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Gene Dmel\chif

General Information
Symbol	Dmel\chif	Species	D. melanogaster
Name	chiffon	Annotation symbol	CG5813
Feature type	protein_coding_gene	FlyBase ID	FBgn0000307
Gene Model Status	Current	Stock availability	14 publicly available
Also Known As	BG:DS09218.1, Dbf4, BG:DS09218.2, CG5817
Genomic Location
Chromosome (arm)	2L	Recombination map	2-53
Cytogenetic map	35F1-35F12	Sequence location	2L:16,342,430..16,352,628 [-]
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 chiffon is referred to in FlyBase by the symbol Dmel\chif (CG5813, FBgn0000307). It is a protein_coding_gene from Drosophila melanogaster. An electronic pipeline based on InterPro domains suggests that it has the molecular function: zinc ion binding; DNA binding. There is experimental evidence that it is involved in the biological process: chorion-containing eggshell formation; eggshell chorion gene amplification; photoreceptor cell axon guidance; muscle cell homeostasis. 22 alleles are reported. The phenotypes of these alleles are annotated with: chorion; eye; trichogen cell; scutellar bristle. It has 3 annotated transcripts and 3 annotated polypeptides. Protein features are: AT hook, DNA-binding motif; Zinc finger, DBF-type. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of low expression. Peak expression observed at stages throughout embryogenesis, in adult female 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 eye, larval/adult central nervous system, adult crop, larval Malpighian tubules, larval fat body, larval/adult salivary gland, larval trachea, adult female reproductive system, larval carcass. Gene sequence location is 2L:16342430..16352628.
User Contributed Data
	Beta version, feedback welcome
External Summaries
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	chif: chiffon (T. Schupbach) Female sterile, homozygous females lay eggs which have thin, fragile chorions and remain unfertilized.
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 35F1-35F12
Experimentally Determined Cytological Location
Cytogenetic map Notes References 35F-36A     (Landis, 1999.6.10) 35F11-35F12   (determined by in situ hybridisation)   (Ashburner et al., 1999) 35F11-35F12     (BDGP Project Members, 1994-1999)
Experimentally Determined Recombination Data
Location	2-53
Left of (cM)	pr
Right of (cM)	b
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\chif 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 5.43 Gene model reviewed during 5.50 Shares 5' UTR with downstream gene; in addition, one transcript isoform shares 3' UTR with downstream gene.
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) chif-RA FBtr0080838  NM_078859   6624   1711 chif-RB FBtr0080839  NM_165156   6575   1695 chif-RD FBtr0321313  NM_001273570   6170   1695
Additional Transcript Data & Comments
Reported size (kB)	6.6, 6.5 (northern blot) (Landis and Tower, 1999)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein chif-PA   FBpp0080396   189.2   1711   8.73     NP_523583   AAF53530 chif-PB   FBpp0080397   188.0   1695   8.92     NP_723965   AAG22437 chif-PD   FBpp0302856   188.0   1695   8.92     NP_001260499   AGB93034
Additional Polypeptide Data & Comments
Reported size (kDa)	1711, 1695 (aa) (Landis and Tower, 1999)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • AT hook, DNA-binding motif (IPR017956) Zinc finger, DBF-type (IPR006572)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA439734   AA540346   AA697589   AA802759   AA803993   AA949224   AE014134 AAF53530   AE014134 AAG22437   AE003416 AAF45010   AE003416 AAF45011   AF158178 AAD48779   AF158179 AAD48780   AE014134 AGB93034   AI062361   AI402606   AQ025739   AQ025889   AW941263   AW942544   AY060919 AAL28467   AY119597 AAM50251   BH615037   BP559294   BP559295   BT128811   CK661016   CO176871   CO177733   CO178884   CO265123   CO266925   CO268696   CO271993   CO273011   CO273115   CO278731   CO281397   CO302342   CO308444   CO311054   CO312390   CO312454   CO322647   CO323622   CO333370   EC073097   EC084119   EC084240   EC089109   EC195642   EC195866   EC197963   EC198280   EC199442   EC202252   EC206029   EC206030   EC209312   EC223523   EC225258   EC231622   EC234540   EC246558   EC251250   EC254485   EC254970   EC258492   GH900163   GH906911   GH947199
UniProtKB/Swiss-Prot	Q9NK54
UniProtKB/TrEMBL
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 1 -- 3   organism | ubiquitous   (Fisher et al., 2012) Comment:maternally deposited embryonic stage 4 -- 6   head mesoderm anlage   (Fisher et al., 2012) Comment:anlage in statu nascendi mesoderm anlage   (Fisher et al., 2012) Comment:anlage in statu nascendi organism | ubiquitous   (Fisher et al., 2012) embryonic stage 7 -- 8   antennal anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage central brain anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage dorsal head epidermis anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage visual anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage organism | ubiquitous   (Fisher et al., 2012) ventral ectoderm   (Fisher et al., 2012) embryonic stage 9 -- 10   antennal primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium central brain primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium visual primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium dorsal head epidermis primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium lateral head epidermis primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium ventral head epidermis primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium organism | ubiquitous   (Fisher et al., 2012) ventral nerve cord primordium   (Fisher et al., 2012) embryonic stage 11 -- 12   anterior midgut primordium   (Fisher et al., 2012) central brain primordium   (Fisher et al., 2012) organism | ubiquitous   (Fisher et al., 2012) posterior midgut primordium   (Fisher et al., 2012) ventral nerve cord primordium   (Fisher et al., 2012) embryonic stage 13 -- 16   embryonic brain   (Fisher et al., 2012) embryonic/larval midgut   (Fisher et al., 2012) organism | faint & ubiquitous   (Fisher et al., 2012) organism | ubiquitous   (Fisher et al., 2012) ventral nerve cord   (Fisher et al., 2012) northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage | early     (Landis and Tower, 1999) adult stage & oogenesis   nurse cell   (Landis and Tower, 1999) follicle cell   (Landis and Tower, 1999) adult stageoogenesis stage S10 -- S11     (Landis and Tower, 1999) adult stageoogenesis stage S13 -- S14     (Landis and Tower, 1999)
Additional Descriptive Data
	Abundant chif transcripts are detected in nurse cells in egg chambers. Low levels of chif transcripts are detected in follicle cells. chif transcripts are detected in egg chambers and very early embryos on northern blots indicating that they are maternally supplied to the embryo. (Landis and Tower, 1999)
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy Stage Tissue/Position (including subcellular localization) Reference day 5 of adulthood & male -- day 7 of adulthood & male   spermatozoon   (Wasbrough et al., 2010)
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
FlyAtlas Anatomical Expression Data (FlyAtlas-RNA.adult) (FlyAtlas-RNA.larva)    Styles Linear Logarithmic Heatmap Back-to-back    Scales gene max expression Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: 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 eye, larval/adult central nervous system, adult crop, larval Malpighian tubules, larval fat body, larval/adult salivary gland, larval trachea, adult female reproductive system, 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) 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    20 central nervous system, larvae L3    39 central nervous system, pupae P8    28 head, virgin 1-day female    12 head, virgin 4-day female    14 head, virgin 20-day female    9 head, mated 1-day female    15 head, mated 4-day female    14 head, mated 20-day female    9 head, mated 1-day male    20 head, mated 4-day male    22 head, mated 20-day male    20 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    15 digestive system, 1-day adult    4 digestive system, 4-day adult    8 digestive system, 20-day adult    5 fat body, larvae L3 wandering    6 fat body, white prepupae    13 fat body, pupae P8    11 carcass, larvae L3 wandering    26 carcass, 1-day adult    8 carcass, 4-day adult    10 carcass, 20-day adult    8 ovary, virgin 4-day female    71 ovary, mated 4-day female    75 testis, mated 4-day male    2 accessory gland, mated 4-day male    3 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    20 central nervous system, larvae L3  (39) central nervous system, pupae P8  (28) head, virgin 1-day female    12 head, virgin 4-day female    14 head, virgin 20-day female    9 head, mated 1-day female    15 head, mated 4-day female    14 head, mated 20-day female    9 head, mated 1-day male    20 head, mated 4-day male    22 head, mated 20-day male    20 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    15 digestive system, 1-day adult    4 digestive system, 4-day adult    8 digestive system, 20-day adult    5 fat body, larvae L3 wandering    6 fat body, white prepupae    13 fat body, pupae P8    11 carcass, larvae L3 wandering  26 carcass, 1-day adult    8 carcass, 4-day adult    10 carcass, 20-day adult    8 ovary, virgin 4-day female  (71) ovary, mated 4-day female  (75) testis, mated 4-day male    2 accessory gland, mated 4-day male    3 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    20 central nervous system, larvae L3    39 central nervous system, pupae P8    28 head, virgin 1-day female    12 head, virgin 4-day female    14 head, virgin 20-day female    9 head, mated 1-day female    15 head, mated 4-day female    14 head, mated 20-day female    9 head, mated 1-day male    20 head, mated 4-day male    22 head, mated 20-day male    20 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    15 digestive system, 1-day adult    4 digestive system, 4-day adult    8 digestive system, 20-day adult    5 fat body, larvae L3 wandering    6 fat body, white prepupae    13 fat body, pupae P8    11 carcass, larvae L3 wandering    26 carcass, 1-day adult    8 carcass, 4-day adult    10 carcass, 20-day adult    8 ovary, virgin 4-day female    71 ovary, mated 4-day female    75 testis, mated 4-day male    2 accessory gland, mated 4-day male    3 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    20 central nervous system, larvae L3    39 central nervous system, pupae P8    28 head, virgin 1-day female    12 head, virgin 4-day female    14 head, virgin 20-day female    9 head, mated 1-day female    15 head, mated 4-day female    14 head, mated 20-day female    9 head, mated 1-day male    20 head, mated 4-day male    22 head, mated 20-day male    20 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    15 digestive system, 1-day adult    4 digestive system, 4-day adult    8 digestive system, 20-day adult    5 fat body, larvae L3 wandering    6 fat body, white prepupae    13 fat body, pupae P8    11 carcass, larvae L3 wandering    26 carcass, 1-day adult    8 carcass, 4-day adult    10 carcass, 20-day adult    8 ovary, virgin 4-day female    71 ovary, mated 4-day female    75 testis, mated 4-day male    2 accessory gland, mated 4-day male    3 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    20 central nervous system, larvae L3    39 central nervous system, pupae P8    28 head, virgin 1-day female    12 head, virgin 4-day female    14 head, virgin 20-day female    9 head, mated 1-day female    15 head, mated 4-day female    14 head, mated 20-day female    9 head, mated 1-day male    20 head, mated 4-day male    22 head, mated 20-day male    20 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    15 digestive system, 1-day adult    4 digestive system, 4-day adult    8 digestive system, 20-day adult    5 fat body, larvae L3 wandering    6 fat body, white prepupae    13 fat body, pupae P8    11 carcass, larvae L3 wandering    26 carcass, 1-day adult    8 carcass, 4-day adult    10 carcass, 20-day adult    8 ovary, virgin 4-day female    71 ovary, mated 4-day female    75 testis, mated 4-day male    2 accessory gland, mated 4-day male    3 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    20 central nervous system, larvae L3  (39) central nervous system, pupae P8  28 head, virgin 1-day female    12 head, virgin 4-day female    14 head, virgin 20-day female    9 head, mated 1-day female    15 head, mated 4-day female    14 head, mated 20-day female    9 head, mated 1-day male    20 head, mated 4-day male    22 head, mated 20-day male    20 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    15 digestive system, 1-day adult    4 digestive system, 4-day adult    8 digestive system, 20-day adult    5 fat body, larvae L3 wandering    6 fat body, white prepupae    13 fat body, pupae P8    11 carcass, larvae L3 wandering  26 carcass, 1-day adult    8 carcass, 4-day adult    10 carcass, 20-day adult    8 ovary, virgin 4-day female  (71) ovary, mated 4-day female  (75) testis, mated 4-day male    2 accessory gland, mated 4-day male    3 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    20 central nervous system, larvae L3    39 central nervous system, pupae P8    28 head, virgin 1-day female    12 head, virgin 4-day female    14 head, virgin 20-day female    9 head, mated 1-day female    15 head, mated 4-day female    14 head, mated 20-day female    9 head, mated 1-day male    20 head, mated 4-day male    22 head, mated 20-day male    20 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    15 digestive system, 1-day adult    4 digestive system, 4-day adult    8 digestive system, 20-day adult    5 fat body, larvae L3 wandering    6 fat body, white prepupae    13 fat body, pupae P8    11 carcass, larvae L3 wandering    26 carcass, 1-day adult    8 carcass, 4-day adult    10 carcass, 20-day adult    8 ovary, virgin 4-day female    71 ovary, mated 4-day female    75 testis, mated 4-day male    2 accessory gland, mated 4-day male    3 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    20 central nervous system, larvae L3    39 central nervous system, pupae P8    28 head, virgin 1-day female    12 head, virgin 4-day female    14 head, virgin 20-day female    9 head, mated 1-day female    15 head, mated 4-day female    14 head, mated 20-day female    9 head, mated 1-day male    20 head, mated 4-day male    22 head, mated 20-day male    20 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    14 digestive system, larvae L3 wandering    15 digestive system, 1-day adult    4 digestive system, 4-day adult    8 digestive system, 20-day adult    5 fat body, larvae L3 wandering    6 fat body, white prepupae    13 fat body, pupae P8    11 carcass, larvae L3 wandering    26 carcass, 1-day adult    8 carcass, 4-day adult    10 carcass, 20-day adult    8 ovary, virgin 4-day female    71 ovary, mated 4-day female    75 testis, mated 4-day male    2 accessory gland, mated 4-day male    3 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Tissue   Expression Level imaginal disc, larvae L3 wandering     central nervous system, larvae L3     central nervous system, pupae P8     head, virgin 1-day female     head, virgin 4-day female     head, virgin 20-day female     head, mated 1-day female     head, mated 4-day female     head, mated 20-day female     head, mated 1-day male     head, mated 4-day male     head, mated 20-day male     salivary gland, larvae L3 wandering     salivary gland, white prepupae     digestive system, larvae L3 wandering     digestive system, 1-day adult     digestive system, 4-day adult     digestive system, 20-day adult     fat body, larvae L3 wandering     fat body, white prepupae     fat body, pupae P8     carcass, larvae L3 wandering     carcass, 1-day adult     carcass, 4-day adult     carcass, 20-day adult     ovary, virgin 4-day female     ovary, mated 4-day female     testis, mated 4-day male     accessory gland, mated 4-day male
modENCODE Development RNA-Seq
modENCODE Temporal Expression Data (modENCODE_mRNA-Seq_U)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of low expression. Peak expression observed at stages throughout embryogenesis, in adult female stages. [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    36 embryo 02-04hr    48 embryo 04-06hr    46 embryo 06-08hr    38 embryo 08-10hr    36 embryo 10-12hr    16 embryo 12-14hr    31 embryo 14-16hr    19 embryo 16-18hr    18 embryo 18-20hr    10 embryo 20-22hr    22 embryo 22-24hr    23 larva L1    7 larva L2    6 larva L3 12hr old    4 larva L3 puffstage 1-2    5 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    16 white prepupae new    16 white prepupae 12hr    14 white prepupae 24hr    15 pupae 2d postWPP    12 pupae 3d postWPP    8 pupae 4d postWPP    4 adult male 01day    6 adult male 05day    5 adult male 30day    5 adult female 01day    11 adult female 05day    29 adult female 30day    28 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (36) embryo 02-04hr  (48) embryo 04-06hr  (46) embryo 06-08hr  (38) embryo 08-10hr  (36) embryo 10-12hr    16 embryo 12-14hr  (31) embryo 14-16hr    19 embryo 16-18hr    18 embryo 18-20hr    10 embryo 20-22hr    22 embryo 22-24hr    23 larva L1    7 larva L2    6 larva L3 12hr old    4 larva L3 puffstage 1-2    5 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    16 white prepupae new    16 white prepupae 12hr    14 white prepupae 24hr    15 pupae 2d postWPP    12 pupae 3d postWPP    8 pupae 4d postWPP    4 adult male 01day    6 adult male 05day    5 adult male 30day    5 adult female 01day    11 adult female 05day  (29) adult female 30day  (28) Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    36 embryo 02-04hr    48 embryo 04-06hr    46 embryo 06-08hr    38 embryo 08-10hr    36 embryo 10-12hr    16 embryo 12-14hr    31 embryo 14-16hr    19 embryo 16-18hr    18 embryo 18-20hr    10 embryo 20-22hr    22 embryo 22-24hr    23 larva L1    7 larva L2    6 larva L3 12hr old    4 larva L3 puffstage 1-2    5 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    16 white prepupae new    16 white prepupae 12hr    14 white prepupae 24hr    15 pupae 2d postWPP    12 pupae 3d postWPP    8 pupae 4d postWPP    4 adult male 01day    6 adult male 05day    5 adult male 30day    5 adult female 01day    11 adult female 05day    29 adult female 30day    28 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    36 embryo 02-04hr    48 embryo 04-06hr    46 embryo 06-08hr    38 embryo 08-10hr    36 embryo 10-12hr    16 embryo 12-14hr    31 embryo 14-16hr    19 embryo 16-18hr    18 embryo 18-20hr    10 embryo 20-22hr    22 embryo 22-24hr    23 larva L1    7 larva L2    6 larva L3 12hr old    4 larva L3 puffstage 1-2    5 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    16 white prepupae new    16 white prepupae 12hr    14 white prepupae 24hr    15 pupae 2d postWPP    12 pupae 3d postWPP    8 pupae 4d postWPP    4 adult male 01day    6 adult male 05day    5 adult male 30day    5 adult female 01day    11 adult female 05day    29 adult female 30day    28 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    36 embryo 02-04hr    48 embryo 04-06hr    46 embryo 06-08hr    38 embryo 08-10hr    36 embryo 10-12hr    16 embryo 12-14hr    31 embryo 14-16hr    19 embryo 16-18hr    18 embryo 18-20hr    10 embryo 20-22hr    22 embryo 22-24hr    23 larva L1    7 larva L2    6 larva L3 12hr old    4 larva L3 puffstage 1-2    5 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    16 white prepupae new    16 white prepupae 12hr    14 white prepupae 24hr    15 pupae 2d postWPP    12 pupae 3d postWPP    8 pupae 4d postWPP    4 adult male 01day    6 adult male 05day    5 adult male 30day    5 adult female 01day    11 adult female 05day    29 adult female 30day    28 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (36) embryo 02-04hr  (48) embryo 04-06hr  (46) embryo 06-08hr  (38) embryo 08-10hr  (36) embryo 10-12hr    16 embryo 12-14hr  31 embryo 14-16hr    19 embryo 16-18hr    18 embryo 18-20hr    10 embryo 20-22hr    22 embryo 22-24hr    23 larva L1    7 larva L2    6 larva L3 12hr old    4 larva L3 puffstage 1-2    5 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    16 white prepupae new    16 white prepupae 12hr    14 white prepupae 24hr    15 pupae 2d postWPP    12 pupae 3d postWPP    8 pupae 4d postWPP    4 adult male 01day    6 adult male 05day    5 adult male 30day    5 adult female 01day    11 adult female 05day  29 adult female 30day  28 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    36 embryo 02-04hr    48 embryo 04-06hr    46 embryo 06-08hr    38 embryo 08-10hr    36 embryo 10-12hr    16 embryo 12-14hr    31 embryo 14-16hr    19 embryo 16-18hr    18 embryo 18-20hr    10 embryo 20-22hr    22 embryo 22-24hr    23 larva L1    7 larva L2    6 larva L3 12hr old    4 larva L3 puffstage 1-2    5 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    16 white prepupae new    16 white prepupae 12hr    14 white prepupae 24hr    15 pupae 2d postWPP    12 pupae 3d postWPP    8 pupae 4d postWPP    4 adult male 01day    6 adult male 05day    5 adult male 30day    5 adult female 01day    11 adult female 05day    29 adult female 30day    28 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    36 embryo 02-04hr    48 embryo 04-06hr    46 embryo 06-08hr    38 embryo 08-10hr    36 embryo 10-12hr    16 embryo 12-14hr    31 embryo 14-16hr    19 embryo 16-18hr    18 embryo 18-20hr    10 embryo 20-22hr    22 embryo 22-24hr    23 larva L1    7 larva L2    6 larva L3 12hr old    4 larva L3 puffstage 1-2    5 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    16 white prepupae new    16 white prepupae 12hr    14 white prepupae 24hr    15 pupae 2d postWPP    12 pupae 3d postWPP    8 pupae 4d postWPP    4 adult male 01day    6 adult male 05day    5 adult male 30day    5 adult female 01day    11 adult female 05day    29 adult female 30day    28 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+    13 Schneider line 2 Sg4    4 embryonic 1182-4H    15 embryonic GM2    13 embryonic Kc167    6 embryonic S1    17 embryonic S3    11 leg disc CME L1    7 wing disc CME-W2    11 wing disc ML-DmD8    14 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    46 wing disc ML-DmD21    3 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11    21 antennal disc ML-DmD20-c5    3 mixed discs ML-DmD4-c1    7 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    14 ovary fGS/OSS    17 ovary OSC    26 ovary OSS    19 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    13 Schneider line 2 Sg4    4 embryonic 1182-4H    15 embryonic GM2    13 embryonic Kc167    6 embryonic S1    17 embryonic S3    11 leg disc CME L1    7 wing disc CME-W2    11 wing disc ML-DmD8    14 wing disc ML-DmD9    17 wing disc ML-DmD16-c3  (46) wing disc ML-DmD21    3 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11    21 antennal disc ML-DmD20-c5    3 mixed discs ML-DmD4-c1    7 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    14 ovary fGS/OSS    17 ovary OSC  26 ovary OSS    19 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    13 Schneider line 2 Sg4    4 embryonic 1182-4H    15 embryonic GM2    13 embryonic Kc167    6 embryonic S1    17 embryonic S3    11 leg disc CME L1    7 wing disc CME-W2    11 wing disc ML-DmD8    14 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    46 wing disc ML-DmD21    3 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11    21 antennal disc ML-DmD20-c5    3 mixed discs ML-DmD4-c1    7 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    14 ovary fGS/OSS    17 ovary OSC    26 ovary OSS    19 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+    13 Schneider line 2 Sg4    4 embryonic 1182-4H    15 embryonic GM2    13 embryonic Kc167    6 embryonic S1    17 embryonic S3    11 leg disc CME L1    7 wing disc CME-W2    11 wing disc ML-DmD8    14 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    46 wing disc ML-DmD21    3 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11    21 antennal disc ML-DmD20-c5    3 mixed discs ML-DmD4-c1    7 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    14 ovary fGS/OSS    17 ovary OSC    26 ovary OSS    19 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    13 Schneider line 2 Sg4    4 embryonic 1182-4H    15 embryonic GM2    13 embryonic Kc167    6 embryonic S1    17 embryonic S3    11 leg disc CME L1    7 wing disc CME-W2    11 wing disc ML-DmD8    14 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    46 wing disc ML-DmD21    3 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11    21 antennal disc ML-DmD20-c5    3 mixed discs ML-DmD4-c1    7 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    14 ovary fGS/OSS    17 ovary OSC    26 ovary OSS    19 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    13 Schneider line 2 Sg4    4 embryonic 1182-4H    15 embryonic GM2    13 embryonic Kc167    6 embryonic S1    17 embryonic S3    11 leg disc CME L1    7 wing disc CME-W2    11 wing disc ML-DmD8    14 wing disc ML-DmD9    17 wing disc ML-DmD16-c3  (46) wing disc ML-DmD21    3 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11    21 antennal disc ML-DmD20-c5    3 mixed discs ML-DmD4-c1    7 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    14 ovary fGS/OSS    17 ovary OSC  26 ovary OSS    19 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    13 Schneider line 2 Sg4    4 embryonic 1182-4H    15 embryonic GM2    13 embryonic Kc167    6 embryonic S1    17 embryonic S3    11 leg disc CME L1    7 wing disc CME-W2    11 wing disc ML-DmD8    14 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    46 wing disc ML-DmD21    3 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11    21 antennal disc ML-DmD20-c5    3 mixed discs ML-DmD4-c1    7 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    14 ovary fGS/OSS    17 ovary OSC    26 ovary OSS    19 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+    13 Schneider line 2 Sg4    4 embryonic 1182-4H    15 embryonic GM2    13 embryonic Kc167    6 embryonic S1    17 embryonic S3    11 leg disc CME L1    7 wing disc CME-W2    11 wing disc ML-DmD8    14 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    46 wing disc ML-DmD21    3 wing disc ML-DmD32    13 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11    21 antennal disc ML-DmD20-c5    3 mixed discs ML-DmD4-c1    7 CNS ML-DmBG1-c1    17 CNS ML-DmBG2-c2    19 tumorous blood cells mbn2    14 ovary fGS/OSS    17 ovary OSC    26 ovary OSS    19 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    19 cold shock, 4-day adult    13 heat shock, 4-day adult    15 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    19 Cadmium 100 mM 48 hrs, 4-day adult    53 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    51 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3    32 Ethanol 5% 3 hrs, larvae L3    6 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    39 Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult    31 Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    19 cold shock, 4-day adult    13 heat shock, 4-day adult    15 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    19 Cadmium 100 mM 48 hrs, 4-day adult  (53) Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult  (51) Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3  (32) Ethanol 5% 3 hrs, larvae L3    6 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult  (39) Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult  (31) Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    19 cold shock, 4-day adult    13 heat shock, 4-day adult    15 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    19 Cadmium 100 mM 48 hrs, 4-day adult    53 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    51 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3    32 Ethanol 5% 3 hrs, larvae L3    6 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    39 Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult    31 Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    2 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    19 cold shock, 4-day adult    13 heat shock, 4-day adult    15 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    19 Cadmium 100 mM 48 hrs, 4-day adult    53 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    51 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3    32 Ethanol 5% 3 hrs, larvae L3    6 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    39 Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult    31 Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    19 cold shock, 4-day adult    13 heat shock, 4-day adult    15 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    19 Cadmium 100 mM 48 hrs, 4-day adult    53 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    51 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3    32 Ethanol 5% 3 hrs, larvae L3    6 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    39 Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult    31 Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    19 cold shock, 4-day adult    13 heat shock, 4-day adult    15 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    19 Cadmium 100 mM 48 hrs, 4-day adult  (53) Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult  (51) Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3  32 Ethanol 5% 3 hrs, larvae L3    6 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult  (39) Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult  31 Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    19 cold shock, 4-day adult    13 heat shock, 4-day adult    15 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    19 Cadmium 100 mM 48 hrs, 4-day adult    53 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    51 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3    32 Ethanol 5% 3 hrs, larvae L3    6 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    39 Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult    31 Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    2 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    19 cold shock, 4-day adult    13 heat shock, 4-day adult    15 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    19 Cadmium 100 mM 48 hrs, 4-day adult    53 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    51 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    20 Ethanol 2.5% 3 hrs, larvae L3    32 Ethanol 5% 3 hrs, larvae L3    6 Ethanol 10% 3 hrs, larvae L3    5 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    39 Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult    31 Paraquat 10 mM 48 hrs, 4-day adult    22 Rotenone 2 μg 12 hrs, larvae L3    5 Rotenone 8 μg 12 hrs, larvae L3    2 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_17 mE1_20_mRNA_expression_cluster_04
External Data & Images
Linkouts	BDGP expression data • LD19808 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0000307 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG5813-RB;CG5813-RA FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for chif Stages(s) 1-3 Stages(s) 4-6 Stages(s) 7-8 Stages(s) 9-10 Stages(s) 11-12 Stages(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele viable, with Scer\GAL4pnr-MD237 chifGD12807 Sterility Allele female sterile chif1 chif3 chif4 chifDB23 chifPS55 chifQY42 chifunspecified female sterile | recessive chifA507 Other Phenotypes Allele visible, with Scer\GAL4pnr-MD237 chifGD12807 visible | recessive chif1 chif4 chifPS55 wild-type chif+t17 chifk08106h Phenotype manifest in Allele chorion chif1 chif3 chif4 chifDB23 chifPS55 chifQY42 eye chif1 chif4 chifPS55 scutellar bristle chif1 chif4 chifPS55 trichogen cell, with Scer\GAL4pnr-MD237 chifGD12807
Classical Alleles ( 17 )
For All Classical Alleles Show
Allele of chif Class Mutagen Stocks Known lesion chifBG02820a P-element activity 3 Yes chif1 hypomorphic allele - genetic evidence ethyl methanesulfonate 2 -- chifA507 P-element activity 2 -- chif5-SZ-3957 1 -- chifBG02484 1 -- chifEY05746 P-element activity 1 -- chif00233 0 -- chif2 ethyl methanesulfonate 0 -- chif3 hypomorphic allele - genetic evidence ethyl methanesulfonate 0 -- chif4 loss of function allele ethyl methanesulfonate 0 Yes chifDB23 hypomorphic allele - genetic evidence ethyl methanesulfonate 0 -- chifETBE3 loss of function allele 0 Yes chifk08106h P-element activity 0 Yes chifk09216 P-element activity 0 -- chifPS55 hypomorphic allele - genetic evidence ethyl methanesulfonate 0 -- chifQY42 hypomorphic allele - genetic evidence ethyl methanesulfonate 0 -- chifunspecified 0 --
Alleles Carried on Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Allele of chif Class Mutagen Stocks Known lesion chifGD12807 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes chifHMS00237 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes chifKK111411 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes chif+t17 in vitro construct - genomic fragment 0 Yes chiftYES9 in vitro construct - genomic fragment 0 Yes
Aneuploid Aberrations
Disrupted in	Df(2L)BSC781 (Christensen et al., 2009.5.6) Df(2L)cact-255rv64 (Tower et al., 1993, Dawson et al., 1995) Df(2L)Exel7065 (Ryder, 2004.4.26) Df(2L)k04216-rv2 (Roote, 2000.6.13) Df(2L)k04216-rv3 (Roote, 2000.6.13) Df(2L)k08106-rv4 (Roote, 2000.6.13) Df(2L)k08106-rv6 (Roote, 1999.7.7, Roote, 2000.6.13) Df(2L)k08106-rv15 (Roote, 1999.7.7, Roote, 2000.6.13) Df(2L)k14608-mr23 (Roote, 2000.6.13) Df(2L)k17027rv2 (Roote, 2000.6.13) Df(2L)r10 (Ashburner et al., 1990, Schupbach and Wieschaus, 1991) Df(2L)RA5 (Eberl et al., 1998, Ashburner et al., 1990, Roote, 1996.8, Levine et al., 2007) Df(2L)RM5 (Ashburner et al., 1990) Df(2L)RN2 (Eberl et al., 1998, Ashburner et al., 1990, Dawson et al., 1995) Df(2L)TE35D-16 (Ashburner et al., 1990) Df(2L)TE35D-21 (Ashburner et al., 1990, Dawson et al., 1995, Roote, 1996.8) Df(2L)TE35D-23 (Ashburner et al., 1990)
Not disrupted in	Df(2L)64j (Ashburner et al., 1990) Df(2L)A72 (Ashburner et al., 1990) Df(2L)A267 (Ashburner et al., 1990) Df(2L)ARR1 (Ashburner et al., 1990) Df(2L)b80e4 (Ashburner et al., 1990) Df(2L)el20 (Ashburner et al., 1990) Df(2L)el28 (Ashburner et al., 1990) Df(2L)fn12 (Ashburner et al., 1990) Df(2L)fn26 (Ashburner et al., 1990) Df(2L)fn27 (Ashburner et al., 1990) Df(2L)H20 (Ashburner et al., 1990) Df(2L)H60-3 (Dawson et al., 1995, Roote, 1996.1.11, Roote, 1996.8) Df(2L)II30 (Roote, 1996.8) Df(2L)III18 (Roote, 1996.8) Df(2L)MN-I (Levine et al., 2007) Df(2L)n78l3 (Ashburner et al., 1990) Df(2L)noc11 (Ashburner et al., 1990) Df(2L)osp29 (Eberl et al., 1998) Df(2L)osp38 (Ashburner et al., 1990) Df(2L)rd9 (Ashburner et al., 1990) Df(2L)Sco7 (Ashburner et al., 1990) Df(2L)Scorv16 (Ashburner et al., 1990) Df(2L)Scorv18 (Ashburner et al., 1990) Df(2L)Scorv19 (Ashburner et al., 1990) Df(2L)Scorv25 (Ashburner et al., 1990) Df(2L)SS1 (Ashburner et al., 1990) Df(2L)TE35BC-3 (Ashburner et al., 1990) Df(2L)TE35BC-4 (Ashburner et al., 1990) Df(2L)TE35BC-34 (Ashburner et al., 1990) Df(2L)TE35D-1 (Ashburner et al., 1990) Df(2L)TE35D-2 (Ashburner et al., 1990) Df(2L)TE35D-3 (Ashburner et al., 1990) Df(2L)TE35D-4 (Ashburner et al., 1990) Df(2L)TE35D-6 (Ashburner et al., 1990) Df(2L)TE35D-13 (Eberl et al., 1998, Ashburner et al., 1990, Dawson et al., 1995) Df(2L)TE35D-14 (Eberl et al., 1998, Ashburner et al., 1990) Df(2L)TE35D-15 (Ashburner et al., 1990) Df(2L)TE35D-19 (Ashburner et al., 1990) Df(2L)TE35D-20 (Ashburner et al., 1990) Df(2L)TE35D-22 (Ashburner et al., 1990) In(2L)dpps22Ldppd36R (Ashburner et al., 1990) In(2L)el18 (Eberl et al., 1998, Ashburner et al., 1990, Dawson et al., 1995) In(2LR)Scorv1-DV7 (Ashburner et al., 1990) T(2;3)Scorv7 (Ashburner et al., 1990)
Duplicated in	Dp(2;3)osp3 (Ashburner et al., 1990)
Not duplicated in	Dp(2;1)Scorv23 (Ashburner et al., 1990) Dp(2;2)GYL (Ashburner et al., 1990) Dp(2;2)TE35B-54L (Ashburner et al., 1990) In(2L)C163.41LC158R (Ashburner et al., 1990) In(2L)Scorv17LC158R (Ashburner et al., 1990)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD12807} NA P{KK111411} NA P{TRiP.HMS00237} NA characterization construct P{chif+t17} NA P{chiftYES9} NA
Insertions
	Type of insertions Name Expression data insertion of mobile activating element P{EPgy2}chifEY05746 NA miscellaneous insertions P{GT1}chifBG02484 NA P{GT1}chifBG02820a NA P{RS5}chif5-SZ-3957 NA insertion of enhancer trap P{lacW}chifk08106h No P{lacW}chifk09216 No P{lacW}l(2)SH1190SH1190 No insertion of enhancer trap binary system P{GawB}ckm175 No
Gene Ontology: Function, Process & Cellular Component ( 8 unique terms )
	There is no information supporting a cellular component term for this gene. (Based on a review of available data on: 2006-10-26)
Terms Based on Experimental Evidence ( 4 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
chorion-containing eggshell formation inferred from mutant phenotype (Schupbach and Wieschaus, 1991) eggshell chorion gene amplification inferred from mutant phenotype (Landis and Tower, 1995, Landis and Tower, 1999, Claycomb et al., 2004, Zhang and Tower, 2004) muscle cell homeostasis inferred from genetic interaction with Dg (Kucherenko et al., 2011) inferred from genetic interaction with Dys (Kucherenko et al., 2011) inferred from mutant phenotype (Kucherenko et al., 2011) photoreceptor cell axon guidance inferred from mutant phenotype (Marrone et al., 2011)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 4 terms )
Molecular Function
CV term Evidence References
DNA binding inferred from electronic annotation with InterPro:IPR017956 (FlyBase Curators et al., 2004-) zinc ion binding inferred from electronic annotation with InterPro:IPR006572 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
eggshell chorion assembly non-traceable author statement (Kim et al., 2002) regulation of DNA replication non-traceable author statement (Landis, 1999.6.10)
Cellular Component ( 0 terms)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions chif allele Gene References
External Data
Linkouts	DroID - A comprehensive database of gene and protein interactions. • FBgn0000307
Orthologs
OrthoDB Orthologs (18) - 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 EOG6M662W Dipteran inclusive ortholog search EOG6V43GN Insect inclusive ortholog search EOG6BK3ZP Arthropod inclusive ortholog search No orthologs identified Metazoa inclusive ortholog search No orthologs identified
Orthologs in Drosophila Species (EOG6M662W)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\chif     Drosophila simulans   Dsim\GD21913 Y   Drosophila sechellia   Dsec\GM17902 Y   Drosophila erecta   Dere\GG20129 Y   Drosophila yakuba   Dyak\GE12819 Y   Drosophila ananassae   Dana\GF20620 Y   Drosophila ananassae   Dana\GF16663     Drosophila pseudoobscura pseudoobscura   Dpse\GA19150 Y   Drosophila persimilis   Dper\GL18484 Y   Drosophila persimilis   Dper\GL17193     Drosophila willistoni   Dwil\GK24327 Y   Drosophila willistoni   Dwil\GK13047     Drosophila virilis   Dvir\GJ17456 Y   Drosophila mojavensis   Dmoj\GI13857 Y   Drosophila grimshawi   Dgri\GH25033 Y   Drosophila grimshawi   Dgri\GH18435
Orthologs in non-Drosophila Dipterans (EOG6V43GN)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ004662
Orthologs in non-Dipteran Insects (EOG6BK3ZP)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Bombyx mori Silkmoth  Bmor\BGIBMGA009897
Orthologs in non-Insect Arthropods (None identified)
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (None identified)
No non-Arthropod Metazoa orthologies identified
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD21913 Drosophila sechellia Dsec\GM17902 Drosophila erecta Dere\GG20129 Drosophila yakuba Dyak\GE12819 Drosophila ananassae Dana\GF20620 Drosophila pseudoobscura pseudoobscura Dpse\GA19150 Drosophila persimilis Dper\GL18484 Drosophila willistoni Dwil\GK24327 Drosophila virilis Dvir\GJ17456 Drosophila mojavensis Dmoj\GI13857 Drosophila grimshawi Dgri\GH25033
Stocks & Reagents
Stocks Listed in FlyBase ( 14 )
Bloomington	12695 w1118; P{GT1}chifBG02484 13134 w1118; P{GT1}chifBG02820a/CyO 15956 y1 w67c23; P{EPgy2}chifEY05746 33365 y1 sc* v1; P{TRiP.HMS00237}attP2 4079 chif1 cn1 sca1 bw1 sp1/CyO 11033 CyO, P{lArB}A507.2M2, chifA507/b1 Adh* cn* l(2)**; ry506
Kyoto	126253 w1118; P{RS5}chif5-SZ-3957 108887 w1118; P{GT1}chifBG02820a/CyO 107575 chif1 cn1 sca1 bw1 sp1/CyO
VDRC	v106508 P{KK111411}VIE-260B v28400 w1118; P{GD12807}v28400 v28401 w1118; P{GD12807}v28401
	More stocks available...
Genomic Clones ( 2 )
	BACR01N08 BACR33A07 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 52 )
	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	GM06264 LD19808 LD45516
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	GH01539 GH21855 GM12481 HL02831 LD14373 LP20081
Other clones	9996 10226 18146 31653 36972 42348 55795 62653 63705 101799 101922 154648 214309.27 214403.30 214471.24 281562 CK01.8C.H1 CK01.67B.D4 CK01.73B.F12 CK01.120D.G5 EK051432 EK054146 EK057842 EK092427 EK105417 EK109230 EK109612 EK131355 EK141560 EK147943 EK157043 EK183943 EK188552 EK190957 EK223233 EK228630 EK228837 EK258164 EK306722 FGM320A09 RP003023703 RP003123057 RP004211884
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0000307 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 34974
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: chif CG5817 (FlyBase, 1996-)
Additional comments	Sequences corresponding to the 5' end of release 2 CG18115 overlap the 3' end of release 3 chif transcript CG5813-RA. (FlyBase Genome Annotators, 2002-2003) Release 1 annotation CG5817 overlaps part of the release 3.2 annotation for chif (CG5813). (FlyBase, 1996-)
Other Comments
	The Hrp59 protein binds preferentially to a subset of mRNAs, including chif mRNA. (Kiesler et al., 2005) Hypomorphic mutations in chif cause thin, fragile chorions and female sterility, and eliminate chorion gene amplification. Null alleles have the additional phenotypes of rough eyes and thin thoracic bristles; phenotypes often associated with disruption of the normal cell cycle. (Landis and Tower, 1999) chif is involved in processes in addition to chorion gene amplification. (Landis and Tower, 1995) Mutations at the chif locus cause defects in midoogenesis. (Schupbach and Wieschaus, 1991) 5 alleles are discussed but are not named. (Ashburner et al., 1990)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_078859 NM_165156 NM_001273570 RefSeq (Proteins) • NP_523583 NP_723965 NP_001260499 DDBJ / EMBL / GenBank • AA439734 AA540346 AA697589 AA802759 AA803993 AA949224 AAD48779 AAD48780 AAF45010 AAF45011 AAF53530 AAG22437 AAL28467 AAM50251 AE003416 AF158178 AF158179 AGB93034 AI062361 AQ025739 AQ025889 AW941263 AW942544 AY060919 AY119597 BH615037 Entrez Gene - A searchable database of RefSeq genes. • 34974 UniProtKB/Swiss-Prot • Q9NK54
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • AT hook, DNA-binding motif (IPR017956) Zinc finger, DBF-type (IPR006572) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • LD19808
Linkouts
	DroID - A comprehensive database of gene and protein interactions. • FBgn0000307 DRSC - Results from RNAi screens. • FBgn0000307 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0000307 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG5813-RB;CG5813-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0000307 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 34974 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /newgene/chiffon1.htm modMine - Data generated by the modENCODE project. • FBgn0000307
Synonyms & Secondary IDs ( 12 )
Reported As
Symbol Synonym	BG:DS09218.1 (Ashburner et al., 1999.10.12, Ashburner et al., 1999, Ashburner et al., 1999, ) BG:DS09218.2 (Ashburner et al., 1999.10.12, Ashburner et al., 1999) CG5813 (Moorman et al., 2006, Keleman et al., 2009.8.5, Ni et al., 2010.12.1) CG5817 (Whitfield, 2000.11.21, Lawniczak and Begun, 2004) chf   chif (Liebl et al., 2006, Georlette et al., 2007, Kucherenko et al., 2008, Christensen et al., 2009.5.6, Roote, 2010.1.4, Levine et al., 2007, Wasbrough et al., 2010, Kucherenko et al., 2011, Marrone et al., 2011, Tunstall et al., 2012) Chif (Cayirlioglu et al., 2003) Dbf4 (Tower, 2004, Georlette et al., 2007) DS09218.1 (Reese et al., 2000) fs(2)chiffon (Orr-Weaver, 1991)
Name Synonym	chiffon (Landis, 1999.6.10, Landis, 1999.6.10, Kiesler et al., 2005, May et al., 2005, Kucherenko et al., 2011, Tunstall et al., 2012) Chiffon (Marrone et al., 2011)
Secondary FlyBase IDs
	FBgn0028842
References ( 70 )
Generate a list of	All references relating to this gene ( 70 )
List References by type	Research paper  ( 26 ) Supplementary material  ( 7 ) Review  ( 6 ) Personal communication to FlyBase  ( 20 ) Abstract  ( 1 ) FlyBase analysis  ( 5 ) DNA/RNA sequence record  ( 2 ) Website  ( 1 ) Curated genome annotation  ( 2 )
Recent research papers ( 3 )
	Tunstall et al., 2012, PLoS ONE 7(4): e35641 A Screen for Genes Expressed in the Olfactory Organs of Drosophila melanogaster Identifies Genes Involved in Olfactory Behaviour. [FBrf0218110] Kucherenko et al., 2011, Dev. Biol. 352(2): 228--242 Stress and muscular dystrophy: a genetic screen for dystroglycan and dystrophin interactors in Drosophila identifies cellular stress response components. [FBrf0214383] Marrone et al., 2011, BMC Neurosci. 12: 93 New Dystrophin/Dystroglycan interactors control neuron behavior in Drosophila eye. [FBrf0216731] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...