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Gene Dmel\nkd

General Information
Symbol	Dmel\nkd	Species	D. melanogaster
Name	naked cuticle	Annotation symbol	CG11614
Feature type	protein_coding_gene	FlyBase ID	FBgn0002945
Gene Model Status	Current	Stock availability	19 publicly available
Genomic Location
Chromosome (arm)	3L	Recombination map	3-47
Cytogenetic map	75F2-75F4	Sequence location	3L:18,996,841..19,038,549 [-]
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 naked cuticle is referred to in FlyBase by the symbol Dmel\nkd (CG11614, FBgn0002945). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: protein binding; zinc ion binding. There is experimental evidence that it is involved in the biological process: neuroblast fate specification; segment polarity determination; Wnt receptor signaling pathway, planar cell polarity pathway. 60 alleles are reported. The phenotypes of these alleles are annotated with: organ system; organ system subdivision; adult segment; larval abdominal segment; acellular anatomical structure; non-connected developing system; thoracic segment; spiracle; portion of tissue; embryonic gnathal segment; abdominal 5 ventral denticle belt; abdominal 3 ventral denticle belt; cephalopharyngeal skeleton; ventral nerve cord primordium; late extended germ band embryo. It has 3 annotated transcripts and 3 annotated polypeptides. Protein features are: EF-hand-like domain. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of very low expression. Peak expression observed within 00-12 hour embryonic stages. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: larval central nervous system. Comments on Affy2 ProbeSet: ProbeSet 1630361_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of nkd. Gene sequence location is 3L:18996841..19038549.
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	nkd: naked cuticle Denticle bands partially deleted. Embryonic lethal. Terminal phenotype partly due to cell death after germ band shortening (Martinez-Arias).
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	Controlled Vocabulary Terms calcium ion binding
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 75F2-75F4   Limits computationally determined from genome sequence between P{lacW}l(3)j4E6j4E6 and P{EP}MESR6EP3142
Experimentally Determined Cytological Location
Cytogenetic map Notes References 75F-75F     (Zeng, 1999.12.7) 75E-75F   (determined by in situ hybridisation)   (Dalton et al., 1987)
Experimentally Determined Recombination Data
Location	3-47 (Tearle and Nusslein-Volhard, 1987)
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\nkd 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 5.45 Low-frequency RNA-Seq exon junction(s) not annotated. Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters. DGC clone appears problematic: incomplete CDS (LD20624)
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) nkd-RA FBtr0075039  NM_080049   5051   928 nkd-RB FBtr0332649  NM_001275100   4674   553 nkd-RC FBtr0332650  NM_001275101   4685   806
Additional Transcript Data & Comments
Reported size (kB)	5.0 (northern blot) (Zeng et al., 2000)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein nkd-PA   FBpp0074806   102.6   928   8.60     NP_524788   AAF49198 nkd-PB   FBpp0304895   60.1   553   9.66     NP_001262029   AGB94722 nkd-PC   FBpp0304896   88.9   806   8.54     NP_001262030   AGB94723
Additional Polypeptide Data & Comments
Reported size (kDa)	928 (aa); 102 (kD predicted) (Zeng et al., 2000)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • EF-hand-like domain (IPR011992)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA540806   AA567710   AE014296 AAF49198   AF213376 AAF34825   AE014296 AGB94722   AE014296 AGB94723   AI293515   AW942574   AY061294 AAL28842   BI237902   BI239767   BI240424   BI242026   BI242453   BI361344   BI373097   BI375464   BI481810   BI577352   BI577412   BI577653   BP560002   BT015258 AAT94487   CO178848   CO179650   CO186239   CO190191   CO196511   CO273648   CO277311   CO278670   CO279237   CO283317   CO285707   CO286061   CO287826   CO287833   CO288298   CO290098   CO295120   CO301682   CO303662   CO306654   CO312010   CO313181   CO313639   CO315097   CO321210   CO324326   CO324394   CO325494   CO328826   CO329721   CZ487548   EC058511   EC058806   EC061263   EC069464   EC069934   EC069968   EC072203   EC076667   EC076960   EC081473   EC083427   EC088053   EC088063   EC195963   EC197170   EC199511   EC200814   EC205979   EC212125   EC214374   EC216442   EC218746   EC225598   EC225951   EC230263   EC230534   EC233208   EC233280   EC236285   EC236957   EC245079   EY199026   GH742368   GH742542   GH744486   GH745725   GH765007
UniProtKB/Swiss-Prot	Q9VVV9
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 regulatory region FBsf0000435043 3L:19,036,493..19,037,199 evidence=Reporter construct (in vivo) (Junion et al., 2012, Halfon, 2012.6.19) regulatory region FBsf0000435554 3L:19,047,520..19,048,605 evidence=Reporter construct (in vitro) (Chang et al., 2008, Halfon, 2012.6.19) regulatory region FBsf0000436186 3L:19,047,736..19,048,605 evidence=Reporter construct (in vivo) (Chang et al., 2008, Halfon, 2012.6.19) regulatory region FBsf0000436424 3L:19,033,127..19,033,995 evidence=Reporter construct (in vivo) (Chang et al., 2008, Halfon, 2012.6.19) regulatory region FBsf0000436511 3L:19,033,127..19,033,381 evidence=Reporter construct (in vivo) (Chang et al., 2008, Halfon, 2012.6.19) regulatory region FBsf0000436700 3L:19,047,520..19,048,138 evidence=Reporter construct (in vivo) (Chang et al., 2008, Halfon, 2012.6.19)
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage | early   organism | gap expression pattern   (Zeng et al., 2000) embryonic stage 4 -- 6   ectoderm anlage   (Fisher et al., 2012) Comment:anlage in statu nascendi organism | intense & ubiquitous   (Fisher et al., 2012) embryonic stage 7 -- 8   organism | intense & ubiquitous   (Fisher et al., 2012) embryonic stage 9 -- 10   organism | intense & ubiquitous   (Fisher et al., 2012) embryonic stage 11 -- 12   dorsal epidermis primordium   (Fisher et al., 2012) dorsal head epidermis primordium   (Fisher et al., 2012) Comment:reported as head epidermis primordium lateral head epidermis primordium   (Fisher et al., 2012) Comment:reported as head epidermis primordium ventral head epidermis primordium   (Fisher et al., 2012) Comment:reported as head epidermis primordium ventral epidermis primordium   (Fisher et al., 2012) embryonic stage 13 -- 16   embryonic dorsal epidermis   (Fisher et al., 2012) embryonic head epidermis   (Fisher et al., 2012) embryonic ventral epidermis   (Fisher et al., 2012) third instar larval stage   wing disc | dorsal/ventral compartment boundary   (Zeng et al., 2000) northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage     (Zeng et al., 2000) organism | segmentally repeated   (Zeng et al., 2000) larval stage   imaginal disc   (Zeng et al., 2000) ventral thoracic disc   (Zeng et al., 2000) wing disc   (Zeng et al., 2000)
Additional Descriptive Data
	nkd RNA is not detected in 0-2hr embryo RNA. It is detected in 2-4hr RNA, peaks in 4-8hr RNA and then declines. By in situ hybridization, nkd transcripts are observed in broad anterior and posterior domains reminiscent of a gap gene pattern in the late cellular blastoderm. During germ band extension, nkd transcription is nearly ubiquitous with higher levels in the 2-3 rows posterior to the hh/en stripe. During full germ band extension, nkd transcript levels are highest just anterior to and lower just posterior to the hh/en stripe. The level is even lower in the hh/en-producing cells. After stage 10, wg and nkd are co-expressed in many tissues. They are expressed in overlapping patterns in imaginal discs and other larval tissues where the nkd domain is slightly broader than the wg domain. (Zeng et al., 2000)
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage   organism | segmentally repeated   (Zeng et al., 2000)
Additional Descriptive Data
	nkd protein is detected in a segmentally repeated cytoplasmic pattern very similar to the mRNA distribution pattern. (Zeng et al., 2000)
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
cytoplasm inferred from direct assay (assigned by UniProtKB) (Waldrop et al., 2006) nucleus inferred from direct assay (assigned by UniProtKB) (Waldrop et al., 2006)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
FlyAtlas Anatomical Expression Data (FlyAtlas-RNA.adult) (FlyAtlas-RNA.larva)    Styles Linear Logarithmic Heatmap Back-to-back    Scales gene max expression Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: larval central nervous system. [download data (TSV)] Guide to FlyAtlas expression level colors   No expression (0 - 9.999)   Low expression (10 - 99.999)   Moderate expression (100 - 499.999)   High level expression (500 - 999.999)   Very high expression (>999.999) Linear, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    167.375 Larval Midgut    19.2 Larval Hindgut    45 Larval Malpighian Tubules    34.5 Larval Fat Body    15.8 Larval Salivary Gland    32 Larval Trachea    49.4 Larval Carcass    45.825 Adult Head    47.6 Adult Eye    38.8 Adult Brain    61 Adult Thoracic-Abdominal Ganglion    51.4 Adult Crop    77.3 Adult Midgut    27.6 Adult Hindgut    73.1 Adult Malpighian Tubules    52.9 Adult Fat Body    22.3 Adult Salivary Gland    34 Adult Heart    35.2 Adult VirginFemale Spermatheca    32.6 Adult InseminatedFemale Spermatheca    36.4 Adult Ovary    2.9 Adult Testis    6.7 Adult Male Accessory Gland    43.1 Adult Carcass    20 Expression Level Scale  None   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    167.375 Larval Midgut    19.2 Larval Hindgut    45 Larval Malpighian Tubules    34.5 Larval Fat Body    15.8 Larval Salivary Gland    32 Larval Trachea    49.4 Larval Carcass    45.825 Adult Head    47.6 Adult Eye    38.8 Adult Brain    61 Adult Thoracic-Abdominal Ganglion    51.4 Adult Crop    77.3 Adult Midgut    27.6 Adult Hindgut    73.1 Adult Malpighian Tubules    52.9 Adult Fat Body    22.3 Adult Salivary Gland    34 Adult Heart    35.2 Adult VirginFemale Spermatheca    32.6 Adult InseminatedFemale Spermatheca    36.4 Adult Ovary    2.9 Adult Testis    6.7 Adult Male Accessory Gland    43.1 Adult Carcass    20 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    167.375 Larval Midgut    19.2 Larval Hindgut    45 Larval Malpighian Tubules    34.5 Larval Fat Body    15.8 Larval Salivary Gland    32 Larval Trachea    49.4 Larval Carcass    45.825 Adult Head    47.6 Adult Eye    38.8 Adult Brain    61 Adult Thoracic-Abdominal Ganglion    51.4 Adult Crop    77.3 Adult Midgut    27.6 Adult Hindgut    73.1 Adult Malpighian Tubules    52.9 Adult Fat Body    22.3 Adult Salivary Gland    34 Adult Heart    35.2 Adult VirginFemale Spermatheca    32.6 Adult InseminatedFemale Spermatheca    36.4 Adult Ovary    2.9 Adult Testis    6.7 Adult Male Accessory Gland    43.1 Adult Carcass    20 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    167.375 Larval Midgut    19.2 Larval Hindgut    45 Larval Malpighian Tubules    34.5 Larval Fat Body    15.8 Larval Salivary Gland    32 Larval Trachea    49.4 Larval Carcass    45.825 Adult Head    47.6 Adult Eye    38.8 Adult Brain    61 Adult Thoracic-Abdominal Ganglion    51.4 Adult Crop    77.3 Adult Midgut    27.6 Adult Hindgut    73.1 Adult Malpighian Tubules    52.9 Adult Fat Body    22.3 Adult Salivary Gland    34 Adult Heart    35.2 Adult VirginFemale Spermatheca    32.6 Adult InseminatedFemale Spermatheca    36.4 Adult Ovary    2.9 Adult Testis    6.7 Adult Male Accessory Gland    43.1 Adult Carcass    20 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    167.375 Larval Midgut    19.2 Larval Hindgut    45 Larval Malpighian Tubules    34.5 Larval Fat Body    15.8 Larval Salivary Gland    32 Larval Trachea    49.4 Larval Carcass    45.825 Adult Head    47.6 Adult Eye    38.8 Adult Brain    61 Adult Thoracic-Abdominal Ganglion    51.4 Adult Crop    77.3 Adult Midgut    27.6 Adult Hindgut    73.1 Adult Malpighian Tubules    52.9 Adult Fat Body    22.3 Adult Salivary Gland    34 Adult Heart    35.2 Adult VirginFemale Spermatheca    32.6 Adult InseminatedFemale Spermatheca    36.4 Adult Ovary    2.9 Adult Testis    6.7 Adult Male Accessory Gland    43.1 Adult Carcass    20 Expression Level Scale  None   Low   Moderate  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    167.375 Larval Midgut    19.2 Larval Hindgut    45 Larval Malpighian Tubules    34.5 Larval Fat Body    15.8 Larval Salivary Gland    32 Larval Trachea    49.4 Larval Carcass    45.825 Adult Head    47.6 Adult Eye    38.8 Adult Brain    61 Adult Thoracic-Abdominal Ganglion    51.4 Adult Crop    77.3 Adult Midgut    27.6 Adult Hindgut    73.1 Adult Malpighian Tubules    52.9 Adult Fat Body    22.3 Adult Salivary Gland    34 Adult Heart    35.2 Adult VirginFemale Spermatheca    32.6 Adult InseminatedFemale Spermatheca    36.4 Adult Ovary    2.9 Adult Testis    6.7 Adult Male Accessory Gland    43.1 Adult Carcass    20 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    167.375 Larval Midgut    19.2 Larval Hindgut    45 Larval Malpighian Tubules    34.5 Larval Fat Body    15.8 Larval Salivary Gland    32 Larval Trachea    49.4 Larval Carcass    45.825 Adult Head    47.6 Adult Eye    38.8 Adult Brain    61 Adult Thoracic-Abdominal Ganglion    51.4 Adult Crop    77.3 Adult Midgut    27.6 Adult Hindgut    73.1 Adult Malpighian Tubules    52.9 Adult Fat Body    22.3 Adult Salivary Gland    34 Adult Heart    35.2 Adult VirginFemale Spermatheca    32.6 Adult InseminatedFemale Spermatheca    36.4 Adult Ovary    2.9 Adult Testis    6.7 Adult Male Accessory Gland    43.1 Adult Carcass    20 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    167.375 Larval Midgut    19.2 Larval Hindgut    45 Larval Malpighian Tubules    34.5 Larval Fat Body    15.8 Larval Salivary Gland    32 Larval Trachea    49.4 Larval Carcass    45.825 Adult Head    47.6 Adult Eye    38.8 Adult Brain    61 Adult Thoracic-Abdominal Ganglion    51.4 Adult Crop    77.3 Adult Midgut    27.6 Adult Hindgut    73.1 Adult Malpighian Tubules    52.9 Adult Fat Body    22.3 Adult Salivary Gland    34 Adult Heart    35.2 Adult VirginFemale Spermatheca    32.6 Adult InseminatedFemale Spermatheca    36.4 Adult Ovary    2.9 Adult Testis    6.7 Adult Male Accessory Gland    43.1 Adult Carcass    20 Expression Level Scale  None   Low   Moderate   High   Very high  Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut     Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body     Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion     Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body     Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca     Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland     Adult Carcass     FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    47.6   NA  Eye    38.8   NA  Brain    61   167.375  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    51.4   NA  Crop    77.3   19.2  Midgut    27.6   45  Hindgut    73.1   34.5  Malpighian Tubules    52.9   no informative data  Fat Body    22.3   32  Salivary Gland    34   NA  Heart    35.2   49.4  Trachea    NA   NA  VirginFemale Spermatheca    32.6   NA  InseminatedFemale Spermatheca    36.4   NA  Ovary    2.9   NA  Testis    6.7   NA  Male Accessory Gland    43.1   45.825  Carcass    no informative data FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
modENCODE Anatomy RNA-Seq
modENCODE Tissue Expression Data (modENCODE_mRNA-Seq_tissues)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    42 central nervous system, larvae L3    22 central nervous system, pupae P8    15 head, virgin 1-day female    4 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    6 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    8 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    2 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    4 carcass, larvae L3 wandering    24 carcass, 1-day adult    3 carcass, 4-day adult    2 carcass, 20-day adult    3 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering  (42) central nervous system, larvae L3    22 central nervous system, pupae P8    15 head, virgin 1-day female    4 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    6 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    8 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    2 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    4 carcass, larvae L3 wandering    24 carcass, 1-day adult    3 carcass, 4-day adult    2 carcass, 20-day adult    3 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    42 central nervous system, larvae L3    22 central nervous system, pupae P8    15 head, virgin 1-day female    4 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    6 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    8 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    2 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    4 carcass, larvae L3 wandering    24 carcass, 1-day adult    3 carcass, 4-day adult    2 carcass, 20-day adult    3 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Tissue   Expression Level imaginal disc, larvae L3 wandering    42 central nervous system, larvae L3    22 central nervous system, pupae P8    15 head, virgin 1-day female    4 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    6 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    8 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    2 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    4 carcass, larvae L3 wandering    24 carcass, 1-day adult    3 carcass, 4-day adult    2 carcass, 20-day adult    3 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    2 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    42 central nervous system, larvae L3    22 central nervous system, pupae P8    15 head, virgin 1-day female    4 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    6 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    8 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    2 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    4 carcass, larvae L3 wandering    24 carcass, 1-day adult    3 carcass, 4-day adult    2 carcass, 20-day adult    3 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering  (42) central nervous system, larvae L3    22 central nervous system, pupae P8    15 head, virgin 1-day female    4 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    6 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    8 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    2 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    4 carcass, larvae L3 wandering    24 carcass, 1-day adult    3 carcass, 4-day adult    2 carcass, 20-day adult    3 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    42 central nervous system, larvae L3    22 central nervous system, pupae P8    15 head, virgin 1-day female    4 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    6 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    8 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    2 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    4 carcass, larvae L3 wandering    24 carcass, 1-day adult    3 carcass, 4-day adult    2 carcass, 20-day adult    3 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Tissue   Expression Level imaginal disc, larvae L3 wandering    42 central nervous system, larvae L3    22 central nervous system, pupae P8    15 head, virgin 1-day female    4 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    6 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    8 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    2 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    4 carcass, larvae L3 wandering    24 carcass, 1-day adult    3 carcass, 4-day adult    2 carcass, 20-day adult    3 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Tissue   Expression Level imaginal disc, larvae L3 wandering     central nervous system, larvae L3     central nervous system, pupae P8     head, virgin 1-day female     head, virgin 4-day female     head, virgin 20-day female     head, mated 1-day female     head, mated 4-day female     head, mated 20-day female     head, mated 1-day male     head, mated 4-day male     head, mated 20-day male     salivary gland, larvae L3 wandering     salivary gland, white prepupae     digestive system, larvae L3 wandering     digestive system, 1-day adult     digestive system, 4-day adult     digestive system, 20-day adult     fat body, larvae L3 wandering     fat body, white prepupae     fat body, pupae P8     carcass, larvae L3 wandering     carcass, 1-day adult     carcass, 4-day adult     carcass, 20-day adult     ovary, virgin 4-day female     ovary, mated 4-day female     testis, mated 4-day male     accessory gland, mated 4-day male
modENCODE Development RNA-Seq
modENCODE Temporal Expression Data (modENCODE_mRNA-Seq_U)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of very low expression. Peak expression observed within 00-12 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    2 embryo 02-04hr    42 embryo 04-06hr    69 embryo 06-08hr    73 embryo 08-10hr    64 embryo 10-12hr    40 embryo 12-14hr    39 embryo 14-16hr    30 embryo 16-18hr    26 embryo 18-20hr    24 embryo 20-22hr    12 embryo 22-24hr    12 larva L1    8 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    12 white prepupae new    15 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    13 pupae 3d postWPP    5 pupae 4d postWPP    6 adult male 01day    3 adult male 05day    3 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr  (42) embryo 04-06hr  (69) embryo 06-08hr  (73) embryo 08-10hr  (64) embryo 10-12hr  (40) embryo 12-14hr  (39) embryo 14-16hr  (30) embryo 16-18hr  26 embryo 18-20hr    24 embryo 20-22hr    12 embryo 22-24hr    12 larva L1    8 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    12 white prepupae new    15 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    13 pupae 3d postWPP    5 pupae 4d postWPP    6 adult male 01day    3 adult male 05day    3 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr    42 embryo 04-06hr    69 embryo 06-08hr    73 embryo 08-10hr    64 embryo 10-12hr    40 embryo 12-14hr    39 embryo 14-16hr    30 embryo 16-18hr    26 embryo 18-20hr    24 embryo 20-22hr    12 embryo 22-24hr    12 larva L1    8 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    12 white prepupae new    15 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    13 pupae 3d postWPP    5 pupae 4d postWPP    6 adult male 01day    3 adult male 05day    3 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 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    2 embryo 02-04hr    42 embryo 04-06hr    69 embryo 06-08hr    73 embryo 08-10hr    64 embryo 10-12hr    40 embryo 12-14hr    39 embryo 14-16hr    30 embryo 16-18hr    26 embryo 18-20hr    24 embryo 20-22hr    12 embryo 22-24hr    12 larva L1    8 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    12 white prepupae new    15 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    13 pupae 3d postWPP    5 pupae 4d postWPP    6 adult male 01day    3 adult male 05day    3 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr    42 embryo 04-06hr    69 embryo 06-08hr    73 embryo 08-10hr    64 embryo 10-12hr    40 embryo 12-14hr    39 embryo 14-16hr    30 embryo 16-18hr    26 embryo 18-20hr    24 embryo 20-22hr    12 embryo 22-24hr    12 larva L1    8 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    12 white prepupae new    15 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    13 pupae 3d postWPP    5 pupae 4d postWPP    6 adult male 01day    3 adult male 05day    3 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr  (42) embryo 04-06hr  (69) embryo 06-08hr  (73) embryo 08-10hr  (64) embryo 10-12hr  (40) embryo 12-14hr  (39) embryo 14-16hr  30 embryo 16-18hr  26 embryo 18-20hr    24 embryo 20-22hr    12 embryo 22-24hr    12 larva L1    8 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    12 white prepupae new    15 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    13 pupae 3d postWPP    5 pupae 4d postWPP    6 adult male 01day    3 adult male 05day    3 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr    42 embryo 04-06hr    69 embryo 06-08hr    73 embryo 08-10hr    64 embryo 10-12hr    40 embryo 12-14hr    39 embryo 14-16hr    30 embryo 16-18hr    26 embryo 18-20hr    24 embryo 20-22hr    12 embryo 22-24hr    12 larva L1    8 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    12 white prepupae new    15 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    13 pupae 3d postWPP    5 pupae 4d postWPP    6 adult male 01day    3 adult male 05day    3 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 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    2 embryo 02-04hr    42 embryo 04-06hr    69 embryo 06-08hr    73 embryo 08-10hr    64 embryo 10-12hr    40 embryo 12-14hr    39 embryo 14-16hr    30 embryo 16-18hr    26 embryo 18-20hr    24 embryo 20-22hr    12 embryo 22-24hr    12 larva L1    8 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    12 white prepupae new    15 white prepupae 12hr    16 white prepupae 24hr    22 pupae 2d postWPP    13 pupae 3d postWPP    5 pupae 4d postWPP    6 adult male 01day    3 adult male 05day    3 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 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+    1 Schneider line 2 Sg4    2 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    3 embryonic S3    0 leg disc CME L1    3 wing disc CME-W2    1 wing disc ML-DmD8    2 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    3 wing disc ML-DmD21    1 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    2 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    2 ovary OSC    4 ovary OSS    2 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    1 Schneider line 2 Sg4    2 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    3 embryonic S3    0 leg disc CME L1    3 wing disc CME-W2    1 wing disc ML-DmD8    2 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    3 wing disc ML-DmD21    1 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    2 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    2 ovary OSC    4 ovary OSS    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    1 Schneider line 2 Sg4    2 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    3 embryonic S3    0 leg disc CME L1    3 wing disc CME-W2    1 wing disc ML-DmD8    2 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    3 wing disc ML-DmD21    1 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    2 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    2 ovary OSC    4 ovary OSS    2 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+    1 Schneider line 2 Sg4    2 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    3 embryonic S3    0 leg disc CME L1    3 wing disc CME-W2    1 wing disc ML-DmD8    2 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    3 wing disc ML-DmD21    1 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    2 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    2 ovary OSC    4 ovary OSS    2 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    1 Schneider line 2 Sg4    2 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    3 embryonic S3    0 leg disc CME L1    3 wing disc CME-W2    1 wing disc ML-DmD8    2 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    3 wing disc ML-DmD21    1 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    2 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    2 ovary OSC    4 ovary OSS    2 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    1 Schneider line 2 Sg4    2 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    3 embryonic S3    0 leg disc CME L1    3 wing disc CME-W2    1 wing disc ML-DmD8    2 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    3 wing disc ML-DmD21    1 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    2 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    2 ovary OSC    4 ovary OSS    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    1 Schneider line 2 Sg4    2 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    3 embryonic S3    0 leg disc CME L1    3 wing disc CME-W2    1 wing disc ML-DmD8    2 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    3 wing disc ML-DmD21    1 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    2 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    2 ovary OSC    4 ovary OSS    2 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+    1 Schneider line 2 Sg4    2 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    3 embryonic S3    0 leg disc CME L1    3 wing disc CME-W2    1 wing disc ML-DmD8    2 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    3 wing disc ML-DmD21    1 wing disc ML-DmD32    1 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    2 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    2 ovary OSC    4 ovary OSS    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Cell Line   Expression Level Schneider line 2 S2R+     Schneider line 2 Sg4     embryonic 1182-4H     embryonic GM2     embryonic Kc167     embryonic S1     embryonic S3     leg disc CME L1     wing disc CME-W2     wing disc ML-DmD8     wing disc ML-DmD9     wing disc ML-DmD16-c3     wing disc ML-DmD21     wing disc ML-DmD32     haltere disc ML-DmD17-c3     eye-antennal disc ML-DmD11     antennal disc ML-DmD20-c5     mixed discs ML-DmD4-c1     CNS ML-DmBG1-c1     CNS ML-DmBG2-c2     tumorous blood cells mbn2     ovary fGS/OSS     ovary OSC     ovary OSS
modENCODE Treatments RNA-Seq
modENCODE Treatment Expression Data (modENCODE_mRNA-Seq_treatments)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    5 cold shock, 4-day adult    4 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    3 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    4 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    3 Rotenone 2 μg 12 hrs, larvae L3    2 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    5 cold shock, 4-day adult    4 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    3 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    4 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    3 Rotenone 2 μg 12 hrs, larvae L3    2 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    5 cold shock, 4-day adult    4 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    3 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    4 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    3 Rotenone 2 μg 12 hrs, larvae L3    2 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    5 cold shock, 4-day adult    4 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    3 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    4 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    3 Rotenone 2 μg 12 hrs, larvae L3    2 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    5 cold shock, 4-day adult    4 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    3 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    4 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    3 Rotenone 2 μg 12 hrs, larvae L3    2 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    5 cold shock, 4-day adult    4 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    3 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    4 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    3 Rotenone 2 μg 12 hrs, larvae L3    2 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    5 cold shock, 4-day adult    4 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    3 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    4 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    3 Rotenone 2 μg 12 hrs, larvae L3    2 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    5 cold shock, 4-day adult    4 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    3 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    4 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    3 Rotenone 2 μg 12 hrs, larvae L3    2 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_11 mE1_20_mRNA_expression_cluster_04
External Data & Images
Linkouts	BDGP expression data • LP04418 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0002945 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG11614-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | embryonic stage | recessive nkd1 nkd2 nkd3 nkd4 nkd5 nkd42J1 nkd04869a nkdunspecified lethal | pharate adult stage, with Scer\GAL4A8 nkdNBam.Scer\UAS.T:Avic\GFP-EGFP nkdNIN3.Scer\UAS.T:Avic\GFP-EGFP nkdR1S.Scer\UAS.T:Hsap\MYC viable, with Scer\GAL4pnr-MD237 nkdGD1496 viable (with Df(3L)ED4782) nkdΔIntE nkdΔUpE Sterility Allele fertile (with Df(3L)ED4782) nkdΔIntE nkdΔUpE Other Phenotypes Allele cell growth defective, with Scer\GAL4ap-md544 nkdScer\UAS.T:Hsap\MYC planar polarity defective, with Scer\GAL4hs.PB nkdScer\UAS.T:Hsap\MYC visible, with Scer\GAL4A8 nkdNIN3.Scer\UAS.T:Avic\GFP-EGFP visible, with Scer\GAL4B119 nkdGFPX.Scer\UAS.T:Avic\GFP-EGFP,T:Hsap\MYC nkdNBam.Scer\UAS.T:Avic\GFP-EGFP nkdNBg.Scer\UAS.T:Avic\GFP-EGFP nkdNBg.Scer\UAS.T:Myr-Src64B,T:Avic\GFP-EGFP nkdNBg.Scer\UAS.T:Myr-Src64B-GA,T:Avic\GFP-EGFP nkdNIN3.Scer\UAS.T:Avic\GFP-EGFP nkdNR1.Scer\UAS.T:Hsap\MYC nkdR1S.Scer\UAS.T:Hsap\MYC nkdScer\UAS.cZa nkdScer\UAS.T:Avic\GFP-EGFP nkdScer\UAS.T:Hsap\MYC nkdSrcRBg.Scer\UAS.T:Myr-Src64B,T:Avic\GFP-EGFP visible, with Scer\GAL4l(2)E105-E105 nkdScer\UAS.cZa visible | somatic clone nkd3 wild-type nkdhs.T:Hsap\MYC wild-type, with Scer\GAL4GMR.PF nkdScer\UAS.T:Hsap\MYC Phenotype manifest in Allele abdominal 1 ventral denticle belt nkd2 abdominal 2 ventral denticle belt nkd2 abdominal 3 ventral denticle belt nkd2 abdominal 4 ventral denticle belt nkd2 abdominal 5 ventral denticle belt nkd2 abdominal 6 ventral denticle belt nkd2 abdominal 7 ventral denticle belt nkd2 abdominal 8 ventral denticle belt nkd2 abdominal sternite bristle, with Scer\GAL4A8 nkdNBam.Scer\UAS.T:Avic\GFP-EGFP nkdNIN3.Scer\UAS.T:Avic\GFP-EGFP abdominal sternite bristle, with Scer\GAL4B119 nkdNBam.Scer\UAS.T:Avic\GFP-EGFP nkdNIN3.Scer\UAS.T:Avic\GFP-EGFP nkdR1S.Scer\UAS.T:Hsap\MYC nkdScer\UAS.T:Hsap\MYC nkdScer\UAS.cZa nkdScer\UAS.T:Avic\GFP-EGFP abdominal sternite bristle, with Scer\GAL4unspecified nkdScer\UAS.cZa abdominal sternite bristle | supernumerary, with Scer\GAL4B119 nkdNR1.Scer\UAS.T:Hsap\MYC abdominal ventral denticle belt nkd2 nkd3 nkd4 nkd42J1 nkd47K1 nkd71-72K1 nkd59-60M1 antenna, with Scer\GAL4unspecified nkdScer\UAS.cZa anterior crossvein | ectopic, with Scer\GAL4unspecified nkdScer\UAS.cZa cephalopharyngeal skeleton nkd2 nkd3 cephalopharyngeal skeleton (with nkd2) nkd3 cephalopharyngeal skeleton (with nkd3) nkd2 cuticle nkd6 denticle belt nkd1 nkd2 nkd3 nkddsRNA.cRa nkdhs.T:Hsap\MYC nkdunspecified denticle belt (with nkd2) nkd3 denticle belt (with nkd3) nkd2 embryonic/first instar larval cuticle nkd04869a nkd2 nkd3 nkd4 nkd42J1 nkd5 embryonic/first instar larval cuticle (with nkd2) nkd3 embryonic/first instar larval cuticle (with nkd3) nkd2 embryonic/larval brain | embryonic stage nkd2 embryonic/larval dorsal vessel nkd2 embryonic/larval somatic muscle nkd2 embryonic/larval spiracle nkd2 embryonic epidermis nkd2 nkd3 nkddsRNA.cRa embryonic epidermis & embryonic abdominal segment nkd2 embryonic gnathal segment nkd2 embryonic head nkd2 embryonic head (with nkd2) nkd3 embryonic head (with nkd3) nkd2 eye | somatic clone nkd3 eye | ventral, with Scer\GAL4B119 nkdScer\UAS.T:Hsap\MYC nkdScer\UAS.T:Avic\GFP-EGFP eye | ventral, with Scer\GAL4unspecified nkdScer\UAS.cZa filzkorper nkd2 nkd3 haltere, with Scer\GAL4unspecified nkdScer\UAS.cZa interommatidial bristle | somatic clone nkd2 Keilin's organ nkd2 nkd3 leg, with Scer\GAL4A8 nkdNBam.Scer\UAS.T:Avic\GFP-EGFP nkdNIN3.Scer\UAS.T:Avic\GFP-EGFP leg, with Scer\GAL4B119 nkdScer\UAS.cZa leg, with Scer\GAL4l(2)E105-E105 nkdScer\UAS.cZa leg, with Scer\GAL4unspecified nkdScer\UAS.cZa leg | ectopic, with Scer\GAL4B119 nkdScer\UAS.cZa leg | ectopic, with Scer\GAL4unspecified nkdScer\UAS.cZa neuroblast NB6-4 | ectopic nkd2 neuroblast NB7-3 nkd2 neuroblast NB7-3 | ectopic, with Scer\GAL4en-e16E nkdScer\UAS.cZa posterior spiracle primordium (with nkd2) nkd3 posterior spiracle primordium (with nkd3) nkd2 presumptive embryonic/larval central nervous system nkd2 presumptive embryonic/larval peripheral nervous system nkd2 primordium of embryonic/larval spiracle (with nkd2) nkd3 primordium of embryonic/larval spiracle (with nkd3) nkd2 scutum | ectopic, with Scer\GAL4unspecified nkdScer\UAS.cZa sternite, with Scer\GAL4B119 nkdNBg.Scer\UAS.T:Avic\GFP-EGFP nkdScer\UAS.T:Avic\GFP-EGFP nkdGFPX.Scer\UAS.T:Avic\GFP-EGFP,T:Hsap\MYC nkdNBg.Scer\UAS.T:Myr-Src64B,T:Avic\GFP-EGFP nkdNBg.Scer\UAS.T:Myr-Src64B-GA,T:Avic\GFP-EGFP nkdSrcRBg.Scer\UAS.T:Myr-Src64B,T:Avic\GFP-EGFP T1 beard nkd89E wing, with Scer\GAL4A8 nkdNBam.Scer\UAS.T:Avic\GFP-EGFP nkdNIN3.Scer\UAS.T:Avic\GFP-EGFP wing, with Scer\GAL4ap-md544 nkdScer\UAS.T:Hsap\MYC nkdScer\UAS.cZa wing, with Scer\GAL4hs.PB nkdScer\UAS.T:Hsap\MYC wing, with Scer\GAL4unspecified nkdScer\UAS.cZa wing disc | dorsal compartment, with Scer\GAL4ap-md544 nkdScer\UAS.T:Hsap\MYC wing hair, with Scer\GAL4hs.PB nkdScer\UAS.T:Hsap\MYC wing margin bristle, with Scer\GAL4unspecified nkdScer\UAS.cZa
Classical Alleles ( 18 )
For All Classical Alleles Show
Allele of nkd Class Mutagen Stocks Known lesion nkd3 ethyl methanesulfonate 4 Yes nkd2 loss of function allele ethyl methanesulfonate 3 Yes nkd04869a P-element activity 1 Yes nkd4 ethyl methanesulfonate 1 Yes nkdf04961 piggyBac transposase 1 -- nkdKG05029 1 -- nkdMI00209 1 -- nkd1 ethyl methanesulfonate 0 -- nkd42J1 0 Yes nkd47K1 0 Yes nkd59-60M1 0 Yes nkd5 ethyl methanesulfonate 0 -- nkd6 ethyl methanesulfonate 0 -- nkd71-72K1 0 Yes nkd89E loss of function allele 0 -- nkdunspecified 0 -- nkdΔIntE 0 Yes nkdΔUpE FLPase 0 Yes
Alleles Carried on Transgenic Constructs ( 42 )
For All Alleles Carried on Transgenic Constructs Show
Allele of nkd Class Mutagen Stocks Known lesion nkdGD1496 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes nkdhs.T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - coding region fusion 1 Yes nkdScer\UAS.cZa in vitro construct - regulatory fusion 1 Yes nkdScer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 1 Yes nkdScer\UAS.T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - coding region fusion 1 Yes nkdΔ30aa.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - deletion 1 Yes nkdΔD6.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 1 Yes nkdΔN.GFPC.Scer\UAS.T:Avic\GFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 1 Yes nkdΔR1S.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - deletion 1 Yes nkd7H.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes nkd7H.Scer\UAS.T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes nkdD201A.Scer\UAS.T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes nkdD213V.Scer\UAS in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes nkddsRNA.cRa in vitro construct - RNAi 0 Yes nkdEFX.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes nkdGFPN.Scer\UAS.T:Avic\GFP-EGFP,T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes nkdGFPX.Scer\UAS.T:Avic\GFP-EGFP,T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes nkdK445A.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - amino acid replacement 0 Yes nkdNBam.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes nkdNBg.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes nkdNBg.Scer\UAS.T:Myr-Src64B,T:Avic\GFP-EGFP in vitro construct - coding region fusion 0 Yes nkdNBg.Scer\UAS.T:Myr-Src64B-GA,T:Avic\GFP-EGFP in vitro construct - amino acid replacement 0 Yes nkdNGA.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes nkdNIG.11614R in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes nkdNIN3.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes nkdNIN4.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes nkdNR1.Scer\UAS.T:Hsap\MYC in vitro construct - regulatory fusion 0 Yes nkdR1S.Scer\UAS.T:Hsap\MYC in vitro construct - regulatory fusion 0 Yes nkdR441A.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - amino acid replacement 0 Yes nkdRAKA.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - amino acid replacement 0 Yes nkdSrcRBg.Scer\UAS.T:Myr-Src64B,T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes nkdΔ30aa.T:SV40\nls2,T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes nkdΔ6Δ30aa.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes nkdΔBBg.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes nkdΔEFX.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes nkdΔR1SΔ30aa.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes nkdΔR1SΔ30aaNLS.Scer\UAS.T:SV40\nls2,T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes nkdΔR1SΔD6.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes nkdΔR1SΔD6Δ30aa.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes nkdΔRB.Scer\UAS.T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes nkdΔRBg.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes nkdΔYS.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes
Aneuploid Aberrations
Not disrupted in	Df(3L)Cat (Cox et al., 2000) Df(3L)fz2 (Bhanot et al., 1999)
Disrupted in	Df(3L)469-6 (Wharton, 2008.8.25) Df(3L)469-13 (Wharton, 2008.8.25) Df(3L)A81 (Jurgens et al., 1984) Df(3L)BSC220 (Gresens and Cook, 2006.12.5) Df(3L)J158 (Jurgens et al., 1984) Ts(YLt;3Rt)L14+Ts(YLt;3Lt)L131 (Jurgens et al., 1984, Tearle and Nusslein-Volhard, 1987)
Partially disrupted in	Df(3L)nkdΔUpE (Chang et al., 2008)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD1496} NA P{NIG.11614R} NA P{UAS-nkd.7H.GFPC} NA P{UAS-nkd.7H.mycC} NA P{UAS-nkd.D201A.mycC} NA P{UAS-nkd.D213V} NA P{UAS-nkd.EFX.GFPC} NA P{UAS-nkd.GFPC} NA P{UAS-nkd.GFPN.mycC} NA P{UAS-nkd.GFPX.mycC} NA P{UAS-nkd.K445A.GFPC} NA P{UAS-nkd.myc} NA P{UAS-nkd.NBam.GFPC} NA P{UAS-nkd.NBg.GFPC} NA P{UAS-nkd.NGA.GFPC} NA P{UAS-nkd.NIN3.GFPC} NA P{UAS-nkd.NIN4.GFPC} NA P{UAS-nkd.NR1.mycC} NA P{UAS-nkd.R1S.mycC} NA P{UAS-nkd.R441A.GFPC} NA P{UAS-nkd.RAKA.GFPC} NA P{UAS-nkd.SrcG2ANBg.GFPC} NA P{UAS-nkd.SrcNBg.GFPC} NA P{UAS-nkd.SrcRBg.GFPC} NA P{UAS-nkd.Z} NA P{UAS-nkd.Δ6Δ30aa.GFPC} NA P{UAS-nkd.Δ30aa.GFPC} NA P{UAS-nkd.ΔBBg.GFPC} NA P{UAS-nkd.ΔD6.GFPC} NA P{UAS-nkd.ΔEFX.GFPC} NA P{UAS-nkd.ΔN.GFPC} NA P{UAS-nkd.ΔR1S.GFPC} NA P{UAS-nkd.ΔR1SΔ30aa.GFPC} NA P{UAS-nkd.ΔR1SΔ30aaNLS.GFPC} NA P{UAS-nkd.ΔR1SΔD6.GFPC} NA P{UAS-nkd.ΔR1SΔD6Δ30aa.GFPC} NA P{UAS-nkd.ΔRB.mycC} NA P{UAS-nkd.ΔRBg.GFPC} NA P{UAS-nkd.ΔYS.GFPC} NA reporter construct P{nkd-lacZ.IntE.255.TCFmut} No P{nkd-lacZ.IntE.255} No P{nkd-lacZ.IntE.869} No P{nkd-lacZ.UpE2.TCFmut} No P{nkd-lacZ.UpE2} No P{nkd-lacZ.UpE+IntE} No P{NKD-lacZ} No heat-shock construct P{hs-nkd.myc} NA characterization construct P{UAS-mNkd1.fNf30aa.GFPC} NA P{UAS-nkd::Btau\recoverin.rEF.mycC} NA P{UAS-nkd::Hsap\NKD2.hEFX2.mycC} NA P{UAS-nkd::Mmus\Nkd1.f30aa.GFPC} NA P{UAS-nkd.m1NΔN.GFPC} NA P{UAS-nkd.Δ6-HSFNLS.GFPC} NA P{UAS-nkd.Δ30aaNLS.GFPC} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions Mi{MIC}nkdMI00209 NA P{SUPor-P}nkdKG05029 NA PBac{WH}nkdf04961 NA insertion of enhancer trap P{PZ}nkd04869a No
Gene Ontology: Function, Process & Cellular Component ( 9 unique terms )
Terms Based on Experimental Evidence ( 7 terms )
Molecular Function
CV term Evidence References
protein binding inferred from physical interaction with UniProtKB:P51140 (assigned by UniProtKB) (Wharton et al., 2001) zinc ion binding inferred from direct assay (assigned by UniProtKB) (Rousset et al., 2002)
Biological Process
CV term Evidence References
neuroblast fate specification inferred from mutant phenotype (assigned by UniProtKB) (Deshpande et al., 2001) segment polarity determination inferred from mutant phenotype (assigned by UniProtKB) (Zeng et al., 2000) Wnt receptor signaling pathway, planar cell polarity pathway inferred from mutant phenotype (assigned by UniProtKB) (Zeng et al., 2000)
Cellular Component
CV term Evidence References
cytoplasm inferred from direct assay (assigned by UniProtKB) (Waldrop et al., 2006) nucleus inferred from direct assay (assigned by UniProtKB) (Waldrop et al., 2006)
Terms Based on Predictions or Assertions ( 2 terms )
Molecular Function
CV term Evidence References
calcium ion binding inferred from electronic annotation with InterPro:IPR011992 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
Wnt receptor signaling pathway non-traceable author statement (Zeng, 1999.12.7)
Cellular Component ( 0 terms)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
nkd - CG15220 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 nkd allele Gene References nkd2 arm (Greaves et al., 1999) ds (Rodriguez, 2004) shi (Moline et al., 1999) tum (Jones and Bejsovec, 2005) wg (Jones and Bejsovec, 2005) nkd3 h (Zeng et al., 2000) nkd4 h (Zeng et al., 2000) nkdhs.T:Hsap\MYC wg (Zeng et al., 2000) nkdScer\UAS.cZa arm (Zeng et al., 2000) dsh (Zeng et al., 2000, Rousset et al., 2001) fz (Rousset et al., 2001) por (Zeng et al., 2000) sgg (Zeng et al., 2000) tum (Jones and Bejsovec, 2005) wg (Zeng et al., 2000, Rousset et al., 2001, Jones and Bejsovec, 2005) nkdunspecified h (Zeng et al., 2000) unspecified arm (Rousset et al., 2001) dsh (Waldrop et al., 2006) fz2 (Rousset et al., 2001) shg (Greaves et al., 1999) tum (Jones et al., 2003)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 69321 DPiM - DPiM, Drosophila Protein interaction Map • FBgn0002945 DroID - A comprehensive database of gene and protein interactions. • FBgn0002945 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 44843 SignaLink - A protein-protein and protein-miRNA interaction database with multi-layered structure and multiple confidence scores. • Q9VVV9
Orthologs
OrthoDB Orthologs (12) - 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 EOG644M4T Dipteran inclusive ortholog search No orthologs identified Insect inclusive ortholog search No orthologs identified Arthropod inclusive ortholog search No orthologs identified Metazoa inclusive ortholog search No orthologs identified
Orthologs in Drosophila Species (EOG644M4T)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\nkd     Drosophila simulans   Dsim\GD12309 Y   Drosophila sechellia   Dsec\GM14900 Y   Drosophila erecta   Dere\GG13431 Y   Drosophila yakuba   Dyak\GE22529 Y   Drosophila ananassae   Dana\GF10788 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA11099 Y   Drosophila persimilis   Dper\GL21953 Y   Drosophila willistoni   Dwil\GK12537 Y   Drosophila virilis   Dvir\GJ13516 Y   Drosophila mojavensis   Dmoj\GI11812 Y   Drosophila grimshawi   Dgri\GH16954 Y
Orthologs in non-Drosophila Dipterans (None identified)
No non-Drosophilid orthologies identified
Orthologs in non-Dipteran Insects (None identified)
No non-Dipteran orthologies identified
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\GD12309 Drosophila sechellia Dsec\GM14900 Drosophila erecta Dere\GG13431 Drosophila yakuba Dyak\GE22529 Drosophila ananassae Dana\GF10788 Drosophila pseudoobscura pseudoobscura Dpse\GA11099 Drosophila persimilis Dper\GL21953 Drosophila willistoni Dwil\GK12537 Drosophila virilis Dvir\GJ13516 Drosophila mojavensis Dmoj\GI11812 Drosophila grimshawi Dgri\GH16954
Stocks & Reagents
Stocks Listed in FlyBase ( 19 )
Bloomington	25384 w*; P{UAS-nkd.GFPC}1 25386 w*; P{UAS-nkd.ΔR1S.GFPC}3 25387 w*; P{UAS-nkd.Δ30aa.GFPC}2 25381 y1 w*; P{hs-nkd.myc}9 25110 nkd2 P{neoFRT}80B/TM3, Sb1 25111 w*; P{PZ}nkd04869a/TM6B, Tb1 13623 y1; P{SUPor-P}nkdKG05029 ry506 25109 h1 nkd4 P{neoFRT}80B/TM6B, Tb1 25112 w*; h1 nkd3 P{neoFRT}80B/TM6B, Tb+
Harvard	- PBac{WH}nkdf04961
VDRC	v3004 w1118; P{GD1496}v3004 v3005 w1118; P{GD1496}v3005
	More stocks available...
Genomic Clones ( 2 )
	BACR09M20 BACR48M06 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 83 )
	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	LD20624 LP04418
Other clones	DPiM_LP04418
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	HL01667 LP06679 RE34234 RE36353 RE37267 RE39242 RE39778 RE45521 RE60314 RE63285 RE64415 RE71018 RE71082 RE71364
Other clones	11471 18243 19936 20000 20671 38296 43370 65759 65820 81666 104191 106322 106370 106496 107721 119577 119990 211272 CK01.18B.E8 CK01.58B.H3 CK01.73B.D6 CK01.76D.F9 CK01.77C.E10 CK01.78C.C6 CK01.79B.D5 CK01.80C.C5 CK01.84A.D5 CK01.84A.F5 CK01.93D.D10 CK01.121C.G7 EK005104 EK017552 EK046930 EK057736 EK060121 EK060451 EK061615 EK066915 EK066923 EK068201 EK073047 EK111733 EK123804 EK130923 EK133849 EK162837 EK181907 EK193231 EK193510 EK196644 EK208701 EK227661 EK231824 EK233627 EK239037 EK242333 EK251702 EK290515 EK291461 EK293605 FGM324B02 RP001014198 RP001016535 RP001017732 RP001025952 RP001026002
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0002945 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 44843
Antibody Information
	polyclonal (Zeng et al., 2000)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: nkd CG18224 CG11614 (Bayraktaroglu, 2000.8.7)
Additional comments	Release 1 annotation CG18224 corresponds to part of the release 3.2 annotation for nkd (CG11614). (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) nkd encodes an inducible antagonist of wg signalling. (Zeng et al., 2000) Wild-type nkd function may contribute to the control of wg protein movement within the epidermal cells of the segment in the embryo. (Moline et al., 1999) Segment polarity gene expression is necessary for the survival of specific rows of epidermal cells. (Pazdera et al., 1998) odd and nkd are required to restrict en expression. odd represses expression of ftz, an activator of en. nkd prevents activation of en by ftz without affecting ftz expression. (Mullen and DiNardo, 1995) Wild type activity of five segment polarity genes, wg, ptc, en, nkd and hh, can account for most of the ventral pattern elements in the embryo. wg is required for naked cuticle and en is required for the first row of denticles in each abdominal denticle belt. Remaining cell types are produced by different combinations of the five gene activities. wg generates the diversity of cell types within the segment but each specific cell identity depends on the activity of ptc, en, nkd and hh. ptc and nkd may affect wg autoregulation, and restrict wg activity within the segment. (Bejsovec and Wieschaus, 1993) Inactivation of late wg function restores denticle cell types to nkd embryos. (Dougan and DiNardo, 1992) Dfd expression unaffected by mutations at this locus. (Gonzalez-Reyes et al., 1992) gsb and nkd segment polarity gene products are responsible for maintaining the AP borders of ac expressing ectodermal cell clusters. (Skeath et al., 1992) Mutations in zygotic polarity gene nkd do not interact with RpII140wimp. (Parkhurst and Ish-Horowicz, 1991) nkd and ptc mutant embryos show ectopic expression of Dll in the limb primordia. There is a correspondence between the Dll expression and the spatial organization of the larval and adult limbs that develop from the primordium. (Cohen, 1990) Mutations of nkd suppress the maternal phenotype of fu mutations. (Preat et al., 1989) nkd mutants display deleted denticle belts. (Jurgens et al., 1984)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_080049 NM_001275100 NM_001275101 RefSeq (Proteins) • NP_524788 NP_001262029 NP_001262030 DDBJ / EMBL / GenBank • AA540806 AAF34825 AAF49198 AAL28842 AAT94487 AF213376 AGB94722 AGB94723 AW942574 AY061294 BT015258 CZ487548 Entrez Gene - A searchable database of RefSeq genes. • 44843 UniProtKB/Swiss-Prot • Q9VVV9
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • EF-hand-like domain (IPR011992) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • LP04418
Linkouts
	BioGRID - A database of protein and genetic interactions • 69321 DPiM - DPiM, Drosophila Protein interaction Map • FBgn0002945 DroID - A comprehensive database of gene and protein interactions. • FBgn0002945 DRSC - Results from RNAi screens. • FBgn0002945 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0002945 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG11614-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0002945 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 44843 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /segment/naked1.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 44843 modMine - Data generated by the modENCODE project. • FBgn0002945 SignaLink - A protein-protein and protein-miRNA interaction database with multi-layered structure and multiple confidence scores. • Q9VVV9
Synonyms & Secondary IDs ( 8 )
Reported As
Symbol Synonym	CG11614   CG18224   naked (Selleck, 2000, ) nkd (Sun et al., 2012, DasGupta et al., 2005, Waldrop et al., 2006, Chan et al., 2007, Mosimann et al., 2006, Gresens and Cook, 2006.12.5, Chang et al., 2007, Parker et al., 2007, Fang et al., 2006, Izutsu et al., 2012, Bhambhani et al., 2008, Chang et al., 2008, Parker et al., 2008, Thompson et al., 2008, Song et al., 2009, Hartmann et al., 2009, Toku et al., 2011, Chan et al., 2007, Chan et al., 2008, Wharton, 2008.8.22, Blauwkamp et al., 2008, Choksi et al., 2006, Tyler and Baker, 2007, Liu et al., 2008, Chang et al., 2008, Vincent et al., 2008, Chang et al., 2008, Wright and Tjian, 2009, Krejcí et al., 2009, Kennell et al., 2008, Li et al., 2007, Hatton-Ellis et al., 2007, DasGupta et al., 2007, Jones et al., 2010, Buechling et al., 2010, Song et al., 2010, Bhambhani et al., 2011, Kim et al., 2012, Japanese National Institute of Genetics, 2012.5.21, Chang et al., 2008) Nkd (Hatini and DiNardo, 2001, Chan et al., 2007, Tolwinski, 2007, Zhang et al., 2006, Sánchez et al., 2008, Immonen and Ritchie, 2012)
Name Synonym	Naked (Hatini and DiNardo, 2001, Zhang et al., 2006) naked (de la Roche and Bienz, 2007, Vincent et al., 2008, Buceta et al., 2007) naked cuticle (Waldrop et al., 2006, Chan et al., 2007, Kennell and Cadigan, 2007, Chang et al., 2007, He and Axelrod, 2006, Kennell and Cadigan, 2008, Parker et al., 2008, Song et al., 2009, Chan et al., 2008, Blauwkamp et al., 2008, Tyler and Baker, 2007, Chang et al., 2008, Chang et al., 2008, Jones et al., 2010, Bhambhani et al., 2011) Naked cuticle (Li et al., 2007, Valenta et al., 2011)
Secondary FlyBase IDs
	FBgn0036840 FBgn0036841
References ( 200 )
Generate a list of	All references relating to this gene ( 200 )
List References by type	Research paper  ( 110 ) Supplementary material  ( 5 ) Review  ( 30 ) Erratum  ( 1 ) Personal communication to FlyBase  ( 12 ) Abstract  ( 29 ) FlyBase analysis  ( 3 ) Conference report  ( 4 ) Stock list  ( 2 ) DNA/RNA sequence record  ( 1 ) Website  ( 1 ) Curated genome annotation  ( 1 ) Book  ( 1 )
Recent research papers ( 9 )
	Yang et al., 2013, Development 140(2): 413--422 Bridging Decapentaplegic and Wingless signaling in Drosophila wings through repression of naked cuticle by Brinker. [FBrf0220401] Immonen and Ritchie, 2012, Proc. Biol. Sci. 279(1732): 1359--1365 The genomic response to courtship song stimulation in female Drosophila melanogaster. [FBrf0217554] Izutsu et al., 2012, PLoS ONE 7(3): e33288 Genome features of "dark-fly", a Drosophila line reared long-term in a dark environment. [FBrf0217825] Junion et al., 2012, Cell 148(3): 473--486 A transcription factor collective defines cardiac cell fate and reflects lineage history. [FBrf0217404] Kim et al., 2012, BMC Syst. Biol. 6: 31 Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster. [FBrf0219366] Sun et al., 2012, PLoS Genet. 8(2): e1002515 Neurophysiological Defects and Neuronal Gene Deregulation in Drosophila mir-124 Mutants. [FBrf0217508] Bhambhani et al., 2011, EMBO J. 30(10): 2031--2043 The oligomeric state of CtBP determines its role as a transcriptional co-activator and co-repressor of Wingless targets. [FBrf0213805] Toku et al., 2011, Comput. Biol. Chem. 35(5): 282--292 Reconstruction and crosstalk of protein-protein interaction networks of Wnt and Hedgehog signaling in Drosophila melanogaster. [FBrf0216393] Valenta et al., 2011, Genes Dev. 25(24): 2631--2643 Probing transcription-specific outputs of β-catenin in vivo. [FBrf0219193] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...