, 1-day adult    13 carcass, 4-day adult    14 carcass, 20-day adult    13 ovary, virgin 4-day female    55 ovary, mated 4-day female    48 testis, mated 4-day male    5 accessory gland, mated 4-day male    7 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    24 central nervous system, larvae L3  (38) central nervous system, pupae P8  (39) head, virgin 1-day female    21 head, virgin 4-day female    20 head, virgin 20-day female    18 head, mated 1-day female    19 head, mated 4-day female    18 head, mated 20-day female    17 head, mated 1-day male  (28) head, mated 4-day male  (28) head, mated 20-day male  (31) salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    11 digestive system, 1-day adult    13 digestive system, 4-day adult    16 digestive system, 20-day adult    17 fat body, larvae L3 wandering    12 fat body, white prepupae    19 fat body, pupae P8    11 carcass, larvae L3 wandering    24 carcass, 1-day adult    13 carcass, 4-day adult    14 carcass, 20-day adult    13 ovary, virgin 4-day female  (55) ovary, mated 4-day female  (48) testis, mated 4-day male    5 accessory gland, mated 4-day male    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    24 central nervous system, larvae L3    38 central nervous system, pupae P8    39 head, virgin 1-day female    21 head, virgin 4-day female    20 head, virgin 20-day female    18 head, mated 1-day female    19 head, mated 4-day female    18 head, mated 20-day female    17 head, mated 1-day male    28 head, mated 4-day male    28 head, mated 20-day male    31 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    11 digestive system, 1-day adult    13 digestive system, 4-day adult    16 digestive system, 20-day adult    17 fat body, larvae L3 wandering    12 fat body, white prepupae    19 fat body, pupae P8    11 carcass, larvae L3 wandering    24 carcass, 1-day adult    13 carcass, 4-day adult    14 carcass, 20-day adult    13 ovary, virgin 4-day female    55 ovary, mated 4-day female    48 testis, mated 4-day male    5 accessory gland, mated 4-day male    7 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    24 central nervous system, larvae L3    38 central nervous system, pupae P8    39 head, virgin 1-day female    21 head, virgin 4-day female    20 head, virgin 20-day female    18 head, mated 1-day female    19 head, mated 4-day female    18 head, mated 20-day female    17 head, mated 1-day male    28 head, mated 4-day male    28 head, mated 20-day male    31 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    11 digestive system, 1-day adult    13 digestive system, 4-day adult    16 digestive system, 20-day adult    17 fat body, larvae L3 wandering    12 fat body, white prepupae    19 fat body, pupae P8    11 carcass, larvae L3 wandering    24 carcass, 1-day adult    13 carcass, 4-day adult    14 carcass, 20-day adult    13 ovary, virgin 4-day female    55 ovary, mated 4-day female    48 testis, mated 4-day male    5 accessory gland, mated 4-day male    7 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    24 central nervous system, larvae L3    38 central nervous system, pupae P8    39 head, virgin 1-day female    21 head, virgin 4-day female    20 head, virgin 20-day female    18 head, mated 1-day female    19 head, mated 4-day female    18 head, mated 20-day female    17 head, mated 1-day male    28 head, mated 4-day male    28 head, mated 20-day male    31 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    11 digestive system, 1-day adult    13 digestive system, 4-day adult    16 digestive system, 20-day adult    17 fat body, larvae L3 wandering    12 fat body, white prepupae    19 fat body, pupae P8    11 carcass, larvae L3 wandering    24 carcass, 1-day adult    13 carcass, 4-day adult    14 carcass, 20-day adult    13 ovary, virgin 4-day female    55 ovary, mated 4-day female    48 testis, mated 4-day male    5 accessory gland, mated 4-day male    7 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    24 central nervous system, larvae L3  (38) central nervous system, pupae P8  (39) head, virgin 1-day female    21 head, virgin 4-day female    20 head, virgin 20-day female    18 head, mated 1-day female    19 head, mated 4-day female    18 head, mated 20-day female    17 head, mated 1-day male  28 head, mated 4-day male  28 head, mated 20-day male  31 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    11 digestive system, 1-day adult    13 digestive system, 4-day adult    16 digestive system, 20-day adult    17 fat body, larvae L3 wandering    12 fat body, white prepupae    19 fat body, pupae P8    11 carcass, larvae L3 wandering    24 carcass, 1-day adult    13 carcass, 4-day adult    14 carcass, 20-day adult    13 ovary, virgin 4-day female  (55) ovary, mated 4-day female  (48) testis, mated 4-day male    5 accessory gland, mated 4-day male    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    24 central nervous system, larvae L3    38 central nervous system, pupae P8    39 head, virgin 1-day female    21 head, virgin 4-day female    20 head, virgin 20-day female    18 head, mated 1-day female    19 head, mated 4-day female    18 head, mated 20-day female    17 head, mated 1-day male    28 head, mated 4-day male    28 head, mated 20-day male    31 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    11 digestive system, 1-day adult    13 digestive system, 4-day adult    16 digestive system, 20-day adult    17 fat body, larvae L3 wandering    12 fat body, white prepupae    19 fat body, pupae P8    11 carcass, larvae L3 wandering    24 carcass, 1-day adult    13 carcass, 4-day adult    14 carcass, 20-day adult    13 ovary, virgin 4-day female    55 ovary, mated 4-day female    48 testis, mated 4-day male    5 accessory gland, mated 4-day male    7 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    24 central nervous system, larvae L3    38 central nervous system, pupae P8    39 head, virgin 1-day female    21 head, virgin 4-day female    20 head, virgin 20-day female    18 head, mated 1-day female    19 head, mated 4-day female    18 head, mated 20-day female    17 head, mated 1-day male    28 head, mated 4-day male    28 head, mated 20-day male    31 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    11 digestive system, 1-day adult    13 digestive system, 4-day adult    16 digestive system, 20-day adult    17 fat body, larvae L3 wandering    12 fat body, white prepupae    19 fat body, pupae P8    11 carcass, larvae L3 wandering    24 carcass, 1-day adult    13 carcass, 4-day adult    14 carcass, 20-day adult    13 ovary, virgin 4-day female    55 ovary, mated 4-day female    48 testis, mated 4-day male    5 accessory gland, mated 4-day male    7 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Tissue   Expression Level imaginal disc, larvae L3 wandering     central nervous system, larvae L3     central nervous system, pupae P8     head, virgin 1-day female     head, virgin 4-day female     head, virgin 20-day female     head, mated 1-day female     head, mated 4-day female     head, mated 20-day female     head, mated 1-day male     head, mated 4-day male     head, mated 20-day male     salivary gland, larvae L3 wandering     salivary gland, white prepupae     digestive system, larvae L3 wandering     digestive system, 1-day adult     digestive system, 4-day adult     digestive system, 20-day adult     fat body, larvae L3 wandering     fat body, white prepupae     fat body, pupae P8     carcass, larvae L3 wandering     carcass, 1-day adult     carcass, 4-day adult     carcass, 20-day adult     ovary, virgin 4-day female     ovary, mated 4-day female     testis, mated 4-day male     accessory gland, mated 4-day male
modENCODE Development RNA-Seq
modENCODE Temporal Expression Data (modENCODE_mRNA-Seq_U)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed within 00-06 hour embryonic stages. [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    53 embryo 02-04hr    43 embryo 04-06hr    12 embryo 06-08hr    9 embryo 08-10hr    13 embryo 10-12hr    9 embryo 12-14hr    18 embryo 14-16hr    23 embryo 16-18hr    19 embryo 18-20hr    12 embryo 20-22hr    23 embryo 22-24hr    22 larva L1    17 larva L2    15 larva L3 12hr old    17 larva L3 puffstage 1-2    14 larva L3 puffstage 3-6    22 larva L3 puffstage 7-9    20 white prepupae new    22 white prepupae 12hr    23 white prepupae 24hr    28 pupae 2d postWPP    20 pupae 3d postWPP    14 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    18 adult male 30day    17 adult female 01day    27 adult female 05day    44 adult female 30day    42 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (53) embryo 02-04hr  (43) embryo 04-06hr    12 embryo 06-08hr    9 embryo 08-10hr    13 embryo 10-12hr    9 embryo 12-14hr    18 embryo 14-16hr    23 embryo 16-18hr    19 embryo 18-20hr    12 embryo 20-22hr    23 embryo 22-24hr    22 larva L1    17 larva L2    15 larva L3 12hr old    17 larva L3 puffstage 1-2    14 larva L3 puffstage 3-6    22 larva L3 puffstage 7-9    20 white prepupae new    22 white prepupae 12hr    23 white prepupae 24hr  (28) pupae 2d postWPP    20 pupae 3d postWPP    14 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    18 adult male 30day    17 adult female 01day  (27) adult female 05day  (44) adult female 30day  (42) Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    53 embryo 02-04hr    43 embryo 04-06hr    12 embryo 06-08hr    9 embryo 08-10hr    13 embryo 10-12hr    9 embryo 12-14hr    18 embryo 14-16hr    23 embryo 16-18hr    19 embryo 18-20hr    12 embryo 20-22hr    23 embryo 22-24hr    22 larva L1    17 larva L2    15 larva L3 12hr old    17 larva L3 puffstage 1-2    14 larva L3 puffstage 3-6    22 larva L3 puffstage 7-9    20 white prepupae new    22 white prepupae 12hr    23 white prepupae 24hr    28 pupae 2d postWPP    20 pupae 3d postWPP    14 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    18 adult male 30day    17 adult female 01day    27 adult female 05day    44 adult female 30day    42 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    53 embryo 02-04hr    43 embryo 04-06hr    12 embryo 06-08hr    9 embryo 08-10hr    13 embryo 10-12hr    9 embryo 12-14hr    18 embryo 14-16hr    23 embryo 16-18hr    19 embryo 18-20hr    12 embryo 20-22hr    23 embryo 22-24hr    22 larva L1    17 larva L2    15 larva L3 12hr old    17 larva L3 puffstage 1-2    14 larva L3 puffstage 3-6    22 larva L3 puffstage 7-9    20 white prepupae new    22 white prepupae 12hr    23 white prepupae 24hr    28 pupae 2d postWPP    20 pupae 3d postWPP    14 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    18 adult male 30day    17 adult female 01day    27 adult female 05day    44 adult female 30day    42 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    53 embryo 02-04hr    43 embryo 04-06hr    12 embryo 06-08hr    9 embryo 08-10hr    13 embryo 10-12hr    9 embryo 12-14hr    18 embryo 14-16hr    23 embryo 16-18hr    19 embryo 18-20hr    12 embryo 20-22hr    23 embryo 22-24hr    22 larva L1    17 larva L2    15 larva L3 12hr old    17 larva L3 puffstage 1-2    14 larva L3 puffstage 3-6    22 larva L3 puffstage 7-9    20 white prepupae new    22 white prepupae 12hr    23 white prepupae 24hr    28 pupae 2d postWPP    20 pupae 3d postWPP    14 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    18 adult male 30day    17 adult female 01day    27 adult female 05day    44 adult female 30day    42 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (53) embryo 02-04hr  (43) embryo 04-06hr    12 embryo 06-08hr    9 embryo 08-10hr    13 embryo 10-12hr    9 embryo 12-14hr    18 embryo 14-16hr    23 embryo 16-18hr    19 embryo 18-20hr    12 embryo 20-22hr    23 embryo 22-24hr    22 larva L1    17 larva L2    15 larva L3 12hr old    17 larva L3 puffstage 1-2    14 larva L3 puffstage 3-6    22 larva L3 puffstage 7-9    20 white prepupae new    22 white prepupae 12hr    23 white prepupae 24hr  28 pupae 2d postWPP    20 pupae 3d postWPP    14 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    18 adult male 30day    17 adult female 01day  27 adult female 05day  (44) adult female 30day  (42) Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    53 embryo 02-04hr    43 embryo 04-06hr    12 embryo 06-08hr    9 embryo 08-10hr    13 embryo 10-12hr    9 embryo 12-14hr    18 embryo 14-16hr    23 embryo 16-18hr    19 embryo 18-20hr    12 embryo 20-22hr    23 embryo 22-24hr    22 larva L1    17 larva L2    15 larva L3 12hr old    17 larva L3 puffstage 1-2    14 larva L3 puffstage 3-6    22 larva L3 puffstage 7-9    20 white prepupae new    22 white prepupae 12hr    23 white prepupae 24hr    28 pupae 2d postWPP    20 pupae 3d postWPP    14 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    18 adult male 30day    17 adult female 01day    27 adult female 05day    44 adult female 30day    42 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    53 embryo 02-04hr    43 embryo 04-06hr    12 embryo 06-08hr    9 embryo 08-10hr    13 embryo 10-12hr    9 embryo 12-14hr    18 embryo 14-16hr    23 embryo 16-18hr    19 embryo 18-20hr    12 embryo 20-22hr    23 embryo 22-24hr    22 larva L1    17 larva L2    15 larva L3 12hr old    17 larva L3 puffstage 1-2    14 larva L3 puffstage 3-6    22 larva L3 puffstage 7-9    20 white prepupae new    22 white prepupae 12hr    23 white prepupae 24hr    28 pupae 2d postWPP    20 pupae 3d postWPP    14 pupae 4d postWPP    12 adult male 01day    18 adult male 05day    18 adult male 30day    17 adult female 01day    27 adult female 05day    44 adult female 30day    42 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+    37 Schneider line 2 Sg4    17 embryonic 1182-4H    43 embryonic GM2    28 embryonic Kc167    18 embryonic S1    37 embryonic S3    31 leg disc CME L1    23 wing disc CME-W2    15 wing disc ML-DmD8    27 wing disc ML-DmD9    32 wing disc ML-DmD16-c3    34 wing disc ML-DmD21    6 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3    49 eye-antennal disc ML-DmD11    34 antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    28 CNS ML-DmBG2-c2    32 tumorous blood cells mbn2    24 ovary fGS/OSS    35 ovary OSC    48 ovary OSS    23 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  (37) Schneider line 2 Sg4    17 embryonic 1182-4H  (43) embryonic GM2  (28) embryonic Kc167    18 embryonic S1  (37) embryonic S3  (31) leg disc CME L1    23 wing disc CME-W2    15 wing disc ML-DmD8  (27) wing disc ML-DmD9  (32) wing disc ML-DmD16-c3  (34) wing disc ML-DmD21    6 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3  (49) eye-antennal disc ML-DmD11  (34) antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1  (28) CNS ML-DmBG2-c2  (32) tumorous blood cells mbn2    24 ovary fGS/OSS  (35) ovary OSC  (48) ovary OSS    23 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    37 Schneider line 2 Sg4    17 embryonic 1182-4H    43 embryonic GM2    28 embryonic Kc167    18 embryonic S1    37 embryonic S3    31 leg disc CME L1    23 wing disc CME-W2    15 wing disc ML-DmD8    27 wing disc ML-DmD9    32 wing disc ML-DmD16-c3    34 wing disc ML-DmD21    6 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3    49 eye-antennal disc ML-DmD11    34 antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    28 CNS ML-DmBG2-c2    32 tumorous blood cells mbn2    24 ovary fGS/OSS    35 ovary OSC    48 ovary OSS    23 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+    37 Schneider line 2 Sg4    17 embryonic 1182-4H    43 embryonic GM2    28 embryonic Kc167    18 embryonic S1    37 embryonic S3    31 leg disc CME L1    23 wing disc CME-W2    15 wing disc ML-DmD8    27 wing disc ML-DmD9    32 wing disc ML-DmD16-c3    34 wing disc ML-DmD21    6 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3    49 eye-antennal disc ML-DmD11    34 antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    28 CNS ML-DmBG2-c2    32 tumorous blood cells mbn2    24 ovary fGS/OSS    35 ovary OSC    48 ovary OSS    23 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    37 Schneider line 2 Sg4    17 embryonic 1182-4H    43 embryonic GM2    28 embryonic Kc167    18 embryonic S1    37 embryonic S3    31 leg disc CME L1    23 wing disc CME-W2    15 wing disc ML-DmD8    27 wing disc ML-DmD9    32 wing disc ML-DmD16-c3    34 wing disc ML-DmD21    6 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3    49 eye-antennal disc ML-DmD11    34 antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    28 CNS ML-DmBG2-c2    32 tumorous blood cells mbn2    24 ovary fGS/OSS    35 ovary OSC    48 ovary OSS    23 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  (37) Schneider line 2 Sg4    17 embryonic 1182-4H  (43) embryonic GM2  28 embryonic Kc167    18 embryonic S1  (37) embryonic S3  31 leg disc CME L1    23 wing disc CME-W2    15 wing disc ML-DmD8  27 wing disc ML-DmD9  32 wing disc ML-DmD16-c3  (34) wing disc ML-DmD21    6 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3  (49) eye-antennal disc ML-DmD11  (34) antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1  28 CNS ML-DmBG2-c2  32 tumorous blood cells mbn2    24 ovary fGS/OSS  (35) ovary OSC  (48) ovary OSS    23 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    37 Schneider line 2 Sg4    17 embryonic 1182-4H    43 embryonic GM2    28 embryonic Kc167    18 embryonic S1    37 embryonic S3    31 leg disc CME L1    23 wing disc CME-W2    15 wing disc ML-DmD8    27 wing disc ML-DmD9    32 wing disc ML-DmD16-c3    34 wing disc ML-DmD21    6 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3    49 eye-antennal disc ML-DmD11    34 antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    28 CNS ML-DmBG2-c2    32 tumorous blood cells mbn2    24 ovary fGS/OSS    35 ovary OSC    48 ovary OSS    23 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+    37 Schneider line 2 Sg4    17 embryonic 1182-4H    43 embryonic GM2    28 embryonic Kc167    18 embryonic S1    37 embryonic S3    31 leg disc CME L1    23 wing disc CME-W2    15 wing disc ML-DmD8    27 wing disc ML-DmD9    32 wing disc ML-DmD16-c3    34 wing disc ML-DmD21    6 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3    49 eye-antennal disc ML-DmD11    34 antennal disc ML-DmD20-c5    15 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    28 CNS ML-DmBG2-c2    32 tumorous blood cells mbn2    24 ovary fGS/OSS    35 ovary OSC    48 ovary OSS    23 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    17 cold shock, 4-day adult    12 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    9 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult    39 Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    22 Zinc 5 mM 12 hrs, larvae L3    9 Zinc 4.5 mM 48 hrs, 4-day adult    17 Ethanol 2.5% 3 hrs, larvae L3    43 Ethanol 5% 3 hrs, larvae L3    12 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    14 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    32 Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult    30 Paraquat 10 mM 48 hrs, 4-day adult    36 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    17 cold shock, 4-day adult    12 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    9 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult  (39) Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    22 Zinc 5 mM 12 hrs, larvae L3    9 Zinc 4.5 mM 48 hrs, 4-day adult    17 Ethanol 2.5% 3 hrs, larvae L3  (43) Ethanol 5% 3 hrs, larvae L3    12 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    14 Caffeine 2.5 mg/ml 48 hrs, 4-day adult  (32) Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult  (30) Paraquat 10 mM 48 hrs, 4-day adult  (36) 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    17 cold shock, 4-day adult    12 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    9 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult    39 Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    22 Zinc 5 mM 12 hrs, larvae L3    9 Zinc 4.5 mM 48 hrs, 4-day adult    17 Ethanol 2.5% 3 hrs, larvae L3    43 Ethanol 5% 3 hrs, larvae L3    12 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    14 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    32 Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult    30 Paraquat 10 mM 48 hrs, 4-day adult    36 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    17 cold shock, 4-day adult    12 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    9 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult    39 Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    22 Zinc 5 mM 12 hrs, larvae L3    9 Zinc 4.5 mM 48 hrs, 4-day adult    17 Ethanol 2.5% 3 hrs, larvae L3    43 Ethanol 5% 3 hrs, larvae L3    12 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    14 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    32 Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult    30 Paraquat 10 mM 48 hrs, 4-day adult    36 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    17 cold shock, 4-day adult    12 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    9 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult    39 Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    22 Zinc 5 mM 12 hrs, larvae L3    9 Zinc 4.5 mM 48 hrs, 4-day adult    17 Ethanol 2.5% 3 hrs, larvae L3    43 Ethanol 5% 3 hrs, larvae L3    12 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    14 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    32 Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult    30 Paraquat 10 mM 48 hrs, 4-day adult    36 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  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    17 cold shock, 4-day adult    12 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    9 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult  (39) Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    22 Zinc 5 mM 12 hrs, larvae L3    9 Zinc 4.5 mM 48 hrs, 4-day adult    17 Ethanol 2.5% 3 hrs, larvae L3  (43) Ethanol 5% 3 hrs, larvae L3    12 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    14 Caffeine 2.5 mg/ml 48 hrs, 4-day adult  32 Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult  30 Paraquat 10 mM 48 hrs, 4-day adult  (36) 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    17 cold shock, 4-day adult    12 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    9 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult    39 Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    22 Zinc 5 mM 12 hrs, larvae L3    9 Zinc 4.5 mM 48 hrs, 4-day adult    17 Ethanol 2.5% 3 hrs, larvae L3    43 Ethanol 5% 3 hrs, larvae L3    12 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    14 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    32 Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult    30 Paraquat 10 mM 48 hrs, 4-day adult    36 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    17 cold shock, 4-day adult    12 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    9 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult    39 Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    22 Zinc 5 mM 12 hrs, larvae L3    9 Zinc 4.5 mM 48 hrs, 4-day adult    17 Ethanol 2.5% 3 hrs, larvae L3    43 Ethanol 5% 3 hrs, larvae L3    12 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    14 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    32 Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult    30 Paraquat 10 mM 48 hrs, 4-day adult    36 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_26 mE1_20_mRNA_expression_cluster_03
External Data & Images
Linkouts	BDGP expression data • RE01547 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0005632 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG1945-RC;CG1945-RC;CG1945-RA FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for faf Stages(s) 4-6 Stages(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | embryonic stage | maternal effect | recessive fafFO8 lethal | embryonic stage | non-rescuable maternal effect (with Df(3R)faf-BP) fafB6 partially lethal - majority die (with Df(3R)faf-BP) fafB3 fafB4 fafB5 fafBX3 fafFO8 partially lethal - majority die (with fafB3) fafFO8 partially lethal - majority die (with fafB4) fafB5 partially lethal - majority die (with fafB5) fafB4 partially lethal - majority die (with fafFO8) fafB3 viable fafBX4 fafEP381 viable, with Scer\GAL4pnr-MD237 fafGD1444 fafGD4722 Sterility Allele female sterile | recessive fafB3 fafB5 fafB6 fafB7 fafB8 fafBX1 fafBX3 fafBX4 fafBX8 fafBX15 fafFBB12 fafFO8 Other Phenotypes Allele neuroanatomy defective, with Scer\GAL4elav-C155 fafEP381 fafEP3520 neuroanatomy defective, with Scer\GAL4Tab2-201Y fafEP381 neuroanatomy defective | larval stage, with Scer\GAL4Ccap.PP fafEP3520 neuroanatomy defective | larval stage, with Scer\GAL4elav-C155 fafEP381 neuroanatomy defective | pharate adult stage, with Scer\GAL4Ccap.PP fafEP3520 neurophysiology defective, with Scer\GAL4elav-C155 fafEP381 fafEP3520 visible fafBX4 visible, with Scer\GAL4ap-md544 fafEP381 visible, with Scer\GAL4sca-537.4 fafEP381 visible (with fafBX4) fafFO8 visible (with fafFO8) fafBX4 visible | recessive fafB3 fafB4 fafB5 fafB6 fafB7 fafB8 fafBX1 fafBX3 fafBX4 fafBX5 fafBX6 fafBX7 fafBX8 fafBX10 fafBX11 fafBX14 fafBX15 fafFBB12 fafFO8 wild-type faf+t13 faf+t14 faf+t17 fafhs.T:Hsap\MYC fafro.T:Hsap\MYC Phenotype manifest in Allele adult abdominal sensillum & trichogen cell, with Scer\GAL4sca-537.4 fafEP381 anterior fascicle & bouton, with Scer\GAL4elav-C155 fafEP381 anterior fascicle & synapse, with Scer\GAL4elav-C155 fafEP381 anterior fascicle & synapse | supernumerary, with Scer\GAL4elav-C155 fafEP381 bouton, with Scer\GAL4elav-C155 fafEP381 bouton | supernumerary, with Scer\GAL4elav-C155 fafEP3520 fafEP381 cone cell (with fafBX3) fafFO8 cone cell (with fafFO8) fafBX3 denticle (with Df(3R)faf-BP) fafB3 fafFO8 denticle (with fafB3) fafFO8 denticle (with fafFO8) fafB3 denticle belt | ectopic (with fafB3) fafFO8 denticle belt | ectopic (with fafFO8) fafB3 denticle belt | ectopic | non-rescuable maternal effect (with fafB3) fafB5 denticle belt | ectopic | non-rescuable maternal effect (with fafB4) fafBX3 fafFO8 denticle belt | ectopic | non-rescuable maternal effect (with fafB5) fafB3 denticle belt | ectopic | non-rescuable maternal effect (with fafBX3) fafB4 denticle belt | ectopic | non-rescuable maternal effect (with fafFO8) fafB4 dorsocentral bristle, with Scer\GAL4sca-537.4 fafEP381 embryonic/first instar larval cuticle (with Df(3R)faf-BP) fafB3 fafFO8 embryonic/first instar larval cuticle (with fafB3) fafFO8 embryonic/first instar larval cuticle (with fafFO8) fafB3 embryonic/first instar larval cuticle | non-rescuable maternal effect (with fafB3) fafB5 embryonic/first instar larval cuticle | non-rescuable maternal effect (with fafB4) fafB5 fafB6 fafBX3 fafFO8 embryonic/first instar larval cuticle | non-rescuable maternal effect (with fafB5) fafB3 fafB4 embryonic/first instar larval cuticle | non-rescuable maternal effect (with fafB6) fafB4 embryonic/first instar larval cuticle | non-rescuable maternal effect (with fafBX3) fafB4 embryonic/first instar larval cuticle | non-rescuable maternal effect (with fafFO8) fafB4 embryonic/larval central nervous system, with Scer\GAL4Ccap.PP fafEP3520 embryonic head (with Df(3R)faf-BP) fafB3 embryonic head | non-rescuable maternal effect (with fafB4) fafB5 fafB6 fafBX3 fafFO8 embryonic head | non-rescuable maternal effect (with fafB5) fafB4 embryonic head | non-rescuable maternal effect (with fafB6) fafB4 embryonic head | non-rescuable maternal effect (with fafBX3) fafB4 embryonic head | non-rescuable maternal effect (with fafFO8) fafB4 eye fafBX4 eye, with Scer\GAL4GMR.PF fafEP381 eye (with fafBX4) fafFO8 eye (with fafFO8) fafBX4 eye photoreceptor cell fafBX3 fafBX4 fafFO8 eye photoreceptor cell (with fafBX4) fafFO8 eye photoreceptor cell (with fafFO8) fafBX4 eye photoreceptor cell & ommatidium | ectopic | somatic clone fafBX4 fafFO8 eye photoreceptor cell | supernumerary fafFO8 eye photoreceptor cell | supernumerary (with fafBX3) fafFO8 eye photoreceptor cell | supernumerary (with fafBX4) fafFO8 eye photoreceptor cell | supernumerary (with fafFO8) fafBX3 fafBX4 filzkorper (with Df(3R)faf-BP) fafB3 fafFO8 filzkorper (with fafB3) fafFO8 filzkorper (with fafFO8) fafB3 filzkorper | non-rescuable maternal effect (with fafB4) fafB5 fafB6 fafBX3 fafFO8 filzkorper | non-rescuable maternal effect (with fafB5) fafB4 filzkorper | non-rescuable maternal effect (with fafB6) fafB4 filzkorper | non-rescuable maternal effect (with fafBX3) fafB4 filzkorper | non-rescuable maternal effect (with fafFO8) fafB4 intersegmental nerve, with Scer\GAL4elav-C155 fafEP381 mushroom body, with Scer\GAL4Tab2-201Y fafEP381 neurite | pharate adult stage, with Scer\GAL4Ccap.PP fafEP3520 neuromuscular junction, with Scer\GAL4elav-C155 fafEP381 ommatidium fafBX4 fafFO8 ommatidium, with Scer\GAL4GMR.PF fafEP381 ommatidium (with fafBX3) fafFO8 ommatidium (with fafBX4) fafFO8 ommatidium (with fafFO8) fafBX3 fafBX4 photoreceptor cell R1 | ectopic fafBX4 photoreceptor cell R2 | ectopic fafBX4 photoreceptor cell R3 | ectopic fafBX4 photoreceptor cell R4 | ectopic fafBX4 photoreceptor cell R5 | ectopic fafBX4 photoreceptor cell R6 | ectopic fafBX4 pole cell fafB3 rhabdomere R7, with Scer\GAL4Rh3.PP fafGS9924 scutellar bristle, with Scer\GAL4sca-537.4 fafEP381 synapse, with Scer\GAL4elav-C155 fafEP381 synapse | supernumerary, with Scer\GAL4elav-C155 fafEP3520 fafEP381 synaptic vesicle, with Scer\GAL4elav-C155 fafEP3520 syncytial blastoderm embryo | maternal effect (with fafBX3) fafFO8 syncytial blastoderm embryo | maternal effect (with fafFO8) fafBX3 trichogen cell, with Scer\GAL4sca-537.4 fafEP381 wing sensillum | ectopic, with Scer\GAL4ap-md544 fafEP381
Classical Alleles ( 31 )
For All Classical Alleles Show
Allele of faf Class Mutagen Stocks Known lesion fafBX4 amorphic allele - genetic evidence, loss of function allele X ray 2 Yes fafB3 amorphic allele - genetic evidence ethyl methanesulfonate 1 Yes fafFO8 amorphic allele - genetic evidence ethyl methanesulfonate 1 Yes fafBX3 loss of function allele X ray 1 Yes fafc06363 piggyBac transposase 1 -- fafd00030 P-element activity 1 -- fafEP381 P-element activity 1 Yes fafEY02018 1 -- fafGS9924 1 Yes fafS063210 P-element activity 1 -- fafB7 amorphic allele - genetic evidence ethyl methanesulfonate 0 Yes fafB8 amorphic allele - genetic evidence ethyl methanesulfonate 0 Yes fafBX15 amorphic allele - genetic evidence X ray 0 Yes fafBX1 amorphic allele - genetic evidence X ray 0 Yes fafBX8 amorphic allele - genetic evidence X ray 0 -- fafFBB12 amorphic allele - genetic evidence ethyl methanesulfonate 0 Yes fafB4 loss of function allele ethyl methanesulfonate 0 Yes fafB5 loss of function allele ethyl methanesulfonate 0 Yes fafB6 loss of function allele ethyl methanesulfonate 0 Yes fafBX10 X ray 0 -- fafBX11 loss of function allele X ray 0 -- fafBX13 0 Yes fafBX14 X ray 0 -- fafBX5 X ray 0 Yes fafBX6 X ray 0 -- fafBX7 loss of function allele X ray 0 -- fafBX9 0 -- fafc01838 piggyBac transposase 0 -- fafEP3520 P-element activity 0 -- fafEP381.faf- ethyl methanesulfonate 0 -- fafunspecified 0 --
Alleles Carried on Transgenic Constructs ( 27 )
For All Alleles Carried on Transgenic Constructs Show
Allele of faf Class Mutagen Stocks Known lesion fafGD1444 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes fafGD4722 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes faf392.T:Ecol\lacZ in vitro construct - coding region fusion 1 Yes fafHMS01470 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes fafKK100775 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes fafScer\UAS.cHa in vitro construct - regulatory fusion 1 Yes faf+t13 in vitro construct - genomic fragment 0 Yes faf+t14 in vitro construct - genomic fragment 0 Yes faf+t17 in vitro construct - genomic fragment 0 Yes faf392.T:Ecol\lacZ,T:Zzzz\nls1 in vitro construct - coding region fusion 0 Yes fafArg1959,Arg1967 in vitro construct - amino acid replacement 0 Yes fafArg1959 in vitro construct - amino acid replacement 0 Yes fafArg1967 in vitro construct - amino acid replacement 0 Yes fafglrl in vitro construct - regulatory fusion 0 Yes fafglrs in vitro construct - regulatory fusion 0 Yes fafhs.T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes fafNIG.1945R in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes fafro.T:Hsap\MYC in vitro construct - regulatory fusion 0 Yes fafSer1677.hs.T:Hsap\MYC in vitro construct - amino acid replacement 0 Yes fafSer1677 in vitro construct - amino acid replacement 0 Yes fafsev.PH in vitro construct - regulatory fusion 0 Yes fafΔ1.ro.T:Hsap\MYC in vitro construct - deletion 0 Yes fafΔ2.ro.T:Hsap\MYC in vitro construct - deletion 0 Yes fafΔ3.ro.T:Hsap\MYC in vitro construct - deletion 0 Yes fafΔ4.ro.T:Hsap\MYC in vitro construct - deletion 0 Yes fafΔ5.ro.T:Hsap\MYC in vitro construct - deletion 0 Yes fafΔ6.ro.T:Hsap\MYC in vitro construct - deletion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3R)E(sina)9 (Wisotzkey et al., 1998, Carthew et al., 1994) Df(3R)Exel6220 (Ryder, 2004.4.26) Df(3R)faf-BP (Fischer-Vize et al., 1992) Df(3R)ttk-Δ1 (Wisotzkey et al., 1998) Df(3R)ttk-Δ2 (Wisotzkey et al., 1998) Df(3R)ttk-Δ3 (Wisotzkey et al., 1998) In(3R)fafBX4 (Fischer-Vize et al., 1992)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data heat-shock construct P{Hs-faf} NA P{Hs-fafSer1677} NA P{ro-faf.H} NA UAS construct P{GD1444} NA P{GD4722} NA P{KK100775} NA P{NIG.1945R} NA P{TRiP.HMS01470} NA P{UAS-faf.H} NA reporter construct P{faf-lacZ.F} No P{faf-lacZ.nls} No characterization construct P{fafArg1959,Arg1967} NA P{fafArg1959} NA P{fafArg1967} NA P{fafSer1677} NA P{fafI} NA P{fafII} NA P{fafIII} NA P{glrl-faf} NA P{glrs-faf} NA P{ro-faf.Δ1} NA P{ro-faf.Δ2} NA P{ro-faf.Δ3} NA P{ro-faf.Δ4} NA P{ro-faf.Δ5} NA P{ro-faf.Δ6} NA P{SEV-faf} NA
Insertions
	Type of insertions Name Expression data insertion of mobile activating element P{EP}fafEP381 NA P{EP}fafEP3520 NA P{EPgy2}fafEY02018 NA P{GSV1}C345C345 NA P{GSV1}GSd315GSd315 NA P{GSV6}fafGS9924 NA P{XP}fafd00030 NA miscellaneous insertions PBac{PB}fafc01838 NA PBac{PB}fafc06363 NA insertion of enhancer trap P{lacW}fafS063210 No
Gene Ontology: Function, Process & Cellular Component ( 15 unique terms )
Terms Based on Experimental Evidence ( 10 terms )
Molecular Function
CV term Evidence References
protein binding inferred from physical interaction with UniProtKB:P09052 (assigned by UniProtKB) (Liu et al., 2003)
Biological Process
CV term Evidence References
cellularization inferred from mutant phenotype (Fischer-Vize et al., 1992) compound eye development inferred from mutant phenotype (Fischer-Vize et al., 1992) dorsal/ventral axis specification inferred from genetic interaction with dpp (Stinchfield et al., 2012) inferred from genetic interaction with Med (Stinchfield et al., 2012) inferred from mutant phenotype (Stinchfield et al., 2012) embryo development inferred from mutant phenotype (Fischer-Vize et al., 1992) mystery cell differentiation inferred from mutant phenotype (Fischer-Vize et al., 1992) nuclear migration inferred from mutant phenotype (Fischer-Vize et al., 1992) protein deubiquitination inferred from direct assay (Huang et al., 1995) inferred from mutant phenotype (Chen et al., 2002) ubiquitin-dependent protein catabolic process inferred from genetic interaction with Pros26 (Huang et al., 1995)
Cellular Component
CV term Evidence References
cytoplasm inferred from direct assay (Fischer-Vize et al., 1992)
Terms Based on Predictions or Assertions ( 7 terms )
Molecular Function
CV term Evidence References
ubiquitin-specific protease activity non-traceable author statement (Swiss-Prot Project Members, 1997.2.1) traceable author statement (Wu et al., 1999, MEROPS Project Members, 1996-) ubiquitin thiolesterase activity inferred from electronic annotation with InterPro:IPR001394, InterPro:IPR018200 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
endocytosis non-traceable author statement (Narayanan and Ramaswami, 2001) germ cell migration traceable author statement (Coffman, 2003) mystery cell differentiation traceable author statement (Ou et al., 2003) negative regulation of proteolysis non-traceable author statement (Narayanan and Ramaswami, 2001) protein deubiquitination non-traceable author statement (Swiss-Prot Project Members, 1997.2.1) traceable author statement (Wu et al., 1999, MEROPS Project Members, 1996-, Ou et al., 2003)
Cellular Component ( 0 terms)
Sequence Ontology: Class of Gene
	gene_with_edited_transcript (Graveley et al., 2011) nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
faf - Ent2 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 faf allele Gene References fafBX3 Chc (Cadavid et al., 2000) E(faf)bE160 (Fischer et al., 1997) E(faf)bE184 (Fischer et al., 1997) E(faf)bE365 (Fischer et al., 1997) eff (Wu et al., 1999) lqf (Fischer et al., 1997, Cadavid et al., 2000) R (Li et al., 1997) Ras85D (Fischer et al., 1997, Li et al., 1997) shi (Cadavid et al., 2000) fafBX4 14-3-3ζ (Isaksson et al., 1997) aop (Isaksson et al., 1997) hiw (DiAntonio et al., 2001) Jra (Isaksson et al., 1997) lqf (Cadavid et al., 2000) pnt (Isaksson et al., 1997) fafEP381 pnr (Pena-Rangel et al., 2002) fafFO8 Chc (Cadavid et al., 2000) DNApol-α60 (Chen et al., 2000) eff (Wu et al., 1999, Chen et al., 2000) hiw (DiAntonio et al., 2001) lqf (Cadavid et al., 2000) Prosβ6 (Huang et al., 1995) R (Li et al., 1997) Ras85D (Li et al., 1997) S(faf)86 (Chen et al., 2000) S(faf)196 (Chen et al., 2000) S(faf)244 (Chen et al., 2000) shi (Cadavid et al., 2000) fafunspecified lqf (Cadavid et al., 2000) unspecified 14-3-3ζ (Li et al., 1997) E(faf)E254 (Fischer et al., 1997) E(faf)E263 (Fischer et al., 1997) E(faf)E306 (Fischer et al., 1997) E(faf)E337 (Fischer et al., 1997) E(faf)E1051 (Fischer et al., 1997) eff (Cadavid et al., 2000) Ppt1 (Buff et al., 2007) Prosβ6 (Cadavid et al., 2000) R (Fischer et al., 1997) rpr (Ryoo et al., 2002)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 68590 DroID - A comprehensive database of gene and protein interactions. • FBgn0005632 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 43749
Orthologs
OrthoDB Orthologs (39) - 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 EOG6SJ602 Dipteran inclusive ortholog search EOG62FSRG Insect inclusive ortholog search EOG6VQ8J2 Arthropod inclusive ortholog search EOG6DFN3B Metazoa inclusive ortholog search EOG612ZZ2
Orthologs in Drosophila Species (EOG6SJ602)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\faf     Drosophila simulans   Dsim\GD21604 Y   Drosophila sechellia   Dsec\GM16452 Y   Drosophila erecta   Dere\GG11832 Y   Drosophila yakuba   Dyak\GE10966 Y   Drosophila ananassae   Dana\GF22987 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA15146 Y   Drosophila persimilis   Dper\GL23356 Y   Drosophila willistoni   Dwil\GK13174 Y   Drosophila virilis   Dvir\GJ24225 Y   Drosophila mojavensis   Dmoj\GI22109 Y   Drosophila grimshawi   Dgri\GH14199 Y
Orthologs in non-Drosophila Dipterans (EOG62FSRG)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL009824   Anopheles gambiae Malaria mosquito  Agam\AGAP010088   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ013863
Orthologs in non-Dipteran Insects (EOG6VQ8J2)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\faf   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG003610   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH19230   Atta cephalotes Leafcutter ant  Acep\ACEP25504   Camponotus floridanus Florida carpenter ant  Cflo\CFLO21780   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL12555   Linepithema humile Argentine ant  Lhum\LH16594   Pogonomyrmex barbatus Red harvester ant  Pbar\PB23206   Solenopsis invicta Red fire ant  Sinv\SINV23524   Acyrthosiphon pisum Pea aphid  Apim\ACYPI008226   Bombyx mori Silkmoth  Bmor\BGIBMGA007507   Pediculus humanus Human body louse  Phum\PHUM076540   Tribolium castaneum Red flour beetle  Tcas\TC010455
Orthologs in non-Insect Arthropods (EOG6DFN3B)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\JGI_V11_306876   Ixodes scapularis Deer tick  Isca\ISCW009097
Orthologs in non-Arthropod Metazoa (EOG612ZZ2)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_002851gn   Danio rerio Zebrafish  Drer\usp9   Xenopus tropicalis Western clawed frog  Xtro\usp9x   Gallus gallus Domestic chicken  Ggal\USP9X   Mus musculus House mouse  Mmus\Usp9x   Mus musculus House mouse  Mmus\Usp9y   Rattus norvegicus Norway rat  Rnor\Usp9x   Homo sapiens Human  Hsap\ENSG00000124486   Homo sapiens Human  Hsap\USP9Y
Human Orthologs (2)
Gene OMIM HGNC Hsap\ENSG00000124486     Hsap\USP9Y
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD21604 Drosophila sechellia Dsec\GM16452 Drosophila erecta Dere\GG11832 Drosophila yakuba Dyak\GE10966 Drosophila ananassae Dana\GF22987 Drosophila pseudoobscura pseudoobscura Dpse\GA15146 Drosophila persimilis Dper\GL23356 Drosophila willistoni Dwil\GK13174 Drosophila virilis Dvir\GJ24225 Drosophila mojavensis Dmoj\GI22109 Drosophila grimshawi Dgri\GH14199
Stocks & Reagents
Stocks Listed in FlyBase ( 18 )
Bloomington	4921 P{faf-lacZ.F}JF1 25100 st1 fafB3/TM6B, Tb1 15390 y1 w67c23; P{EPgy2}fafEY02018 25101 w*; st1 fafBX3/TM6B, Tb1 25107 w*; st1 fafBX4/TM6B, Tb1
Harvard	- P{XP}fafd00030 - PBac{PB}fafc06363
VDRC	v107716 P{KK100775}VIE-260B v2955 w1118; P{GD1444}v2955 v2956 w1118; P{GD1444}v2956 v30679 w1118; P{GD4722}v30679 v30680 w1118; P{GD4722}v30680/TM3
	More stocks available...
Genomic Clones ( 2 )
	BACR16F16 BACR48C22 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 57 )
	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	LD22582 RE01547 RH55725 RH57784
Other clones	MIP20638
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	HL03201 HL05495 LD01196 LD01464 LD10138 LD42278 LD45480 LP11865 RH18208 RH18777 RH19867 RH20158 RH44042 SD14182
Other clones	16708 30173 63203 172634 174225 211084.1 214475.29 214569.29 283737 CK01157 CK01328 EC13340 EC34576 EK149009 EK211502 EK251606 EK272661 EK291227 EK309325 EP12324 IP15360 IP15560 LD44432 RC0-DP0007-150700-011-F05 RH01039 RH01063 RP004122917 RP004149594 RP004241926 RP004256704 RP004267732 RP004386772 RP004450066 RP004468124 RP004471534 RP004515297 RP004528087 RP004531309
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0005632 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 43749
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: faf CG1945 (Zhao, 1999.11)
Source for database merge of	Source for merge of: faf BcDNA:LD22582 (FlyBase, 1996-)
Additional comments	Source for merge of faf BcDNA:LD22582 was sequence comparison (date:990717). (FlyBase, 1996-)
Other Comments
	dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology. (Kiger et al., 2003) lqf is ubiquitinated in vivo and is deubiquitinated by faf. (Chen et al., 2002) faf de-ubiquitination has a role in controlling the level of activity of critical regulatory molecules at the synapse. (DiAntonio et al., 2001) faf and lqf facilitate endocytosis and antagonise ubiquitination. They function in common cells to generate an inhibitory signal that prevents ectopic photoreceptor cell determination. (Cadavid et al., 2000) faf gene activity antagonises Ubi-p63E mediated proteolysis. (Wu et al., 1999) Analysis of genetic interactions among faf and R and Ras85D reveals that in addition to its critical role anterior to the morphogenetic furrow, faf has a function in undifferentiated cells alter in eye development that involves, probably indirectly, Ras85D and R. These results suggest that cells outside the facet influence cell fates within the facet. (Li et al., 1997) Shows no genetic interaction with sdk. (Nguyen et al., 1997) faf is essential only early in eye development and only outside of the 7-cell precluster and cone cell precursors. The critical role of faf in eye development is not in the regulation of argos, aop or Gap1 activities, nor in the regulation of any other protein that functions within cells of the developing facets. Undifferentiated cells outside the facet precluster direct ommatidial assembly by sending to the mystery cells and other cells an inhibitory signal, regulated by faf protein. (Huang and Fischer-Vize, 1996) The faf protein acts as a regulatory Ubiquitin-specific protease that prevents degradation of its substrate by the proteasome. The faf Ubiquitin-specific protease is cell type- and substrate-specific and regulates cell fate decisions. (Huang et al., 1995) faf is required for cell interactions that prevent particular cells in the developing eye from becoming photoreceptors. Mosaic analysis indicates that faf is required in cells close to, but outside the normal developing photoreceptors and also outside the ectopic photoreceptors in mutant facets. The faf product is also required during oogenesis (embryos from faf mutant mothers never cellularize, except for the pole cells), but is not required for nos localization or function. The faf gene has been cloned, and all regions essential for its function identified by transformation rescue of the mutant phenotypes. faf-Ecol\lacZ chimeric proteins become posteriorly localized in oocytes, and the first 392 amino acids of faf protein is sufficient for this localization. (Fischer-Vize et al., 1992)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_079873 NM_170576 NM_001260458 NM_001260459 NM_001260461 RefSeq (Proteins) • NP_524612 NP_733455 NP_001247387 NP_001247388 NP_001247390 DDBJ / EMBL / GenBank • AA817335 AAD38652 AAF01345 AAF01346 AAF01347 AAF01348 AAF57198 AAN14291 AF145677 AFH06704 AFH06705 AFH06706 AFH06707 AI455285 AQ025072 AQ254727 AY075439 BI162152 BI623462 BI628999 CZ467486 CZ470631 CZ471337 CZ471338 L04958 L04959 L04960 Entrez Gene - A searchable database of RefSeq genes. • 43749 UniProtKB/Swiss-Prot • P55824
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (IPR018200) Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (IPR001394) Armadillo-type fold (IPR016024) MEROPS - An information resource for peptidases and the proteins that inhibit them • C19.007 BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • RE01547
Linkouts
	BioGRID - A database of protein and genetic interactions • 68590 DroID - A comprehensive database of gene and protein interactions. • FBgn0005632 DRSC - Results from RNAi screens. • FBgn0005632 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0005632 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG1945-RC;CG1945-RC;CG1945-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0005632 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 43749 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /dbzhnsky/fatfac1.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 43749 modMine - Data generated by the modENCODE project. • FBgn0005632
Synonyms & Secondary IDs ( 9 )
Reported As
Symbol Synonym	BcDNA:LD22582   BcDNA.LD22582 (Rubin, 1999.4.23) CG1945 (Kraut et al., 2001, Kraut et al., 2001, Molnar et al., 2006, Zhang et al., 2012, Keleman et al., 2009.8.5, Klement et al., 2010, Tsou et al., 2012, Hernandez et al., 2004, Ni et al., 2011.7.19, Kanuka et al., 2005) faf (Collins et al., 2006, Zhao et al., 2008, Buff et al., 2007, Molnar et al., 2006, Murphey and Godenschwege, 2002, Millard and Wood, 2006, Minidorff et al., 2007, Kaltenbach et al., 2007, Minidorff et al., 2007, Zhang et al., 2012, Zhang et al., 2012, Viquez et al., 2006, Horiuchi et al., 2007, Tripodi et al., 2008, Uthaman et al., 2008, Reiter et al., 2006, Kim et al., 2010, Tsou et al., 2012, Hazelett et al., 2009, Cho and Fischer, 2011, Kanuka et al., 2005, Japanese National Institute of Genetics, 2012.5.21, Senthilan et al., 2012, Stinchfield et al., 2012) Faf (Xia et al., 2012, Murphey and Godenschwege, 2002, Cronin et al., 2009, Kugler et al., 2010) Fat (Klement et al., 2010)
Name Synonym	fat facets (Kraut et al., 2001, Kraut et al., 2001, Collins et al., 2006, Zhao et al., 2008, Millard and Wood, 2006, Kaltenbach et al., 2007, Horiuchi et al., 2007, Uthaman et al., 2008, Reiter et al., 2006, Viquez et al., 2006, Klement et al., 2010) Fat facets (Buff et al., 2007, Murphey and Godenschwege, 2002, Kugler et al., 2010) fat-facets (Tripodi et al., 2008)
Secondary FlyBase IDs
References ( 130 )
Generate a list of	All references relating to this gene ( 130 )
List References by type	Research paper  ( 66 ) Supplementary material  ( 8 ) Review  ( 26 ) Erratum  ( 1 ) Personal communication to FlyBase  ( 11 ) Abstract  ( 7 ) FlyBase analysis  ( 2 ) DNA/RNA sequence record  ( 3 ) Stock list  ( 1 ) Curated genome annotation  ( 3 ) Protein sequence record  ( 1 ) Website  ( 1 )
Recent research papers ( 7 )
	Crawford et al., 2012, Cell Death Differ. 19(12): 2040--2048 Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis. [FBrf0220233] Senthilan et al., 2012, Cell 150(5): 1042--1054 Drosophila auditory organ genes and genetic hearing defects. [FBrf0219321] Stinchfield et al., 2012, Development 139(15): 2721--2729 Fat facets deubiquitylation of Medea/Smad4 modulates interpretation of a Dpp morphogen gradient. [FBrf0219593] Tsou et al., 2012, PLoS ONE 7(8): e43112 Systematic Analysis of the Physiological Importance of Deubiquitinating Enzymes. [FBrf0219256] Xia et al., 2012, PLoS Biol. 10(1): e1001238 USP8 promotes smoothened signaling by preventing its ubiquitination and changing its subcellular localization. [FBrf0218247] Zhang et al., 2012, G3 (Bethesda) 2(12): 1563--1575 A Targeted In Vivo RNAi Screen Reveals Deubiquitinases as New Regulators of Notch Signaling. [FBrf0220374] Cho and Fischer, 2011, Development 138(7): 1349--1359 Ral GTPase promotes asymmetric Notch activation in the Drosophila eye in response to Frizzled/PCP signaling by repressing ligand-independent receptor activation. [FBrf0213208] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...