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Gene Dmel\kn

General Information
Symbol	Dmel\kn	Species	D. melanogaster
Name	knot	Annotation symbol	CG10197
Feature type	protein_coding_gene	FlyBase ID	FBgn0001319
Gene Model Status	Current	Stock availability	12 publicly available
Also Known As	Col
Genomic Location
Chromosome (arm)	2R	Recombination map	2-72.3
Cytogenetic map	51C2-51C3	Sequence location	2R:10,660,155..10,694,566 [-]
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 knot is referred to in FlyBase by the symbol Dmel\kn (CG10197, FBgn0001319). It is a protein_coding_gene from Drosophila melanogaster. It is reported to have molecular function: sequence-specific DNA binding transcription factor activity. There is experimental evidence for 13 unique biological process terms, many of which group under: single-organism developmental process; biological regulation; system development; post-embryonic organ morphogenesis; immune response; response to other organism; muscle cell differentiation; segment specification; cellular component organization or biogenesis; response to stimulus; embryonic pattern specification. 28 alleles are reported. The phenotypes of these alleles are annotated with: ISN innervated muscle of A1-7; organ system; adult segment; organ system subdivision; hypodermal muscle of larval abdomen; thoracic segment; cephalopharyngeal skeleton; peripheral nervous system; pharyngeal sclerite; hypodermal muscle of metathorax; embryonic/larval hemocoel; cell part. It has 5 annotated transcripts and 5 annotated polypeptides. Protein features are: Cell surface receptor IPT/TIG; Immunoglobulin E-set; Immunoglobulin-like fold; Myc-type, basic helix-loop-helix (bHLH) domain; Transcription factor COE; Transcription factor COE, conserved site. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of extremely low expression. Peak expression observed at stages throughout embryogenesis. 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: larval/adult central nervous system, adult heart. Gene sequence location is 2R:10660155..10694566.
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	kn: knot Veins L3 and L4 shifted closer together in region of anterior crossvein, which is either extremely thick or eliminated by regional fusion of L3 and L4. Frequently, extra crossvein between L3 and L4 near end of wing. Shift in positions of sensilla and extra chaetae accompanies shift in vein positions. Wing narrowed. Head narrowed and flattened, so the long axis of eye is at oblique angle. May overlap wild type at high temperatures and in late counts. Best at 19. RK2.
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 51C2-51C3   Limits computationally determined from genome sequence between P{lacW}Rpn6k00103 and P{PZ}chn02064
Experimentally Determined Cytological Location
Cytogenetic map Notes References 51C1-51C2   (determined by in situ hybridisation)   (Crozatier et al., 1999) 51E-51F   (determined by in situ hybridisation)   (Kania et al., 1995) 51C1-51C2   (determined by in situ hybridisation)   (Vincent, 1995) 51B10-51C1   Placed in 51B10--51C1 by deficiency mapping (details unspecified).   (Crozatier et al., 1996)
Experimentally Determined Recombination Data
Location	2-72.3
Left of (cM)
Right of (cM)	L (Nestoras et al., 1997)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\kn 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 5.44 Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters. Gene model reviewed during 5.50
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) kn-RA FBtr0087465  NM_080074   3460   557 kn-RB FBtr0112809  NM_166070   3926   575 kn-RC FBtr0112810  NM_001103847   3339   689 kn-RD FBtr0301400  NM_137146   3457   556 kn-RE FBtr0329882  NM_001274051   2927   524
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein kn-PA   FBpp0086595   60.5   557   8.69     NP_524813   AAF58204 kn-PB   FBpp0111721   62.5   575   8.53     NP_725419   AAM68551 kn-PC   FBpp0111722   74.8   689   8.41     NP_001097317   ABV53800 kn-PD   FBpp0290614   60.4   556   8.69     NP_610990   AAF58203 kn-PE   FBpp0302917   57.5   524   8.64     NP_001260980   AGB93512
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Transcription factor COE, conserved site (IPR018350) Cell surface receptor IPT/TIG (IPR002909) Transcription factor COE (IPR003523) Immunoglobulin E-set (IPR014756) Myc-type, basic helix-loop-helix (bHLH) domain (IPR011598) Immunoglobulin-like fold (IPR013783)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE013599 AAF58203   AE013599 AAF58204   AE013599 AAM68551   AE013599 ABV53800   AE013599 AGB93512   AI258364   AY119102 AAM50962   BI164134   BI234222   BI240518   BI577611   BI577655   BI592030   CL526130   CO179589   CO179722   CO266449   CO285735   CO288277   CO289739   CO311535   CO333844   EC058463   EC067982   EC069932   EC087092   EC196710   EC207762   EC213599   EC218811   EC218974   EC244867   GH951451   GH961873   GH963624   GH963776   GH964755   GH965185   GH967794   GH970818   GH971176   GH971218   GH979459   GH979625   GH984554   X97803
UniProtKB/Swiss-Prot	P56721
UniProtKB/TrEMBL	A1Z9V2 A8DYD9 E2QCN0
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 FBsf0000435067 2R:10,699,246..10,700,536 evidence=Reporter construct (in vivo) (Hersh and Carroll, 2005, Halfon, 2012.6.19) regulatory region FBsf0000435540 2R:10,699,246..10,699,402 evidence=Reporter construct (in vivo) (Hersh and Carroll, 2005, Halfon, 2012.6.19) regulatory region FBsf0000435686 2R:10,687,374..10,689,097 evidence=Reporter construct (in vivo) (Enriquez et al., 2010, Halfon, 2012.6.19) regulatory region FBsf0000435784 2R:10,688,155..10,689,154 evidence=Reporter construct (in vivo) (Dubois et al., 2007, Halfon, 2012.6.19) regulatory region FBsf0000435858 2R:10,699,359..10,700,536 evidence=Reporter construct (in vivo) (Hersh and Carroll, 2005, Halfon, 2012.6.19) regulatory region FBsf0000435969 2R:10,685,887..10,689,154 evidence=Reporter construct (in vivo) (Dubois et al., 2007, Halfon, 2012.6.19) regulatory region FBsf0000436193 2R:10,686,886..10,695,954 evidence=Reporter construct (in vivo) (Dubois et al., 2007, Halfon, 2012.6.19) regulatory region FBsf0000436284 2R:10,686,886..10,689,739 evidence=Reporter construct (in vivo) (Dubois et al., 2007, Halfon, 2012.6.19) regulatory region FBsf0000436299 2R:10,699,246..10,699,638 evidence=Reporter construct (in vivo) (Hersh and Carroll, 2005, Halfon, 2012.6.19) regulatory region FBsf0000436420 2R:10,699,402..10,700,536 evidence=Reporter construct (in vivo) (Hersh and Carroll, 2005, Halfon, 2012.6.19) regulatory region FBsf0000436705 2R:10,686,886..10,689,073 evidence=Reporter construct (in vivo) (Dubois et al., 2007, Halfon, 2012.6.19) regulatory region FBsf0000436749 2R:10,664,067..10,666,462 evidence=Reporter construct (in vivo) (Enriquez et al., 2010, Halfon, 2012.6.19)
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage   head mesoderm   (Seecoomar et al., 2000) embryonic mandibular segment   (Seecoomar et al., 2000) embryonic stage 4 -- 6   head mesoderm anlage   (Fisher et al., 2012) hypopharynx anlage in statu nascendi   (Fisher et al., 2012) organism | subset   (Fisher et al., 2012) embryonic stage 4 -- 7   intercalary segment | precursor   (Crozatier et al., 1999) Comment:reference states "parasegment 0" parasegment 1 | anterior to   (Crozatier et al., 1999) embryonic stage 7 -- 8   head mesoderm   (Fisher et al., 2012) hypopharynx anlage   (Fisher et al., 2012) embryonic stage 8 -- 11   embryonic mandibular segment   (Seecoomar et al., 2000) mitotic domain 2 of embryonic mandibular segment   (Seecoomar et al., 2000) embryonic mandibular segment | anterior   (Seecoomar et al., 2000) embryonic stage 9 -- 10   head mesoderm   (Fisher et al., 2012) hypopharynx inclusive primordium   (Fisher et al., 2012) dorsal ectoderm   (Fisher et al., 2012) trunk mesoderm   (Fisher et al., 2012) embryonic stage 10 -- 11   hypopharyngeal lobe | restricted   (Crozatier et al., 1999) embryonic stage 11 -- 12   central brain primordium   (Fisher et al., 2012) dorsal sensory complex primordium   (Fisher et al., 2012) head mesoderm   (Fisher et al., 2012) hypopharynx proper primordium   (Fisher et al., 2012) trunk mesoderm   (Fisher et al., 2012) ventral nerve cord primordium   (Fisher et al., 2012) ventral sensory complex anlage   (Fisher et al., 2012) corpus cardiacum primordium   (Fisher et al., 2012) dorsal epidermis primordium   (Fisher et al., 2012) fat body/gonad primordium   (Fisher et al., 2012) lateral cord glial cell   (Fisher et al., 2012) lateral cord neuron   (Fisher et al., 2012) stomatogastric nervous system primordium   (Fisher et al., 2012) embryonic stage 13 -- 16   dorsal sensory complex proper primordium   (Fisher et al., 2012) Comment:reported as dorsal/lateral sensory complexes embryonic brain   (Fisher et al., 2012) embryonic head sensory system   (Fisher et al., 2012) embryonic/larval lymph gland   (Fisher et al., 2012) embryonic/larval muscle system   (Fisher et al., 2012) embryonic/larval pericardial cell   (Fisher et al., 2012) embryonic/larval somatic muscle   (Fisher et al., 2012) ventral nerve cord   (Fisher et al., 2012) ventral sensory complex primordium   (Fisher et al., 2012) embryonic central brain   (Fisher et al., 2012) embryonic central brain glial cell   (Fisher et al., 2012) embryonic central brain neuron   (Fisher et al., 2012) embryonic stomatogastric nervous system   (Fisher et al., 2012) embryonic/larval corpus cardiacum   (Fisher et al., 2012) embryonic/larval nervous system   (Fisher et al., 2012) lateral cord glial cell   (Fisher et al., 2012) lateral cord neuron   (Fisher et al., 2012) sensory nervous system primordium   (Fisher et al., 2012) embryonic stage 16   dendritic arborizing neuron | subset   (Jinushi-Nakao et al., 2007) abdominal dorsal multidendritic neuron ddaC   (Jinushi-Nakao et al., 2007) abdominal anterior ventral multidendritic neuron vdaa   (Jinushi-Nakao et al., 2007) abdominal ventral multidendritic neuron vdaB   (Jinushi-Nakao et al., 2007) third instar larval stage   wing disc | anterior/posterior compartment boundary   (Glise et al., 2002)
Additional Descriptive Data
	Transcript is detected in 7 cells anterior to the A/P boundary in third instar wing discs. However, expression is excluded from the D/V boundary that will form the wing margin. (Glise et al., 2002) kn transcripts are expressed in the anterior-most regions of the mandibular segment and also in the cephalic mesoderm. (Seecoomar et al., 2000)
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage 12 -- 16   eo neuron   (Orgogozo et al., 2004) embryonic stage 15 -- larval stage   Tvb neuron   (Baumgardt et al., 2007) Tv neuron   (Baumgardt et al., 2007) embryonic stage 16   abdominal anterior ventral multidendritic neuron vdaa   (Jinushi-Nakao et al., 2007) third instar larval stage   wing disc | anterior/posterior compartment boundary   (Glise et al., 2002)
Additional Descriptive Data
	Protein is detected in 7 cells anterior to the A/P boundary in third instar wing discs. However, expression is excluded from the D/V boundary that will form the wing margin. (Glise et al., 2002)
Marker for
	eo neuron
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: larval/adult central nervous system, adult heart. [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    6 central nervous system, larvae L3    15 central nervous system, pupae P8    12 head, virgin 1-day female    3 head, virgin 4-day female    3 head, virgin 20-day female    2 head, mated 1-day female    3 head, mated 4-day female    2 head, mated 20-day female    1 head, mated 1-day male    4 head, mated 4-day male    4 head, mated 20-day male    3 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    4 carcass, larvae L3 wandering    4 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    6 central nervous system, larvae L3    15 central nervous system, pupae P8    12 head, virgin 1-day female    3 head, virgin 4-day female    3 head, virgin 20-day female    2 head, mated 1-day female    3 head, mated 4-day female    2 head, mated 20-day female    1 head, mated 1-day male    4 head, mated 4-day male    4 head, mated 20-day male    3 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    4 carcass, larvae L3 wandering    4 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    6 central nervous system, larvae L3    15 central nervous system, pupae P8    12 head, virgin 1-day female    3 head, virgin 4-day female    3 head, virgin 20-day female    2 head, mated 1-day female    3 head, mated 4-day female    2 head, mated 20-day female    1 head, mated 1-day male    4 head, mated 4-day male    4 head, mated 20-day male    3 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    4 carcass, larvae L3 wandering    4 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Tissue   Expression Level imaginal disc, larvae L3 wandering    6 central nervous system, larvae L3    15 central nervous system, pupae P8    12 head, virgin 1-day female    3 head, virgin 4-day female    3 head, virgin 20-day female    2 head, mated 1-day female    3 head, mated 4-day female    2 head, mated 20-day female    1 head, mated 1-day male    4 head, mated 4-day male    4 head, mated 20-day male    3 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    4 carcass, larvae L3 wandering    4 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    6 central nervous system, larvae L3    15 central nervous system, pupae P8    12 head, virgin 1-day female    3 head, virgin 4-day female    3 head, virgin 20-day female    2 head, mated 1-day female    3 head, mated 4-day female    2 head, mated 20-day female    1 head, mated 1-day male    4 head, mated 4-day male    4 head, mated 20-day male    3 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    4 carcass, larvae L3 wandering    4 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    6 central nervous system, larvae L3    15 central nervous system, pupae P8    12 head, virgin 1-day female    3 head, virgin 4-day female    3 head, virgin 20-day female    2 head, mated 1-day female    3 head, mated 4-day female    2 head, mated 20-day female    1 head, mated 1-day male    4 head, mated 4-day male    4 head, mated 20-day male    3 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    4 carcass, larvae L3 wandering    4 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    6 central nervous system, larvae L3    15 central nervous system, pupae P8    12 head, virgin 1-day female    3 head, virgin 4-day female    3 head, virgin 20-day female    2 head, mated 1-day female    3 head, mated 4-day female    2 head, mated 20-day female    1 head, mated 1-day male    4 head, mated 4-day male    4 head, mated 20-day male    3 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    4 carcass, larvae L3 wandering    4 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Tissue   Expression Level imaginal disc, larvae L3 wandering    6 central nervous system, larvae L3    15 central nervous system, pupae P8    12 head, virgin 1-day female    3 head, virgin 4-day female    3 head, virgin 20-day female    2 head, mated 1-day female    3 head, mated 4-day female    2 head, mated 20-day female    1 head, mated 1-day male    4 head, mated 4-day male    4 head, mated 20-day male    3 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    4 carcass, larvae L3 wandering    4 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Tissue   Expression Level imaginal disc, larvae L3 wandering     central nervous system, larvae L3     central nervous system, pupae P8     head, virgin 1-day female     head, virgin 4-day female     head, virgin 20-day female     head, mated 1-day female     head, mated 4-day female     head, mated 20-day female     head, mated 1-day male     head, mated 4-day male     head, mated 20-day male     salivary gland, larvae L3 wandering     salivary gland, white prepupae     digestive system, larvae L3 wandering     digestive system, 1-day adult     digestive system, 4-day adult     digestive system, 20-day adult     fat body, larvae L3 wandering     fat body, white prepupae     fat body, pupae P8     carcass, larvae L3 wandering     carcass, 1-day adult     carcass, 4-day adult     carcass, 20-day adult     ovary, virgin 4-day female     ovary, mated 4-day female     testis, mated 4-day male     accessory gland, mated 4-day male
modENCODE Development RNA-Seq
modENCODE Temporal Expression Data (modENCODE_mRNA-Seq_U)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of extremely low expression. Peak expression observed at stages throughout embryogenesis. [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    0 embryo 02-04hr    1 embryo 04-06hr    6 embryo 06-08hr    8 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    13 embryo 14-16hr    13 embryo 16-18hr    11 embryo 18-20hr    11 embryo 20-22hr    7 embryo 22-24hr    7 larva L1    5 larva L2    1 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    2 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    0 adult female 01day    0 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    1 embryo 04-06hr    6 embryo 06-08hr    8 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    13 embryo 14-16hr    13 embryo 16-18hr    11 embryo 18-20hr    11 embryo 20-22hr    7 embryo 22-24hr    7 larva L1    5 larva L2    1 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    2 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    0 adult female 01day    0 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    1 embryo 04-06hr    6 embryo 06-08hr    8 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    13 embryo 14-16hr    13 embryo 16-18hr    11 embryo 18-20hr    11 embryo 20-22hr    7 embryo 22-24hr    7 larva L1    5 larva L2    1 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    2 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    0 adult female 01day    0 adult female 05day    0 adult female 30day    0 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    0 embryo 02-04hr    1 embryo 04-06hr    6 embryo 06-08hr    8 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    13 embryo 14-16hr    13 embryo 16-18hr    11 embryo 18-20hr    11 embryo 20-22hr    7 embryo 22-24hr    7 larva L1    5 larva L2    1 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    2 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    0 adult female 01day    0 adult female 05day    0 adult female 30day    0 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    1 embryo 04-06hr    6 embryo 06-08hr    8 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    13 embryo 14-16hr    13 embryo 16-18hr    11 embryo 18-20hr    11 embryo 20-22hr    7 embryo 22-24hr    7 larva L1    5 larva L2    1 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    2 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    0 adult female 01day    0 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    1 embryo 04-06hr    6 embryo 06-08hr    8 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    13 embryo 14-16hr    13 embryo 16-18hr    11 embryo 18-20hr    11 embryo 20-22hr    7 embryo 22-24hr    7 larva L1    5 larva L2    1 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    2 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    0 adult female 01day    0 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    1 embryo 04-06hr    6 embryo 06-08hr    8 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    13 embryo 14-16hr    13 embryo 16-18hr    11 embryo 18-20hr    11 embryo 20-22hr    7 embryo 22-24hr    7 larva L1    5 larva L2    1 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    2 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    0 adult female 01day    0 adult female 05day    0 adult female 30day    0 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    0 embryo 02-04hr    1 embryo 04-06hr    6 embryo 06-08hr    8 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    13 embryo 14-16hr    13 embryo 16-18hr    11 embryo 18-20hr    11 embryo 20-22hr    7 embryo 22-24hr    7 larva L1    5 larva L2    1 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    2 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    0 adult female 01day    0 adult female 05day    0 adult female 30day    0 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 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 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_06
External Data & Images
Linkouts	BDGP expression data • CG10197 RE03728 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0001319 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • HDC06452;CG10197-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | embryonic stage knSA1 lethal | embryonic stage | heat sensitive knhs.PS lethal | embryonic stage | heat sensitive, with Scer\GAL4srp.D.cCa knScer\UAS.cVa lethal | embryonic stage | recessive knKN1 knKN2 knKN3 knKN4 knunspecified lethal | late embryonic stage (with kn1) knKN2 lethal | late embryonic stage (with knKN2) kn1 lethal | recessive kncol-1 kncol-2 kncol-3 viable knSA2 viable, with Scer\GAL4pnr-MD237 knGD4730 Other Phenotypes Allele immune response defective, with kn+m5 kncol-1 immune response defective, with kncol-1 kn+m5 neuroanatomy defective, with Scer\GAL4221 knScer\UAS.cMa neuroanatomy defective, with Scer\GAL4smid-C161 knScer\UAS.cMa neuroanatomy defective | somatic clone kn1 knKN2 neuroanatomy defective | somatic clone, with Scer\GAL421-7 knScer\UAS.cMa neuroanatomy defective | somatic clone (with kn1) knKN2 neuroanatomy defective | somatic clone (with knKN2) kn1 smell perception defective kncol-85 visible kn1 kn+m5 knunspecified visible, with kn+m5 kncol-1 visible, with kncol-1 kn+m5 visible, with Scer\GAL4Bx-MS1096 knScer\UAS.cMa visible, with Scer\GAL4dpp.blk1 knScer\UAS.cMa visible (with kn1) kncol-1 visible (with kncol-1) kn1 visible | cell non-autonomous | recessive | somatic clone knKN4 visible | recessive kn1 knSA1 visible | somatic clone kncol-1 knKN1 knKN2 knKN3 knKN4 knunspecified wild-type kn+m5 Phenotype manifest in Allele 1st posterior cell kn+m5 kn1 knSA1 kncol-1 1st posterior cell, with kn+m5 kncol-1 1st posterior cell, with kncol-1 kn+m5 1st posterior cell (with kn1) kncol-1 1st posterior cell (with kncol-1) kn1 2nd posterior cell, with kn+m5 kncol-1 2nd posterior cell, with kncol-1 kn+m5 2nd posterior cell (with kn1) kncol-1 2nd posterior cell (with kncol-1) kn1 3rd posterior cell, with kn+m5 kncol-1 3rd posterior cell, with kncol-1 kn+m5 3rd posterior cell (with kn1) kncol-1 3rd posterior cell (with kncol-1) kn1 A1-7 dorsal acute muscle 2, with Scer\GAL4twi.PB knScer\UAS.cVa A1-7 dorsal acute muscle 2 | ectopic kncol85-GAL4 kncol-1 A1-7 dorsal acute muscle 2 | ectopic (with kncol-1) kncol85-GAL4 A1-7 dorsal acute muscle 2 | ectopic (with kncol85-GAL4) kncol-1 A1-7 dorsal acute muscle 3 kncol85-GAL4 kncol-1 A1-7 dorsal acute muscle 3 (with kncol-1) kncol85-GAL4 A1-7 dorsal acute muscle 3 (with kncol85-GAL4) kncol-1 A1-7 dorsal acute muscle 3 | ectopic kncol-1 A1-7 dorsal acute muscle 3 | ectopic, with Scer\GAL4twi.PB knScer\UAS.cVa A1-7 dorsal oblique muscle 4 kncol-1 A1-7 dorsal oblique muscle 5 | ectopic kncol-1 A1-7 lateral longitudinal muscle 1 kncol-1 abdominal 1 dorsal acute muscle 3 kncol-1 kncol-2 kncol-3 knhs.PS abdominal 1 dorsal oblique muscle 5 knhs.PS abdominal 2 dorsal acute muscle 3 kncol-1 kncol-2 kncol-3 knhs.PS abdominal 2 dorsal oblique muscle 5 knhs.PS abdominal 3 dorsal acute muscle 3 kncol-1 kncol-2 kncol-3 knhs.PS abdominal 3 dorsal oblique muscle 5 knhs.PS abdominal 4 dorsal acute muscle 3 kncol-1 kncol-2 kncol-3 knhs.PS abdominal 4 dorsal oblique muscle 5 knhs.PS abdominal 5 dorsal acute muscle 3 kncol-1 kncol-2 kncol-3 knhs.PS abdominal 5 dorsal oblique muscle 5 knhs.PS abdominal 6 dorsal acute muscle 3 kncol-1 kncol-2 kncol-3 knhs.PS abdominal 6 dorsal oblique muscle 5 knhs.PS abdominal 7 dorsal acute muscle 3 kncol-1 kncol-2 kncol-3 knhs.PS abdominal 7 dorsal oblique muscle 5 knhs.PS anterior crossvein kn+m5 kn1 kncol-1 cephalopharyngeal skeleton knKN2 knKN4 kncol-1 kncol-2 kncol-3 cephalopharyngeal skeleton | heat sensitive knhs.PS class I dendritic arborizing neuron, with Scer\GAL4221 knScer\UAS.cMa class II dendritic arborizing neuron, with Scer\GAL4smid-C161 knScer\UAS.cMa class III dendritic arborizing neuron, with Scer\GAL4smid-C161 knScer\UAS.cMa class IV dendritic arborizing neuron | somatic clone kn1 class IV dendritic arborizing neuron | somatic clone (with kn1) knKN2 class IV dendritic arborizing neuron | somatic clone (with knKN2) kn1 crystal cell, with Scer\GAL4srp.D.cCa knScer\UAS.cVa dendrite, with Scer\GAL4221 knScer\UAS.cMa dendrite, with Scer\GAL4smid-C161 knScer\UAS.cMa dendrite | somatic clone kn1 knKN2 dendrite | somatic clone (with kn1) knKN2 dendrite | somatic clone (with knKN2) kn1 dendritic arborizing neuron | somatic clone, with Scer\GAL421-7 knScer\UAS.cMa dorsal multidendritic neuron ddaC | somatic clone kn1 knKN2 dorsal multidendritic neuron ddaC | somatic clone (with kn1) knKN2 dorsal multidendritic neuron ddaC | somatic clone (with knKN2) kn1 embryonic/larval lymph gland kncol-1 embryonic/larval lymph gland, with Scer\GAL4dome-PG125 knScer\UAS.cVa embryonic/larval somatic muscle kncol-1 kncol-2 kncol-3 embryonic head kncol-1 kncol-2 kncol-3 hypopharyngeal lobe knKN4 hypostomal sclerite | heat sensitive knhs.PS lamellocyte | supernumerary, with Scer\GAL4srp.D.cCa knScer\UAS.cVa lateral process knKN2 knKN4 kna.hs kncol-1 kncol-2 kncol-3 lateral process | heat sensitive knhs.PS macrochaeta | ectopic | somatic clone knKN1 knKN2 knKN3 knKN4 melanotic mass | ectopic, with Scer\GAL4srp.D.cCa knScer\UAS.cVa mesothoracic dorsal acute muscle 4 kncol-1 kncol-2 kncol-3 metathoracic dorsal acute muscle 4 kncol-1 kncol-2 kncol-3 posterior crossvein kn+m5 kncol-1 posterior signalling centre of anterior lymph gland pair | ectopic, with Scer\GAL4kn-col85-GAL4 knScer\UAS.cVa sensillum campaniformium of dorsal radius | ectopic knKN1 knKN2 knKN3 knKN4 submarginal cell, with kn+m5 kncol-1 submarginal cell, with kncol-1 kn+m5 ventral arm of pharyngeal sclerite knKN2 knKN4 wing knSA2 knunspecified wing, with kn+m5 kncol-1 wing, with kncol-1 kn+m5 wing | anterior compartment | somatic clone knKN1 knKN2 knKN3 knKN4 wing | cell non-autonomous | somatic clone knKN4 wing | P-stage, with kn+m5 kncol-1 wing | P-stage, with kncol-1 kn+m5 wing | P-stage (with kn1) kncol-1 wing | P-stage (with kncol-1) kn1 wing basal cell 1 kn1 knSA1 wing cell knSA2 wing cell & wing vein L3 & wing vein L4 kn1 wing cell & wing vein L3 & wing vein L4 | somatic clone knKN1 knKN2 knKN3 knKN4 wing margin bristle | somatic clone knKN1 knKN2 knKN3 knKN4 wing vein kn+m5 kncol-1 knunspecified wing vein | cell non-autonomous | ectopic | somatic clone knKN4 wing vein | ectopic knKN1 knKN2 knKN3 knKN4 wing vein | ectopic | somatic clone knKN1 knKN2 knKN3 knKN4 knunspecified wing vein L2, with Scer\GAL4Bx-MS1096 knScer\UAS.cMa wing vein L3 kn+m5 kn1 knSA1 kncol-1 wing vein L3, with kn+m5 kncol-1 wing vein L3, with kncol-1 kn+m5 wing vein L3, with Scer\GAL4ap-md544 kndsRNA.Scer\UAS wing vein L3, with Scer\GAL4Bx-MS1096 knScer\UAS.cMa wing vein L3 | distal, with Scer\GAL4dpp.blk1 knScer\UAS.cMa wing vein L3 | somatic clone knunspecified wing vein L4 kn+m5 kn1 knSA1 kncol-1 wing vein L4, with kn+m5 kncol-1 wing vein L4, with kncol-1 kn+m5 wing vein L4, with Scer\GAL4ap-md544 kndsRNA.Scer\UAS wing vein L4 | cell non-autonomous | somatic clone knKN1 knKN2 knKN3 knKN4 wing vein L4 | distal, with Scer\GAL4Bx-MS1096 knScer\UAS.cMa wing vein L4 | proximal, with Scer\GAL4Bx-MS1096 knScer\UAS.cMa wing vein L4 | somatic clone kncol-1 knunspecified wing vein L5, with Scer\GAL4en-e16E knScer\UAS.cVa wing vein L5 | distal, with Scer\GAL4Bx-MS1096 knScer\UAS.cMa wing vein L5 | proximal, with Scer\GAL4Bx-MS1096 knScer\UAS.cMa
Classical Alleles ( 15 )
For All Classical Alleles Show
Allele of kn Class Mutagen Stocks Known lesion kncol-1 amorphic allele - genetic evidence, loss of function allele ethyl methanesulfonate 2 Yes kn1 2 -- knEY09641 P-element activity 1 -- knKN4 ethyl methanesulfonate 1 -- knMI02387 1 -- knSA2 gamma ray 1 Yes kncol-2 loss of function allele ethyl methanesulfonate 0 -- kncol-3 loss of function allele ethyl methanesulfonate 0 -- kncol-85 P-element activity 0 -- kncol85-GAL4 0 -- knKN1 ethyl methanesulfonate 0 -- knKN2 ethyl methanesulfonate 0 -- knKN3 ethyl methanesulfonate 0 -- knSA1 X ray 0 -- knunspecified 0 --
Alleles Carried on Transgenic Constructs ( 13 )
For All Alleles Carried on Transgenic Constructs Show
Allele of kn Class Mutagen Stocks Known lesion knJF02206 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes knKK114322 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes knScer\UAS.cMa in vitro construct - regulatory fusion 1 Yes knT:Avic\GFP-SF,T:Zzzz\FLAG,T:Zzzz\PSP.CS,T:Zzzz\TEV.CS,T:Zzzz\BLRP in vitro construct - coding region fusion 1 Yes kn+m5 in vitro construct - regulatory fusion 0 Yes kna.hs in vitro construct - regulatory fusion 0 Yes kndsRNA.Scer\UAS in vitro construct - regulatory fusion in vitro construct - RNAi 0 Yes knGD4730 in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes knhs.PS in vitro construct - regulatory fusion 0 Yes knKK109184 in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes knScer\UAS.cVa in vitro construct - regulatory fusion 0 Yes knScer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes knt5 in vitro construct - genomic fragment 0 Yes
Aneuploid Aberrations
Disrupted in	Df(2R)BSC429 (Christensen et al., 2008.4.15) Df(2R)BSC858 (Christensen et al., 2009.7.22) Df(2R)knSA3 (Mohler, 1997.8.7) In(2R)knSA1 (Nestoras et al., 1997) T(1;2)knSA2 (Seecoomar et al., 2000)
Not disrupted in	Df(2R)Jp1 (Nestoras et al., 1997) Df(2R)trix (Nestoras et al., 1997)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data reporter construct P{col5-lacZ.C} No P{col-lacZ.0.9} No P{col-lacZ.1.6} No P{col-lacZ.2.3} No P{col-lacZ.2.6} No P{col-lacZ.9} No P{kn-lacZ.1-2330} No P{kn-lacZ.2.6-0.9.Hox1} No P{kn-lacZ.2.6-0.9.Hox2} No P{kn-lacZ.2.6-0.9} No P{kn-lacZ.2.6.col} No P{kn-lacZ.2.6.nau} No P{kn-lacZ.4-0.9.intron} No P{kn-lacZ.4-0.9} No P{kn-lacZ.-20} No P{kn-lacZ.224-1426} No P{kn-lacZ.701-1835} No P{kn-lacZ.701-1991.Ci1047} No P{kn-lacZ.701-1991.Ci1341} No P{kn-lacZ.701-1991.Ci1680} No P{kn-lacZ.701-1991.KO} No P{kn-lacZ.701-1991.KOmut} No P{kn-lacZ.701-1991.mut} No P{kn-lacZ.701-1991.UBX1KO} No P{kn-lacZ.701-1991.UBX2KO} No P{kn-lacZ.701-1991.UBX3KO} No P{kn-lacZ.701-1991.UBX4KO} No P{kn-lacZ.701-1991} No P{kn-lacZ.1599-1991} No P{kn-lacZ.composite} No P{kn-lacZ.compositeKO} No P{kn-lacZ.CRM276.intron} No P{kn-lacZ.CRM276} No heat-shock construct P{hs-col.S} NA P{HscolA} NA UAS construct P{GD4730} NA P{GD7846} NA P{GD17582} NA P{KK109184} NA P{KK114322} NA P{TRiP.JF02206} NA P{UAS-col.dsRNA} NA P{UAS-kn.HA} NA P{UAS-kn.M} NA P{UAS-kn.V} NA GAL4 construct P{kn-GAL4.2.6-1.6} No P{kn-GAL4.9} No characterization construct P{C4-gBF} NA P{col5-cDNA.C} NA PBac{kn-GFP.FPTB} NA
Insertions
	Type of insertions Name Expression data insertion of mobile activating element P{EPgy2}knEY09641 NA insertion of enhancer trap P{lArB}kncol-85 No insertion of enhancer trap binary system P{GAL4}col85 No miscellaneous insertions Mi{MIC}knMI02387 NA
Gene Ontology: Function, Process & Cellular Component ( 22 unique terms )
Terms Based on Experimental Evidence ( 13 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
dendrite morphogenesis inferred from genetic interaction with ct (Jinushi-Nakao et al., 2007) inferred from mutant phenotype (Jinushi-Nakao et al., 2007) determination of muscle attachment site inferred from mutant phenotype (Enriquez et al., 2012) embryonic development via the syncytial blastoderm inferred from mutant phenotype (Crozatier et al., 1999) head segmentation inferred from mutant phenotype (Crozatier et al., 1999) imaginal disc-derived wing vein specification inferred from mutant phenotype (Crozatier et al., 2002) innate immune response inferred from mutant phenotype (Crozatier et al., 2004) larval somatic muscle development inferred from mutant phenotype (Enriquez et al., 2012) muscle cell fate specification inferred from mutant phenotype (Enriquez et al., 2012) positive regulation of JAK-STAT cascade inferred from mutant phenotype (Muller et al., 2005) regulation of lamellocyte differentiation inferred from mutant phenotype (Crozatier et al., 2004) regulation of transcription, DNA-dependent inferred from mutant phenotype (Crozatier et al., 1999) response to symbiont inferred from mutant phenotype (Crozatier et al., 2004) specification of segmental identity, intercalary segment inferred from mutant phenotype (Crozatier et al., 1999)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 10 terms )
Molecular Function
CV term Evidence References
DNA binding inferred from electronic annotation with InterPro:IPR003523 (FlyBase Curators et al., 2004-) protein dimerization activity inferred from electronic annotation with InterPro:IPR011598 (FlyBase Curators et al., 2004-) sequence-specific DNA binding transcription factor activity non-traceable author statement (Swiss-Prot Project Members, 2001.8.20)
Biological Process
CV term Evidence References
anterior head segmentation traceable author statement (Peel, 2004) blastoderm segmentation traceable author statement (Urbach and Technau, 2004) imaginal disc-derived wing morphogenesis traceable author statement (de Celis, 2003) pattern specification process traceable author statement (Potter and Xu, 2001) posterior head segmentation traceable author statement (Peel, 2004) regulation of transcription, DNA-dependent traceable author statement (de Celis, 2003)
Cellular Component
CV term Evidence References
nucleus non-traceable author statement (Swiss-Prot Project Members, 2001.8.20)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
kn - CG17323 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 kn allele Gene References kn1 Egfr (Diaz-Benjumea and Garcia-Bellido, 1990) hh (Vervoort et al., 1999) ptc (Nestoras et al., 1997) kncol-1 fu (Vervoort et al., 1999) hh (Vervoort et al., 1999) knKN4 ptc (Nestoras et al., 1997) knScer\UAS.cVa ci (Vervoort et al., 1999) unspecified rho (Sturtevant and Bier, 1995)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 69588 DroID - A comprehensive database of gene and protein interactions. • FBgn0001319 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 45318 SignaLink - A protein-protein and protein-miRNA interaction database with multi-layered structure and multiple confidence scores. • P56721
Orthologs
OrthoDB Orthologs (57) - 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 EOG6BVSD7 Dipteran inclusive ortholog search EOG67H5Z7 Insect inclusive ortholog search EOG6H18R4 Arthropod inclusive ortholog search EOG6GTHV8 Metazoa inclusive ortholog search EOG6PCPPK
Orthologs in Drosophila Species (EOG6BVSD7)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\kn     Drosophila simulans   Dsim\GD25656 Y   Drosophila sechellia   Dsec\GM20182 Y   Drosophila erecta   Dere\GG22397 Y   Drosophila yakuba   Dyak\GE12286 Y   Drosophila ananassae   Dana\GF11778 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA24435 Y   Drosophila persimilis   Dper\GL10656 Y   Drosophila willistoni   Dwil\GK23295 Y   Drosophila virilis   Dvir\GJ21945 Y   Drosophila mojavensis   Dmoj\GI21022 Y   Drosophila grimshawi   Dgri\GH20479 Y
Orthologs in non-Drosophila Dipterans (EOG67H5Z7)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL003436   Anopheles gambiae Malaria mosquito  Agam\AGAP011437   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ010142
Orthologs in non-Dipteran Insects (EOG6H18R4)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\GB42304   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG000666   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH12943   Atta cephalotes Leafcutter ant  Acep\ACEP22948   Camponotus floridanus Florida carpenter ant  Cflo\CFLO19433   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL16900   Linepithema humile Argentine ant  Lhum\LH17960   Pogonomyrmex barbatus Red harvester ant  Pbar\PB25446   Acyrthosiphon pisum Pea aphid  Apim\ACYPI007722   Bombyx mori Silkmoth  Bmor\BGIBMGA011565   Pediculus humanus Human body louse  Phum\PHUM119360   Tribolium castaneum Red flour beetle  Tcas\kn
Orthologs in non-Insect Arthropods (EOG6GTHV8)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\JGI_V11_22285   Ixodes scapularis Deer tick  Isca\ISCW021817   Ixodes scapularis Deer tick  Isca\ISCW021819
Orthologs in non-Arthropod Metazoa (EOG6PCPPK)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Caenorhabditis elegans Nematode  Cele\unc-3   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_004702gn   Danio rerio Zebrafish  Drer\si:ch211-51e8.2   Danio rerio Zebrafish  Drer\ENSDARG00000069196   Danio rerio Zebrafish  Drer\ENSDARG00000016116   Danio rerio Zebrafish  Drer\ENSDARG00000091287   Danio rerio Zebrafish  Drer\coe2   Danio rerio Zebrafish  Drer\ebf3   Xenopus tropicalis Western clawed frog  Xtro\ebf2   Xenopus tropicalis Western clawed frog  Xtro\ebf3   Xenopus tropicalis Western clawed frog  Xtro\ENSXETG00000030294   Xenopus tropicalis Western clawed frog  Xtro\ENSXETG00000031092   Gallus gallus Domestic chicken  Ggal\EBF3   Gallus gallus Domestic chicken  Ggal\EBF2   Gallus gallus Domestic chicken  Ggal\EBF1   Mus musculus House mouse  Mmus\Ebf1   Mus musculus House mouse  Mmus\Ebf4   Mus musculus House mouse  Mmus\Ebf2   Mus musculus House mouse  Mmus\Ebf3   Rattus norvegicus Norway rat  Rnor\Ebf1   Rattus norvegicus Norway rat  Rnor\Ebf3   Rattus norvegicus Norway rat  Rnor\Ebf2   Rattus norvegicus Norway rat  Rnor\Ebf4   Homo sapiens Human  Hsap\EBF2   Homo sapiens Human  Hsap\EBF3   Homo sapiens Human  Hsap\EBF1   Homo sapiens Human  Hsap\EBF4
Human Orthologs (4)
Gene OMIM HGNC Hsap\EBF2     Hsap\EBF3     Hsap\EBF1     Hsap\EBF4
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD25656 Drosophila sechellia Dsec\GM20182 Drosophila erecta Dere\GG22397 Drosophila yakuba Dyak\GE12286 Drosophila ananassae Dana\GF11778 Drosophila pseudoobscura pseudoobscura Dpse\GA24435 Drosophila persimilis Dper\GL10656 Drosophila willistoni Dwil\GK23295 Drosophila virilis Dvir\GJ21945 Drosophila mojavensis Dmoj\GI21022 Drosophila grimshawi Dgri\GH20479
Stocks & Reagents
Stocks Listed in FlyBase ( 12 )
Bloomington	316 kn1 9551 w*; P{UAS-kn.M}15+9/SM1 38658 w1118; PBac{kn-GFP.FPTB}VK00033 31916 y1 v1; P{TRiP.JF02206}attP2 35112 y1 w*; Mi{MIC}knMI02387 17588 y1 w67c23; P{EPgy2}knEY09641/CyO 9550 y1 w*; P{FRT(whs)}G13 knKN4/CyO, y+ 9574 y1 w*; T(1;2)knSA2, Tp(1;2)TE21F22A, knSA2/CyO
Kyoto	105853 kn1 109022 w*; kncol-1/CyO 109023 w*; kncol-1 / CyO; P{col5-cDNA.C} / TM6B
VDRC	v103837 P{KK114322}VIE-260B
Genomic Clones ( 1 )
	BACR03K23 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 38 )
	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	RE03728
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	LP01538 RE29885 RE37371 RE71320 RE71366 RH09628
Other clones	35309 79394 102015 282419 CK01.76C.G11 CK01.77C.B12 CK01.77C.D11 CK01.86B.A2 CK01.92A.A6 CK01.102B.G1 EK059921 EK060416 EK060540 EK068133 EK071935 EK146441 EK225216 EK308146 RP004160971 RP004197458 RP004248059 RP004250178 RP004415877 RP004416515 RP004421517 RP004463221 RP004494327 RP004499452 RP004510863 RP004513340 RP004531072
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0001319 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 45318
Antibody Information
	polyclonal (Jinushi-Nakao et al., 2007)
Other Information
Discoverer
	Nichols-Skoog, 1st Aug. 1931.
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: kn CG10197 (Bayraktaroglu, 2000.4.3) Source for merge of: kn col (Vervoort et al., 1999)
Additional comments
Other Comments
	DNA-protein interactions: genome-wide binding profile assayed for kn protein in 0-12 hr embryos; see mE1_TFBS_kn collection report. (Negre et al., 2011) Ectopic expression of kn increases arbor length and represses filopodia/spike formation in class III neurons. (Jinushi-Nakao et al., 2007) 10 alleles of kn have been recovered in a screen for mutations with smo-like mutant phenotypes in clones in the wing. (Vegh and Basler, 2003) kn is required for the proper positioning of veins 3 and 4 in the wing and to prevent ectopic venation between them. (Mohler et al., 2000) kn is required for the formation of the hypopharyngeal lobe and for subsequent differentiation of the ventral arms and lateralgrate of the pharyngeal head skeleton. (Seecoomar et al., 2000) kn shows lineage-specific restriction of transcription to the founder of muscle DA3A during muscle development, which depends on the asymmetric segregation of numb gene product and involves repression by N signalling. (Crozatier and Vincent, 1999) In kn mutant embryos the DA3A founder cells form but do not maintain kn transcription and are unable to fuse with neighboring myoblasts, leading to a loss-of-muscle DA3A phenotype. (Crozatier and Vincent, 1999) The specification of the DA3A muscle lineage requires both kn and at least one other transcription factor. (Crozatier and Vincent, 1999) kn is required for the establishment of the PS(-1)/PS0 parasegmental border and formation of the intercalary segment. (Crozatier et al., 1999) kn is a mediator of the short range organizing activity of hh in the wing. (Vervoort et al., 1999) kn has a specific role in hh-mediated patterning of the wing with no appreciable effect on general dpp-mediated wing organisation. kn acts in the hh-responsive cells at the posterior edge of the anterior compartment of the wing, primarily by preventing vein formation by these cells, thus forming a distinct intervein region between veins 3 and 4. (Nestoras et al., 1997) Mutants display hyperplastic phenotype, showing tissue overgrowth in mitotic recombination clones. (Mechler, 1994) Mutations in kn cause extra longitudinal or transverse veins with plexated vein phenotypes. kn, fu and shf act synergistically against Px, px, net, dsr and emc. (Diaz-Benjumea and Garcia-Bellido, 1990) The kn and fu loci belong to the knot phenotypic group within the 'excess-of-vein' mutant class. Mutants generate a medial shift in the position of the longitudinal veins, sensilla and chaetae. Double mutants are superadditive in vein pattern defects. (Diaz-Benjumea et al., 1989)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_080074 NM_137146 NM_166070 NM_001103847 NM_001274051 RefSeq (Proteins) • NP_524813 NP_610990 NP_725419 NP_001097317 NP_001260980 DDBJ / EMBL / GenBank • AAF58203 AAF58204 AAM50962 AAM68551 ABV53800 AGB93512 AY119102 BI164134 CL526130 X97803 Entrez Gene - A searchable database of RefSeq genes. • 45318 UniProtKB/Swiss-Prot • P56721 UniProtKB/TrEMBL • A1Z9V2 A8DYD9 E2QCN0
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Transcription factor COE, conserved site (IPR018350) Cell surface receptor IPT/TIG (IPR002909) Transcription factor COE (IPR003523) Immunoglobulin E-set (IPR014756) Myc-type, basic helix-loop-helix (bHLH) domain (IPR011598) Immunoglobulin-like fold (IPR013783) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • CG10197 RE03728
Linkouts
	BioGRID - A database of protein and genetic interactions • 69588 DroID - A comprehensive database of gene and protein interactions. • FBgn0001319 DRSC - Results from RNAi screens. • FBgn0001319 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0001319 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • HDC06452;CG10197-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0001319 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 45318 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /gene/collier1.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 45318 modMine - Data generated by the modENCODE project. • FBgn0001319 REDfly - A database of transcriptional regulatory elements. • FBgn0001319 SignaLink - A protein-protein and protein-miRNA interaction database with multi-layered structure and multiple confidence scores. • P56721
Synonyms & Secondary IDs ( 16 )
Reported As
Symbol Synonym	CG10197 (Klebes et al., 2005, Mohit et al., 2006, Keleman et al., 2009.8.5, Perkins et al., 2009, Marcu et al., 2011) coe (Daburon et al., 2008) Col (Torroja et al., 2004, Daoud and Blanchet-Tournier, 2005, Briscoe, 2004, Anonymous, 2005, Apionishev et al., 2005, Jia et al., 2004, Perrin et al., 2004, Orgogozo et al., 2004, Vincent et al., 2004, Han et al., 2004, Crozatier et al., 2003, Dubois and Vincent, 2001, Crozatier et al., 2001, Crozatier et al., 2001, Crozatier and Vincent, 1999, Crozatier et al., 2005, Kulkarni et al., 2011, Du et al., 2011, Hattori et al., 2007, Callejo et al., 2011, Su et al., 2011, Katanaev et al., 2008, Márkus et al., 2009, Dawber et al., 2005, Nahmad and Stathopoulos, 2009, Enriquez et al., 2010, Cheng et al., 2010, Yan et al., 2010, Wojcinski et al., 2011, Cheng et al., 2012, Pennetier et al., 2012) col (Panakova et al., 2005, Crozatier et al., 2004, Crozatier et al., 2004, Casali and Struhl, 2004, Rajewsky and Socci, 2004, Ogden et al., 2004, Hooper, 2003, Crozatier et al., 2003, Vegh and Basler, 2003, Kambris et al., 2002, Glise et al., 2002, Tallafuss and Bally-Cuif, 2002, Amanai and Jiang, 2001, Johnson et al., 2002, Ingham and McMahon, 2001, Haas et al., 2001, Capdevila and Johnson, 2000, Johnson et al., 2000, Vervoort, 2000, Crozatier et al., 1999, Vervoort et al., 1999, Crozatier and Vincent, 1999, Son, 1999.3.8, Chang et al., 1999, Vervoort et al., 1998, Crozatier et al., 1998, Dubois et al., 1998, Crozatier et al., 1997, Crozatier et al., 1996, Vincent, 1995, Gorfinkiel et al., 2005, Baumgardt et al., 2007, Bartscherer et al., 2006, Dubois et al., 2007, Mandal et al., 2007, Krzemień et al., 2007, Jones, 2007, Boukhatmi et al., 2012, Baumgardt et al., 2009, Enriquez et al., 2012, Wendler et al., 2006, Baumgardt et al., 2008, Enriquez et al., 2008, Seong et al., 2010, Torroja et al., 2005, Daburon et al., 2008, Benito-Sipos et al., 2011, Ruel et al., 2007, Dubois et al., 2007, Claret et al., 2007, Crozatier and Vincent, 2008, Cheng et al., 2010, Mosimann et al., 2009, Tokusumi et al., 2009, Glise et al., 2005, Karlsson et al., 2010, Losada-Pérez et al., 2010, Tokusumi et al., 2012) Col/Kn (Crozatier and Vincent, 2008) collier (Govind and Nehm, 2004) DmCOE (Daburon et al., 2008) Kn (Crozatier et al., 2001, Molnar and de Celis, 2006, Ye et al., 2011, Shimono et al., 2009, Molnar et al., 2007) kn (Ramos and Mohler, 2006, Gilbert et al., 2006, Ramos et al., 2006, Mohit et al., 2006, Christensen et al., 2008.4.15, Hattori et al., 2007, Seong et al., 2010, Stofanko et al., 2010, Frise et al., 2010, Nègre et al., 2011, Pavlopoulos and Akam, 2011, Tokusumi et al., 2010, Karim and Moore, 2011, Sandmann et al., 2006, Choksi et al., 2006, Jinushi-Nakao et al., 2007, Liu et al., 2009, Economou and Telford, 2009, Hurlbut et al., 2009, Christensen et al., 2009.7.22, Mosimann et al., 2009, Zeitlinger et al., 2007, Glise et al., 2005, Long et al., 2009, Usha and Shashidhara, 2010, Spokony and White, 2012.5.22, Beltran et al., 2007, The modENCODE Consortium, 2010, The modENCODE Consortium, 2010, Muller et al., 2005, Busser et al., 2012, Manning et al., 2012) knot (Lelli et al., 2011)
Name Synonym	collier (Mosimann et al., 2009, Peel, 2004, Urbach and Technau, 2004, Baylies and Michelson, 2001, Potter and Xu, 2001, Martin et al., 2001, Ledent and Vervoort, 2001, Bier, 2000, Crozatier, 1996.5.13, Frasch, 1999, Crozatier et al., 2004, Ogden et al., 2004, Vervoort, 2000, Baumgardt et al., 2007, Baumgardt et al., 2007, Bartscherer et al., 2006, Dubois et al., 2007, Jones, 2007, Baumgardt et al., 2009, Du et al., 2011, Wendler et al., 2006, Ulvklo et al., 2008, Hattori et al., 2007, Torroja et al., 2005, Ntini and Wimmer, 2011, Callejo et al., 2006, Eugster et al., 2007, Ruel et al., 2007, Dubois et al., 2007, Claret et al., 2007, Márkus et al., 2009, Cheng et al., 2010, Colomb et al., 2008, Usha and Shashidhara, 2010, Marcu et al., 2011, Tokusumi et al., 2012) Collier (Torroja et al., 2004, Anonymous, 2005, Orgogozo and Schweisguth, 2004, Crozatier et al., 2003, Dubois and Vincent, 2001, Crozatier et al., 2001, Crozatier et al., 2005, Vincent et al., 2007, Enriquez et al., 2012, Enriquez et al., 2008, Cheng et al., 2012, Beckett and Baylies, 2007, Crozatier and Vincent, 2008, Orgogozo and Grueber, 2005, Dawber et al., 2005, Tokusumi et al., 2009, Shimono et al., 2009, Nahmad and Stathopoulos, 2009, Cheng et al., 2010, Yan et al., 2010, Losada-Pérez et al., 2010, Wojcinski et al., 2011) collier/knot (Nilsson et al., 2007, Karlsson et al., 2010) Collier/Knot (Crozatier and Vincent, 2008) Collier-Knot (Miller et al., 2003) knot (Mosimann et al., 2009, Pearson et al., 2005, Ulvklo et al., 2008, Ntini and Wimmer, 2011, Pavlopoulos and Akam, 2011, Economou and Telford, 2009, Hurlbut et al., 2009, Usha and Shashidhara, 2010) Knot (Crozatier et al., 2001, Dubois et al., 2007, Ye et al., 2011, Hattori et al., 2007, Cheng et al., 2012, Long et al., 2009, Shimono et al., 2009, Molnar et al., 2007, Losada-Pérez et al., 2010) knotted (Miller and Blair, 1997, Miller and Blair, 1997)
Secondary FlyBase IDs
	FBgn0014142 FBgn0033967
References ( 203 )
Generate a list of	All references relating to this gene ( 203 )
List References by type	Research paper  ( 119 ) Supplementary material  ( 9 ) Review  ( 24 ) Personal communication to FlyBase  ( 15 ) Abstract  ( 29 ) FlyBase analysis  ( 1 ) DNA/RNA sequence record  ( 1 ) Protein sequence record  ( 1 ) Website  ( 1 ) Book  ( 1 ) Curated genome annotation  ( 1 )
Recent research papers ( 24 )
	Benmimoun et al., 2012, Development 139(10): 1713--1717 Dual role for Insulin/TOR signaling in the control of hematopoietic progenitor maintenance in Drosophila. [FBrf0218049] Boukhatmi et al., 2012, Development 139(19): 3572--3582 Tup/Islet1 integrates time and position to specify muscle identity in Drosophila. [FBrf0219376] Busser et al., 2012, PLoS Genet. 8(3): e1002531 A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis. [FBrf0217716] Cheng et al., 2012, Development 139(1): 85--94 Drosophila G-protein-coupled receptor kinase 2 regulates cAMP-dependent Hedgehog signaling. [FBrf0216860] Eade et al., 2012, PLoS Genet. 8(2): e1002501 Developmental transcriptional networks are required to maintain neuronal subtype identity in the mature nervous system. [FBrf0217668] Enriquez et al., 2012, Dev. Biol. 363(1): 27--39 Combinatorial coding of Drosophila muscle shape by Collier and Nautilus. [FBrf0217465] Manning et al., 2012, Cell Rep. 2(4): 1002--1013 A Resource for Manipulating Gene Expression and Analyzing cis-Regulatory Modules in the Drosophila CNS. [FBrf0219785] Pennetier et al., 2012, Proc. Natl. Acad. Sci. U.S.A. 109(9): 3389--3394 Size control of the Drosophila hematopoietic niche by bone morphogenetic protein signaling reveals parallels with mammals. [FBrf0217568] Tokusumi et al., 2012, PLoS ONE 7(7): e41604 Gene regulatory networks controlling hematopoietic progenitor niche cell production and differentiation in the Drosophila lymph gland. [FBrf0219204] Benito-Sipos et al., 2011, Development 138(24): 5311--5320 Seven up acts as a temporal factor during two different stages of neuroblast 5-6 development. [FBrf0216799] Callejo et al., 2011, Proc. Natl. Acad. Sci. U.S.A. 108(31): 12591--12598 Feature Article: From the Cover: Dispatched mediates Hedgehog basolateral release to form the long-range morphogenetic gradient in the Drosophila wing disk epithelium. [FBrf0214615] Demilly et al., 2011, PLoS ONE 6(6): e21213 Coe genes are expressed in differentiating neurons in the central nervous system of protostomes. [FBrf0214030] Du et al., 2011, PLoS ONE 6(9): e24168 In Vivo RNAi Screen Reveals Neddylation Genes as Novel Regulators of Hedgehog Signaling. [FBrf0215574] Gabilondo et al., 2011, Mech. Dev. 128(3-4): 208--221 A targeted genetic screen identifies crucial players in the specification of the Drosophila abdominal Capaergic neurons. [FBrf0213290] Karim and Moore, 2011, J. Neurosci. 31(47): 17017--17027 Convergent local identity and topographic projection of sensory neurons. [FBrf0216770] Kulkarni et al., 2011, PLoS ONE 6(11): e27667 Asrij Maintains the Stem Cell Niche and Controls Differentiation during Drosophila Lymph Gland Hematopoiesis. [FBrf0216819] Marcu et al., 2011, PLoS ONE 6(1): e15361 Innate Immune Responses of Drosophila melanogaster Are Altered by Spaceflight. [FBrf0212851] Ntini and Wimmer, 2011, Dev. Biol. 360(2): 403--414 Second order regulator Collier directly controls intercalary-specific segment polarity gene expression. [FBrf0216616] Nègre et al., 2011, Nature 471(7339): 527--531 A cis-regulatory map of the Drosophila genome. [FBrf0213303] Pavlopoulos and Akam, 2011, Proc. Natl. Acad. Sci. U.S.A. 108(7): 2855--2860 Hox gene Ultrabithorax regulates distinct sets of target genes at successive stages of Drosophila haltere morphogenesis. [FBrf0213089] Quan et al., 2011, Nat. Biotechnol. 29(5): 449--452 Parallel on-chip gene synthesis and application to optimization of protein expression. [FBrf0213642] Su et al., 2011, Sci. Signal. 4(180): ra43 Sequential phosphorylation of smoothened transduces graded hedgehog signaling. [FBrf0216577] Wojcinski et al., 2011, Dev. Biol. 358(1): 168--180 DSulfatase-1 fine-tunes Hedgehog patterning activity through a novel regulatory feedback loop. [FBrf0215253] Ye et al., 2011, J. Neurosci. 31(9): 3309--3319 Differential regulation of dendritic and axonal development by the novel kruppel-like factor dar1. [FBrf0213162] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...