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Gene Dmel\kni

General Information
Symbol	Dmel\kni	Species	D. melanogaster
Name	knirps	Annotation symbol	CG4717
Feature type	protein_coding_gene	FlyBase ID	FBgn0001320
Gene Model Status	Current	Stock availability	340 publicly available
Also Known As	ri
Genomic Location
Chromosome (arm)	3L	Recombination map
Cytogenetic map	77E3-77E3	Sequence location	3L:20,685,430..20,688,478 [-]
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 knirps is referred to in FlyBase by the symbol Dmel\kni (CG4717, FBgn0001320). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription; sequence-specific DNA binding transcription factor activity; repressing transcription factor binding. There is experimental evidence that it is involved in the biological process: dendrite morphogenesis; regulation of mitosis; muscle organ development; epidermis development. 108 alleles are reported. The phenotypes of these alleles are annotated with: multicellular structure; anatomical structure; abdominal segment; organ system; adult segment; thoracic segment; organ system subdivision; late extended germ band embryo; embryonic abdominal segment 1; abdominal segment 10; dorsal trunk primordium; dorsal branch primordium; embryonic/larval hemocoel. It has one annotated transcript and one annotated polypeptide. Protein features are: Zinc finger, NHR/GATA-type; Zinc finger, nuclear hormone receptor-type. 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 00-06 hour embryonic stages. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: adult crop, adult hindgut, larval trachea. Comments on Affy2 ProbeSet: ProbeSet 1629097_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of kni. Gene sequence location is 3L:20685430..20688478.
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	kni: knirps Zygotic gap gene whose mutants are homozygous lethal; their denticle belts in segments one through seven are fused into a single field (Nusslein-Volhard and Wieschaus, 1980), but the head, thorax, eighth abdominal segment, and tail region appear normal. Embryos homozygous for a strong kni mutant show a wide band of ftz staining instead of the normal number of ftz stripes (Carroll and Scott, 1986). ri: radius incompletus ri: radius incompletus From Edith M. Wallace, unpublished. Vein L2 interrupted. Wings slightly warped and blunt. Acts during contraction period in D. simulans, inhibiting fusion of small spaces into a vein (Waddington, 1940, J. Genet. 41: 75-139). RK1.
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 77E3-77E3   Limits computationally determined from genome sequence between P{EP}trblEP3519 and P{EP}fngEP3082&P{lacW}skdL7062
Experimentally Determined Cytological Location
Cytogenetic map Notes References 77E1-77E2   (determined by in situ hybridisation)   (Ranz et al., 1997) 77E1-77E2   (determined by in situ hybridisation)   (Nauber et al., 1988)
Experimentally Determined Recombination Data
Location	2-47 (Kalisch and Rasmuson, 1974) 3-47 (Duncan and Kaufman, 1975) 3-46.8 (Arajarvi and Hannah-Alava, 1969) 3-47.0 (Tearle and Nusslein-Volhard, 1987) 3-47.1 (Meyer, 1952)
Left of (cM)	Pc (Puro and Nygren, 1975) Su(var)3-3 (Reuter et al., 1986)
Right of (cM)	Sgs3 (Kokoza et al., 1982)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\kni 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 5.46
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) kni-RA FBtr0078283  NM_079463   2100   429
Additional Transcript Data & Comments
Reported size (kB)	2.5, 2.2 (northern blot) (Nauber et al., 1988)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein kni-PA   FBpp0077941   45.6   429   8.35     NP_524187   AAF51629
Additional Polypeptide Data & Comments
Reported size (kDa)	429 (aa); 45.6 (kD predicted) (Nauber et al., 1988)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Zinc finger, nuclear hormone receptor-type (IPR001628) Zinc finger, NHR/GATA-type (IPR013088)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA540371   AE014296 AAF51629   AI388412   AY118798 AAM50658   CO289698   CO329526   EC059958   EC070261   EC239345   EC240792   EC240793   EC242701   X13331 CAA31709
UniProtKB/Swiss-Prot	P10734
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 protein binding site FBsf0000160106 3L:20,700,420..20,700,428 bound_moiety=sd-XP comment=A mutation in this site along with two other Sd-binding sites in a kni wing reporter construct leads to complete loss of wing disc expression. evidence=experimental bound_moiety=Sd-XP (Bergman et al., 2005, Lunde et al., 2003) protein binding site FBsf0000160107 3L:20,700,350..20,700,358 bound_moiety=sd-XP bound_moiety=Sd-XP comment=A mutation in this site along with two other Sd-binding sites in a kni wing reporter construct leads to complete loss of wing disc expression.(binding site reported on opposite strand with respect to kni gene transcription) evidence=experimental (Lunde et al., 2003, Bergman et al., 2005) protein binding site FBsf0000160108 3L:20,700,303..20,700,311 bound_moiety=sd-XP bound_moiety=Sd-XP comment=(binding site reported on opposite strand with respect to kni gene transcription) evidence=experimental (Lunde et al., 2003, Bergman et al., 2005) protein binding site FBsf0000160109 3L:20,700,243..20,700,251 bound_moiety=Sd-XP bound_moiety=sd-XP evidence=experimental (Lunde et al., 2003, Bergman et al., 2005) protein binding site FBsf0000160110 3L:20,700,051..20,700,068 bound_moiety=sd-XP comment=Tandem Sd-binding site. A mutation in this site along with two other Sd-binding sites in a kni wing reporter construct leads to complete loss of wing disc expression. (binding site reported on opposite strand with respect to kni gene transcription) evidence=experimental bound_moiety=Sd-XP (Bergman et al., 2005, Lunde et al., 2003) protein binding site FBsf0000160111 3L:20,690,647..20,690,657 bound_moiety=cad-XP comment=cad binding site 1 evidence=experimental (Bergman et al., 2005, Rivera-Pomar et al., 1995) protein binding site FBsf0000160112 3L:20,690,610..20,690,622 bound_moiety=cad-XP comment=cad binding site 2. The binding site has two extra T residues in the reference sequence relative to the reported sequence. evidence=experimental (Rivera-Pomar et al., 1995) protein binding site FBsf0000160113 3L:20,690,583..20,690,593 bound_moiety=cad-XP comment=cad binding site 3 evidence=experimental (Rivera-Pomar et al., 1995) protein binding site FBsf0000160114 3L:20,690,557..20,690,567 bound_moiety=cad-XP comment=cad binding site 4 evidence=experimental (Rivera-Pomar et al., 1995) protein binding site FBsf0000160115 3L:20,690,527..20,690,537 bound_moiety=cad-XP comment=cad binding site 5 evidence=experimental (Rivera-Pomar et al., 1995) protein binding site FBsf0000160116 3L:20,690,504..20,690,513 bound_moiety=bcd-XP comment=bcd binding site 1 evidence=experimental (Rivera-Pomar et al., 1995) protein binding site FBsf0000160117 3L:20,690,494..20,690,503 bound_moiety=bcd-XP comment=bcd binding site 2 evidence=experimental (Rivera-Pomar et al., 1995) protein binding site FBsf0000160118 3L:20,690,492..20,690,502 bound_moiety=cad-XP comment=cad binding site 6 evidence=experimental (Rivera-Pomar et al., 1995) protein binding site FBsf0000160119 3L:20,690,483..20,690,492 bound_moiety=bcd-XP comment=bcd binding site 3 evidence=experimental (Rivera-Pomar et al., 1995) protein binding site FBsf0000160120 3L:20,690,468..20,690,482 bound_moiety=bcd-XP comment=bcd binding site 4 evidence=experimental (Rivera-Pomar et al., 1995) protein binding site FBsf0000160121 3L:20,690,462..20,690,471 bound_moiety=bcd-XP comment=bcd binding site 5 evidence=experimental (Rivera-Pomar et al., 1995) protein binding site FBsf0000160122 3L:20,690,452..20,690,461 bound_moiety=bcd-XP comment=bcd binding site 6 evidence=experimental (Rivera-Pomar et al., 1995) protein binding site FBsf0000160123 3L:20,690,400..20,690,407 bound_moiety=hb-XP comment=hb binding site 1 evidence=experimental (Pankratz et al., 1992) protein binding site FBsf0000160124 3L:20,690,359..20,690,366 bound_moiety=hb-XP comment=hb binding site 2 evidence=experimental (Pankratz et al., 1992) protein binding site FBsf0000160125 3L:20,690,221..20,690,228 bound_moiety=hb-XP comment=hb binding site 3 evidence=experimental (Pankratz et al., 1992, Bergman et al., 2005) protein binding site FBsf0000160126 3L:20,690,190..20,690,197 bound_moiety=hb-XP comment=hb binding site 4 evidence=experimental (Pankratz et al., 1992, Bergman et al., 2005) protein binding site FBsf0000160127 3L:20,690,054..20,690,061 bound_moiety=hb-XP comment=hb binding site 5 evidence=experimental (Pankratz et al., 1992) protein binding site FBsf0000160128 3L:20,690,032..20,690,039 bound_moiety=hb-XP comment=hb binding site 6 (weak site) evidence=experimental (Pankratz et al., 1992, Bergman et al., 2005) protein binding site FBsf0000160129 3L:20,689,985..20,689,993 bound_moiety=tll-XP comment=tll binding site 1 evidence=experimental (Pankratz et al., 1992) protein binding site FBsf0000160130 3L:20,689,961..20,689,969 bound_moiety=tll-XP comment=tll binding site 2 (last base differs from that reported in FBrf0057643). evidence=experimental (Pankratz et al., 1992) protein binding site FBsf0000160131 3L:20,689,859..20,689,867 bound_moiety=tll-XP comment=tll binding site 3 evidence=experimental (Pankratz et al., 1992) protein binding site FBsf0000160132 3L:20,689,798..20,689,808 bound_moiety=Kr-XP comment=Kr binding site K1 evidence=experimental (Pankratz et al., 1989) protein binding site FBsf0000160133 3L:20,689,768..20,689,778 bound_moiety=Kr-XP comment=Kr binding site K2 evidence=experimental (Pankratz et al., 1989) protein binding site FBsf0000160134 3L:20,689,643..20,689,651 bound_moiety=tll-XP comment=tll binding site 4 evidence=experimental (Pankratz et al., 1992) protein binding site FBsf0000160831 3L:20,689,688..20,689,713 bound_moiety=tll-XP evidence=experimental (Pankratz et al., 1992, Bergman et al., 2005) protein binding site FBsf0000160832 3L:20,690,695..20,690,707 bound_moiety=hb-XP evidence=experimental (Bergman et al., 2005, Rivera-Pomar et al., 1995) protein binding site FBsf0000160833 3L:20,689,735..20,689,750 bound_moiety=tll-XP evidence=experimental (Bergman et al., 2005, Pankratz et al., 1992) protein binding site FBsf0000160834 3L:20,689,700..20,689,725 bound_moiety=hb-XP evidence=experimental (Rivera-Pomar et al., 1995, Bergman et al., 2005) protein binding site FBsf0000160835 3L:20,690,704..20,690,712 bound_moiety=cad-XP evidence=experimental (Rivera-Pomar et al., 1995, Bergman et al., 2005) protein binding site FBsf0000160836 3L:20,689,701..20,689,724 bound_moiety=Kr-XP evidence=experimental (Rivera-Pomar et al., 1995, Bergman et al., 2005) protein binding site FBsf0000160837 3L:20,690,525..20,690,540 bound_moiety=hb-XP evidence=experimental (Rivera-Pomar et al., 1995, Bergman et al., 2005) protein binding site FBsf0000160838 3L:20,690,503..20,690,509 bound_moiety=His2B-XP evidence=experimental (Kerrigan and Kadonaga, 1992, Bergman et al., 2005) protein binding site FBsf0000160839 3L:20,690,492..20,690,499 bound_moiety=His2B-XP evidence=experimental (Bergman et al., 2005, Kerrigan and Kadonaga, 1992) protein binding site FBsf0000160840 3L:20,690,484..20,690,489 bound_moiety=His2B-XP evidence=experimental (Kerrigan and Kadonaga, 1992, Bergman et al., 2005) protein binding site FBsf0000160841 3L:20,690,473..20,690,480 bound_moiety=His2B-XP evidence=experimental (Kerrigan and Kadonaga, 1992, Bergman et al., 2005) protein binding site FBsf0000160842 3L:20,690,462..20,690,468 evidence=experimental bound_moiety=His2B-XP (Bergman et al., 2005, Kerrigan and Kadonaga, 1992) protein binding site FBsf0000160843 3L:20,690,058..20,690,072 bound_moiety=gt-XP evidence=experimental (Rivera-Pomar et al., 1995, Bergman et al., 2005) protein binding site FBsf0000160844 3L:20,690,035..20,690,046 bound_moiety=gt-XP evidence=experimental (Bergman et al., 2005, Rivera-Pomar et al., 1995) protein binding site FBsf0000160845 3L:20,689,796..20,689,814 bound_moiety=Kr-XP evidence=experimental (Bergman et al., 2005, Rivera-Pomar et al., 1995) protein binding site FBsf0000160846 3L:20,689,776..20,689,792 evidence=experimental bound_moiety=tll-XP (Bergman et al., 2005, Pankratz et al., 1992) protein binding site FBsf0000160847 3L:20,689,764..20,689,783 bound_moiety=Kr-XP evidence=experimental (Bergman et al., 2005, Rivera-Pomar et al., 1995) protein binding site FBsf0000160848 3L:20,689,632..20,689,649 evidence=experimental bound_moiety=Kr-XP (Bergman et al., 2005, Rivera-Pomar et al., 1995) protein binding site FBsf0000160849 3L:20,689,636..20,689,649 bound_moiety=hb-XP evidence=experimental (Rivera-Pomar et al., 1995, Bergman et al., 2005) protein binding site FBsf0000160850 3L:20,689,640..20,689,656 bound_moiety=tll-XP evidence=experimental (Bergman et al., 2005, Pankratz et al., 1992) protein binding site FBsf0000160851 3L:20,689,819..20,689,839 bound_moiety=Kr-XP evidence=experimental (Bergman et al., 2005, Rivera-Pomar et al., 1995) protein binding site FBsf0000160852 3L:20,689,743..20,689,766 bound_moiety=hb-XP evidence=experimental (Bergman et al., 2005, Pankratz et al., 1992) regulatory region FBsf0000161371 3L:20,699,781..20,701,141 comment=Region sufficient to direct the correct spatial pattern of kni expression in the wing vein L2 primordium in wing imaginal discs. linked_to=XhoI-EcoRI_rfrag (Lunde et al., 2003) regulatory region FBsf0000161372 3L:20,688,236..20,693,017 comment=Region sufficient to direct the correct spatial pattern of kni expression in the anterior and posterior domains in the blastoderm embryo. evidence=experimental linked_to=BamHI-NruI_rfrag (Pankratz et al., 1989) regulatory region FBsf0000161373 3L:20,689,640..20,690,516 comment=Fragment directs kni wild-type-like abdominal expression pattern in blastoderm embryos. linked_to=KpnI-DraI_rfrag (Pankratz et al., 1992) regulatory region FBsf0000161374 3L:20,690,014..20,690,464 comment=Fragment required for setting the anterior boundary of kni expression in the abdomen in blastoderm embryos. evidence=experimental linked_to=PstI-EcoRI_rfrag (Pankratz et al., 1992) regulatory region FBsf0000161375 3L:20,689,640..20,690,019 comment=Fragment required for setting the posterior boundary of kni expression in the abdomen in blastoderm embryos. linked_to=EcoRI-DraI_rfrag (Pankratz et al., 1992) regulatory region FBsf0000435379 3L:20,699,781..20,701,140 evidence=Reporter construct (in vivo) (Lunde et al., 2003, Halfon, 2012.6.19) regulatory region FBsf0000435448 3L:20,690,515..20,690,671 evidence=Reporter construct (in vivo) (Rivera-Pomar et al., 1995, Halfon, 2012.6.19) regulatory region FBsf0000435642 3L:20,699,782..20,700,468 evidence=Reporter construct (in vivo) (Lunde et al., 2003, Halfon, 2012.6.19) regulatory region FBsf0000435648 3L:20,692,222..20,693,787 evidence=Reporter construct (in vivo) (Zeitlinger et al., 2007, Halfon, 2012.6.19) regulatory region FBsf0000435664 3L:20,689,649..20,690,495 evidence=Reporter construct (in vivo) (Rivera-Pomar et al., 1995, Halfon, 2012.6.19) regulatory region FBsf0000435789 3L:20,694,631..20,694,937 evidence=Reporter construct (in vivo) (Weiss et al., 2010, Halfon, 2012.6.19) regulatory region FBsf0000435983 3L:20,670,880..20,672,890 evidence=Reporter construct (in vivo) (Weiss et al., 2010, Halfon, 2012.6.19) regulatory region FBsf0000436358 3L:20,692,603..20,694,005 evidence=Reporter construct (in vivo) (Schroeder et al., 2004, Halfon, 2012.6.19) regulatory region FBsf0000436440 3L:20,689,643..20,690,512 evidence=Reporter construct (in vivo) (Pankratz et al., 1992, Halfon, 2012.6.19) regulatory region FBsf0000436448 3L:20,687,687..20,688,345 evidence=Reporter construct (in vivo) (Perry et al., 2011, Halfon, 2012.6.19) regulatory region FBsf0000436465 3L:20,699,782..20,704,709 evidence=Reporter construct (in vivo) (Lunde et al., 2003, Halfon, 2012.6.19) regulatory region FBsf0000436639 3L:20,690,449..20,690,515 evidence=Reporter construct (in vivo) (Rivera-Pomar et al., 1995, 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 | anterior   (Gavis and Lehmann, 1992) embryonic stage 1 -- 3   organism   (Fisher et al., 2012) Comment:maternally deposited blastoderm stage   organism | 30-50% egg length   (Hulskamp et al., 1990) Comment:30-45% egg length embryonic stage 4   organism | 30-50% egg length   (Boring et al., 1993) organism | 20-40% egg length   (Rivera-Pomar et al., 1995) organism | anterior   (Boring et al., 1993, Rivera-Pomar et al., 1995) organism | 70-100% egg length   (Rivera-Pomar et al., 1995, Boring et al., 1993) embryonic stage 4 -- 6   anterior endoderm anlage   (Fisher et al., 2012) Comment:anlage in statu nascendi clypeo-labral anlage in statu nascendi   (Fisher et al., 2012) dorsal ectoderm anlage   (Fisher et al., 2012) Comment:anlage in statu nascendi endoderm anlage   (Fisher et al., 2012) Comment:anlage in statu nascendi foregut anlage in statu nascendi   (Fisher et al., 2012) head mesoderm anlage   (Fisher et al., 2012) Comment:anlage in statu nascendi mesoderm anlage   (Fisher et al., 2012) Comment:anlage in statu nascendi organism | gap expression pattern   (Fisher et al., 2012) ventral ectoderm anlage   (Fisher et al., 2012) Comment:anlage in statu nascendi embryonic stage 5   organism | gap expression pattern   (Capovilla et al., 1992) embryonic stage 7 -- 8   anterior endoderm anlage   (Fisher et al., 2012) clypeo-labral anlage   (Fisher et al., 2012) dorsal ectoderm   (Fisher et al., 2012) foregut anlage   (Fisher et al., 2012) head mesoderm   (Fisher et al., 2012) organism | gap expression pattern   (Fisher et al., 2012) trunk mesoderm   (Fisher et al., 2012) ventral ectoderm   (Fisher et al., 2012) embryonic stage 9 -- 10   clypeo-labral primordium   (Fisher et al., 2012) dorsal ectoderm   (Fisher et al., 2012) dorsal epidermis primordium   (Fisher et al., 2012) Comment:reported as dorsal epidermis anlage foregut primordium   (Fisher et al., 2012) ventral epidermis primordium   (Fisher et al., 2012) embryonic stage 10   esophagus primordium   (Fuss et al., 2001) hindgut proper primordium   (Fuss et al., 2001) Comment:rectum and small intestine primordia embryonic stage 10 -- 15   tracheal pit   (Fuss et al., 2001) embryonic stage 11 -- 12   atrium | precursor   (Fisher et al., 2012) Comment:reported as atrium primordium clypeo-labral primordium   (Fisher et al., 2012) 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 foregut primordium   (Fisher et al., 2012) hindgut proper primordium   (Fisher et al., 2012) ventral epidermis primordium   (Fisher et al., 2012) visceral branch primordium   (Fisher et al., 2012) Comment:reported as visceral branch specific anlage embryonic stage 13 -- 15   embryonic large intestine | restricted   (Fuss et al., 2001) Comment:two lateral cells rows on either side of embryonic large intestine embryonic stage 13 -- 16   atrium   (Fisher et al., 2012) embryonic dorsal epidermis   (Fisher et al., 2012) embryonic esophagus   (Fisher et al., 2012) embryonic head epidermis   (Fisher et al., 2012) embryonic hindgut   (Fisher et al., 2012) embryonic proventriculus   (Fisher et al., 2012) embryonic ventral epidermis   (Fisher et al., 2012) embryonic/larval visceral branch   (Fisher et al., 2012) labral segment   (Fisher et al., 2012) third instar larval stage   wing vein L2 | precursor   (Lunde et al., 1998) northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage     (Nauber et al., 1988) embryonic stage 5     (Nauber et al., 1988)
Additional Descriptive Data
	kni is expressed in the third instar wing disc in a narrow stripe corresponding to the position of the L2 primordium. (Lunde et al., 1998) kni is expressed in the blastoderm embryo from approximately 30-45% egg length. (Hulskamp et al., 1990)
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage 5   organism | gap expression pattern   (Capovilla et al., 1992, Langeland et al., 1994) embryonic stage 11   foregut primordium   (Fuss et al., 2001) embryonic stage 11 -- 13   hindgut proper primordium   (Fuss et al., 2001) in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 11   embryonic foregut   (Brown et al., 2001) embryonic hindgut   (Brown et al., 2001) tracheal pit   (Brown et al., 2001)
Additional Descriptive Data
Marker for
	embryonic tracheal pit
Subcellular Localization (GO Cellular Component)
CV term Evidence References
Expression Deduced from Reporters
Reporter: P{kni(4.4)-lacZ} Stage Tissue/Position (including subcellular localization) Reference embryonic stage 5   organism | 30-50% egg length   (Pankratz et al., 1989) Comment:30-45% egg length organism | anterior   (Pankratz et al., 1989) Reporter: P{kni-lacZ.2R} Stage Tissue/Position (including subcellular localization) Reference embryonic stage 3   organism | anterior posterior gradient   (Burz et al., 1998) organism | 40-100% egg length   (Burz et al., 1998) Reporter: P{kni-lacZ.Ψ} Stage Tissue/Position (including subcellular localization) Reference embryonic stage 3   organism | 0-100% egg length   (Burz et al., 1998) organism | anterior posterior gradient   (Burz et al., 1998) Reporter: P{kni64} Stage Tissue/Position (including subcellular localization) Reference embryonic stage 3   organism | anterior posterior gradient   (Burz et al., 1998)
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: adult crop, adult hindgut, larval trachea. [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    5.35 Larval Midgut    12.1 Larval Hindgut    68 Larval Malpighian Tubules    3.4 Larval Fat Body    2.6 Larval Salivary Gland    4.5 Larval Trachea    158.775 Larval Carcass    19.3 Adult Head    54.4 Adult Eye    5.85 Adult Brain    5.1 Adult Thoracic-Abdominal Ganglion    5.8 Adult Crop    402.9 Adult Midgut    6.5 Adult Hindgut    165 Adult Malpighian Tubules    4.8 Adult Fat Body    9.8 Adult Salivary Gland    11.5 Adult Heart    7.875 Adult VirginFemale Spermatheca    4.6 Adult InseminatedFemale Spermatheca    3.6 Adult Ovary    1.2 Adult Testis    11 Adult Male Accessory Gland    4.9 Adult Carcass    33.8 Expression Level Scale  None   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    5.35 Larval Midgut    12.1 Larval Hindgut    68 Larval Malpighian Tubules    3.4 Larval Fat Body    2.6 Larval Salivary Gland    4.5 Larval Trachea    158.775 Larval Carcass    19.3 Adult Head    54.4 Adult Eye    5.85 Adult Brain    5.1 Adult Thoracic-Abdominal Ganglion    5.8 Adult Crop    402.9 Adult Midgut    6.5 Adult Hindgut    165 Adult Malpighian Tubules    4.8 Adult Fat Body    9.8 Adult Salivary Gland    11.5 Adult Heart    7.875 Adult VirginFemale Spermatheca    4.6 Adult InseminatedFemale Spermatheca    3.6 Adult Ovary    1.2 Adult Testis    11 Adult Male Accessory Gland    4.9 Adult Carcass    33.8 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    5.35 Larval Midgut    12.1 Larval Hindgut    68 Larval Malpighian Tubules    3.4 Larval Fat Body    2.6 Larval Salivary Gland    4.5 Larval Trachea    158.775 Larval Carcass    19.3 Adult Head    54.4 Adult Eye    5.85 Adult Brain    5.1 Adult Thoracic-Abdominal Ganglion    5.8 Adult Crop    402.9 Adult Midgut    6.5 Adult Hindgut    165 Adult Malpighian Tubules    4.8 Adult Fat Body    9.8 Adult Salivary Gland    11.5 Adult Heart    7.875 Adult VirginFemale Spermatheca    4.6 Adult InseminatedFemale Spermatheca    3.6 Adult Ovary    1.2 Adult Testis    11 Adult Male Accessory Gland    4.9 Adult Carcass    33.8 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    5.35 Larval Midgut    12.1 Larval Hindgut    68 Larval Malpighian Tubules    3.4 Larval Fat Body    2.6 Larval Salivary Gland    4.5 Larval Trachea    158.775 Larval Carcass    19.3 Adult Head    54.4 Adult Eye    5.85 Adult Brain    5.1 Adult Thoracic-Abdominal Ganglion    5.8 Adult Crop    402.9 Adult Midgut    6.5 Adult Hindgut    165 Adult Malpighian Tubules    4.8 Adult Fat Body    9.8 Adult Salivary Gland    11.5 Adult Heart    7.875 Adult VirginFemale Spermatheca    4.6 Adult InseminatedFemale Spermatheca    3.6 Adult Ovary    1.2 Adult Testis    11 Adult Male Accessory Gland    4.9 Adult Carcass    33.8 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    5.35 Larval Midgut    12.1 Larval Hindgut    68 Larval Malpighian Tubules    3.4 Larval Fat Body    2.6 Larval Salivary Gland    4.5 Larval Trachea    158.775 Larval Carcass    19.3 Adult Head    54.4 Adult Eye    5.85 Adult Brain    5.1 Adult Thoracic-Abdominal Ganglion    5.8 Adult Crop    402.9 Adult Midgut    6.5 Adult Hindgut    165 Adult Malpighian Tubules    4.8 Adult Fat Body    9.8 Adult Salivary Gland    11.5 Adult Heart    7.875 Adult VirginFemale Spermatheca    4.6 Adult InseminatedFemale Spermatheca    3.6 Adult Ovary    1.2 Adult Testis    11 Adult Male Accessory Gland    4.9 Adult Carcass    33.8 Expression Level Scale  None   Low   Moderate   High  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    5.35 Larval Midgut    12.1 Larval Hindgut    68 Larval Malpighian Tubules    3.4 Larval Fat Body    2.6 Larval Salivary Gland    4.5 Larval Trachea    158.775 Larval Carcass    19.3 Adult Head    54.4 Adult Eye    5.85 Adult Brain    5.1 Adult Thoracic-Abdominal Ganglion    5.8 Adult Crop    402.9 Adult Midgut    6.5 Adult Hindgut    165 Adult Malpighian Tubules    4.8 Adult Fat Body    9.8 Adult Salivary Gland    11.5 Adult Heart    7.875 Adult VirginFemale Spermatheca    4.6 Adult InseminatedFemale Spermatheca    3.6 Adult Ovary    1.2 Adult Testis    11 Adult Male Accessory Gland    4.9 Adult Carcass    33.8 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    5.35 Larval Midgut    12.1 Larval Hindgut    68 Larval Malpighian Tubules    3.4 Larval Fat Body    2.6 Larval Salivary Gland    4.5 Larval Trachea    158.775 Larval Carcass    19.3 Adult Head    54.4 Adult Eye    5.85 Adult Brain    5.1 Adult Thoracic-Abdominal Ganglion    5.8 Adult Crop    402.9 Adult Midgut    6.5 Adult Hindgut    165 Adult Malpighian Tubules    4.8 Adult Fat Body    9.8 Adult Salivary Gland    11.5 Adult Heart    7.875 Adult VirginFemale Spermatheca    4.6 Adult InseminatedFemale Spermatheca    3.6 Adult Ovary    1.2 Adult Testis    11 Adult Male Accessory Gland    4.9 Adult Carcass    33.8 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    5.35 Larval Midgut    12.1 Larval Hindgut    68 Larval Malpighian Tubules    3.4 Larval Fat Body    2.6 Larval Salivary Gland    4.5 Larval Trachea    158.775 Larval Carcass    19.3 Adult Head    54.4 Adult Eye    5.85 Adult Brain    5.1 Adult Thoracic-Abdominal Ganglion    5.8 Adult Crop    402.9 Adult Midgut    6.5 Adult Hindgut    165 Adult Malpighian Tubules    4.8 Adult Fat Body    9.8 Adult Salivary Gland    11.5 Adult Heart    7.875 Adult VirginFemale Spermatheca    4.6 Adult InseminatedFemale Spermatheca    3.6 Adult Ovary    1.2 Adult Testis    11 Adult Male Accessory Gland    4.9 Adult Carcass    33.8 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    54.4   NA  Eye    5.85   NA  Brain    5.1   5.35  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    5.8   NA  Crop    402.9   no informative data  Midgut    6.5   68  Hindgut    165   3.4  Malpighian Tubules    4.8   2.6  Fat Body    9.8   4.5  Salivary Gland    no informative data   NA  Heart    7.875   158.775  Trachea    NA   NA  VirginFemale Spermatheca    4.6   NA  InseminatedFemale Spermatheca    3.6   NA  Ovary    1.2   NA  Testis    11   NA  Male Accessory Gland    4.9   19.3  Carcass    33.8 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    12 central nervous system, larvae L3    3 central nervous system, pupae P8    2 head, virgin 1-day female    7 head, virgin 4-day female    6 head, virgin 20-day female    5 head, mated 1-day female    7 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    7 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    3 fat body, larvae L3 wandering    0 fat body, white prepupae    3 fat body, pupae P8    21 carcass, larvae L3 wandering    11 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    12 central nervous system, larvae L3    3 central nervous system, pupae P8    2 head, virgin 1-day female    7 head, virgin 4-day female    6 head, virgin 20-day female    5 head, mated 1-day female    7 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    7 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    3 fat body, larvae L3 wandering    0 fat body, white prepupae    3 fat body, pupae P8    21 carcass, larvae L3 wandering    11 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    12 central nervous system, larvae L3    3 central nervous system, pupae P8    2 head, virgin 1-day female    7 head, virgin 4-day female    6 head, virgin 20-day female    5 head, mated 1-day female    7 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    7 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    3 fat body, larvae L3 wandering    0 fat body, white prepupae    3 fat body, pupae P8    21 carcass, larvae L3 wandering    11 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 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    12 central nervous system, larvae L3    3 central nervous system, pupae P8    2 head, virgin 1-day female    7 head, virgin 4-day female    6 head, virgin 20-day female    5 head, mated 1-day female    7 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    7 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    3 fat body, larvae L3 wandering    0 fat body, white prepupae    3 fat body, pupae P8    21 carcass, larvae L3 wandering    11 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    12 central nervous system, larvae L3    3 central nervous system, pupae P8    2 head, virgin 1-day female    7 head, virgin 4-day female    6 head, virgin 20-day female    5 head, mated 1-day female    7 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    7 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    3 fat body, larvae L3 wandering    0 fat body, white prepupae    3 fat body, pupae P8    21 carcass, larvae L3 wandering    11 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    12 central nervous system, larvae L3    3 central nervous system, pupae P8    2 head, virgin 1-day female    7 head, virgin 4-day female    6 head, virgin 20-day female    5 head, mated 1-day female    7 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    7 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    3 fat body, larvae L3 wandering    0 fat body, white prepupae    3 fat body, pupae P8    21 carcass, larvae L3 wandering    11 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    12 central nervous system, larvae L3    3 central nervous system, pupae P8    2 head, virgin 1-day female    7 head, virgin 4-day female    6 head, virgin 20-day female    5 head, mated 1-day female    7 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    7 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    3 fat body, larvae L3 wandering    0 fat body, white prepupae    3 fat body, pupae P8    21 carcass, larvae L3 wandering    11 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 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    12 central nervous system, larvae L3    3 central nervous system, pupae P8    2 head, virgin 1-day female    7 head, virgin 4-day female    6 head, virgin 20-day female    5 head, mated 1-day female    7 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    7 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    2 digestive system, 1-day adult    3 digestive system, 4-day adult    3 digestive system, 20-day adult    3 fat body, larvae L3 wandering    0 fat body, white prepupae    3 fat body, pupae P8    21 carcass, larvae L3 wandering    11 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 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 00-06 hour embryonic stages. [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    4 embryo 02-04hr    70 embryo 04-06hr    24 embryo 06-08hr    37 embryo 08-10hr    39 embryo 10-12hr    40 embryo 12-14hr    22 embryo 14-16hr    11 embryo 16-18hr    7 embryo 18-20hr    7 embryo 20-22hr    6 embryo 22-24hr    5 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    6 white prepupae new    6 white prepupae 12hr    4 white prepupae 24hr    12 pupae 2d postWPP    12 pupae 3d postWPP    7 pupae 4d postWPP    2 adult male 01day    4 adult male 05day    4 adult male 30day    5 adult female 01day    3 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    4 embryo 02-04hr  (70) embryo 04-06hr    24 embryo 06-08hr  (37) embryo 08-10hr  (39) embryo 10-12hr  (40) embryo 12-14hr    22 embryo 14-16hr    11 embryo 16-18hr    7 embryo 18-20hr    7 embryo 20-22hr    6 embryo 22-24hr    5 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    6 white prepupae new    6 white prepupae 12hr    4 white prepupae 24hr    12 pupae 2d postWPP    12 pupae 3d postWPP    7 pupae 4d postWPP    2 adult male 01day    4 adult male 05day    4 adult male 30day    5 adult female 01day    3 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    4 embryo 02-04hr    70 embryo 04-06hr    24 embryo 06-08hr    37 embryo 08-10hr    39 embryo 10-12hr    40 embryo 12-14hr    22 embryo 14-16hr    11 embryo 16-18hr    7 embryo 18-20hr    7 embryo 20-22hr    6 embryo 22-24hr    5 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    6 white prepupae new    6 white prepupae 12hr    4 white prepupae 24hr    12 pupae 2d postWPP    12 pupae 3d postWPP    7 pupae 4d postWPP    2 adult male 01day    4 adult male 05day    4 adult male 30day    5 adult female 01day    3 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    4 embryo 02-04hr    70 embryo 04-06hr    24 embryo 06-08hr    37 embryo 08-10hr    39 embryo 10-12hr    40 embryo 12-14hr    22 embryo 14-16hr    11 embryo 16-18hr    7 embryo 18-20hr    7 embryo 20-22hr    6 embryo 22-24hr    5 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    6 white prepupae new    6 white prepupae 12hr    4 white prepupae 24hr    12 pupae 2d postWPP    12 pupae 3d postWPP    7 pupae 4d postWPP    2 adult male 01day    4 adult male 05day    4 adult male 30day    5 adult female 01day    3 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    4 embryo 02-04hr    70 embryo 04-06hr    24 embryo 06-08hr    37 embryo 08-10hr    39 embryo 10-12hr    40 embryo 12-14hr    22 embryo 14-16hr    11 embryo 16-18hr    7 embryo 18-20hr    7 embryo 20-22hr    6 embryo 22-24hr    5 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    6 white prepupae new    6 white prepupae 12hr    4 white prepupae 24hr    12 pupae 2d postWPP    12 pupae 3d postWPP    7 pupae 4d postWPP    2 adult male 01day    4 adult male 05day    4 adult male 30day    5 adult female 01day    3 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    4 embryo 02-04hr  (70) embryo 04-06hr    24 embryo 06-08hr  (37) embryo 08-10hr  (39) embryo 10-12hr  (40) embryo 12-14hr    22 embryo 14-16hr    11 embryo 16-18hr    7 embryo 18-20hr    7 embryo 20-22hr    6 embryo 22-24hr    5 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    6 white prepupae new    6 white prepupae 12hr    4 white prepupae 24hr    12 pupae 2d postWPP    12 pupae 3d postWPP    7 pupae 4d postWPP    2 adult male 01day    4 adult male 05day    4 adult male 30day    5 adult female 01day    3 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    4 embryo 02-04hr    70 embryo 04-06hr    24 embryo 06-08hr    37 embryo 08-10hr    39 embryo 10-12hr    40 embryo 12-14hr    22 embryo 14-16hr    11 embryo 16-18hr    7 embryo 18-20hr    7 embryo 20-22hr    6 embryo 22-24hr    5 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    6 white prepupae new    6 white prepupae 12hr    4 white prepupae 24hr    12 pupae 2d postWPP    12 pupae 3d postWPP    7 pupae 4d postWPP    2 adult male 01day    4 adult male 05day    4 adult male 30day    5 adult female 01day    3 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    4 embryo 02-04hr    70 embryo 04-06hr    24 embryo 06-08hr    37 embryo 08-10hr    39 embryo 10-12hr    40 embryo 12-14hr    22 embryo 14-16hr    11 embryo 16-18hr    7 embryo 18-20hr    7 embryo 20-22hr    6 embryo 22-24hr    5 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    6 white prepupae new    6 white prepupae 12hr    4 white prepupae 24hr    12 pupae 2d postWPP    12 pupae 3d postWPP    7 pupae 4d postWPP    2 adult male 01day    4 adult male 05day    4 adult male 30day    5 adult female 01day    3 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 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    2 cold shock, 4-day adult    1 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    2 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    1 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    2 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    1 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    2 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 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    2 cold shock, 4-day adult    1 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    2 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    1 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    2 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    1 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    2 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    1 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    2 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 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    2 cold shock, 4-day adult    1 heat shock, 4-day adult    2 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    2 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 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_31 mE1_20_mRNA_expression_cluster_05
External Data & Images
Linkouts	BDGP expression data • GH19318 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0001320 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG4717-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal kni2FKE.eve lethal | embryonic stage, with Scer\GAL4pnr-MD237 kniScer\UAS.cLa lethal | embryonic stage | gap | recessive kniunspecified lethal | embryonic stage | recessive kni3 lethal | pupal stage, with Scer\GAL4pnr-MD237 kniGD1470 viable knid10922 kniri-53j kniri-92f kniri-M3 kniriM kniri-XT2 Sterility Allele fertile knid10922 Other Phenotypes Allele embryonic/larval segmentation phenotype | dominant kni1 mitotic cell cycle defective, with Scer\GAL4fkh.14-3 kniScer\UAS.cCa visible kniri-1 kniri-2 kniri-51k kniri-53j kniri-92f kniri-M1 kniri-M2 kniri-M3 kniri-M4 kniriM kniri-XT2 visible, with Scer\GAL4Bx-MS1096 kniScer\UAS.cLa visible | heat sensitive knihs.PR visible | recessive kniri-1 kniri-92f kniri-XT2 wild-type knitRa Phenotype manifest in Allele abdomen kni1 kni3 abdominal segment kniT abdominal segment 1 kni11 kni2 kni8 abdominal segment 2 kni11 kni2 kni8 abdominal segment 3 kni11 kni2 kni8 abdominal segment 4 kni11 kni2 kni8 abdominal segment 5 kni11 kni2 kni8 abdominal segment 6 kni11 kni2 kni8 abdominal segment 7 kni11 kni2 kni8 adherens junction & embryonic dorsal trunk, with Scer\GAL4btl.PS kniScer\UAS.cCa adult thorax & macrochaeta, with Scer\GAL4Bx-MS1096 kniScer\UAS.cLa dorsal branch primordium knitRa dorsal trunk primordium, with Scer\GAL4btl.PS kniScer\UAS.cCa embryo | gap kniunspecified embryonic/first instar larval cuticle & abdominal segment 1 kniunspecified embryonic/first instar larval cuticle & abdominal segment 2 kniunspecified embryonic/first instar larval cuticle & abdominal segment 3 kniunspecified embryonic/first instar larval cuticle & abdominal segment 4 kniunspecified embryonic/first instar larval cuticle & abdominal segment 5 kniunspecified embryonic/first instar larval cuticle & abdominal segment 6 kniunspecified embryonic/first instar larval cuticle & abdominal segment 7 kniunspecified embryonic/larval dorsal anastomosis, with Scer\GAL4btl.PS kniScer\UAS.cCa embryonic abdominal segment 1 kniIIIE48 embryonic abdominal segment 2 kniIIIE48 embryonic abdominal segment 3 kniIIIE48 embryonic abdominal segment 4 kni1 kniIIIE48 embryonic abdominal segment 5 kniIIIE48 embryonic abdominal segment 6 kniIIIE48 embryonic abdominal segment 7 kniIIIE48 embryonic abdominal segment 8 kniIIIE48 embryonic abdominal segment 9 kniIIIE48 embryonic abdominal segment 10 kniIIIE48 embryonic abdominal segment 11 kniIIIE48 extended germ band embryo kni10 kni2 macrophage kniunspecified mesothoracic segment kni2FKE.eve mesothoracic segment | ventral kni2FKE.eve mesothoracic ventral denticle belt kni2FKE.eve metathoracic femur, with Scer\GAL4Bx-MS1096 kniScer\UAS.cLa wing kniri-1 kniri-2 kniri-51k wing, with Scer\GAL4Bx-MS1096 kniScer\UAS.cLa wing | heat sensitive knihs.PR wing vein | ectopic | heat sensitive knihs.PR wing vein | heat sensitive knihs.PR wing vein L2 kniri-1 kniri-2 kniri-51k kniri-53j kniri-92f kniri-M1 kniri-M2 kniri-M3 kniri-M4 kniri-XT2 kniriM wing vein L2 | distal kniri-1
Classical Alleles ( 35 )
For All Classical Alleles Show
Allele of kni Class Mutagen Stocks Known lesion kniri-1 spontaneous 328 Yes kni6 loss of function allele ethyl methanesulfonate 3 Yes kni9 loss of function allele ethyl methanesulfonate 3 -- kni10 amorphic allele - genetic evidence, loss of function allele ethyl methanesulfonate 2 -- knid10922 P-element activity 2 -- kni1 ethyl methanesulfonate 1 Yes kni5 loss of function allele ethyl methanesulfonate 1 Yes kni8 amorphic allele - genetic evidence, loss of function allele X ray 0 Yes kni11 loss of function allele ethyl methanesulfonate 0 Yes kni12 ethyl methanesulfonate 0 Yes kni2 loss of function allele ethyl methanesulfonate 0 Yes kni3 ethyl methanesulfonate 0 Yes kni4 ethyl methanesulfonate 0 -- kni5H 0 -- kni7 loss of function allele ethyl methanesulfonate 0 Yes kniDD48 0 -- kniEP P-element activity 0 -- kniIIID 0 -- kniIIIE48 0 -- kniP5 hypomorphic allele - genetic evidence Delta2-3 0 Yes kniri-2 0 -- kniri-51k spontaneous 0 -- kniri-53j spontaneous 0 Yes kniri-60b2 X ray 0 -- kniri-92f spontaneous 0 Yes kniri-M1 0 -- kniri-M2 0 -- kniri-M3 0 Yes kniri-M4 0 -- kniri-XT101 0 -- kniri-XT2 0 Yes kniriM 0 Yes kniSchuh P-element activity 0 -- kniT ethyl methanesulfonate 0 Yes kniunspecified ethyl methanesulfonate 0 --
Alleles Carried on Transgenic Constructs ( 73 )
For All Alleles Carried on Transgenic Constructs Show
Allele of kni Class Mutagen Stocks Known lesion kniGD1470 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes kniHMS01184 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes kniJF02544 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes kni139-330.Kr.T:Scer\GAL4,T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes kni139-330.T:Scer\GAL4,T:Zzzz\FLAG in vitro construct - deletion 0 Yes kni169-330.T:Scer\GAL4,T:Zzzz\FLAG in vitro construct - deletion 0 Yes kni188-429.T:Scer\GAL4,T:Zzzz\FLAG,T:Zzzz\His6 in vitro construct - site directed mutagenesis in vitro construct - deletion 0 Yes kni189-254.Act5C.T:Scer\GAL4 in vitro construct - coding region fusion in vitro construct - regulatory fusion 0 Yes kni189-254.Act5C in vitro construct - regulatory fusion 0 Yes kni189-254.T:Scer\GAL4,T:Zzzz\FLAG,T:Zzzz\His6 in vitro construct - deletion 0 Yes kni189-254.T:Scer\GAL4 in vitro construct - coding region fusion 0 Yes kni189-330.Kr.T:Scer\GAL4,T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes kni189-330.T:Scer\GAL4,T:Zzzz\FLAG in vitro construct - deletion 0 Yes kni202-358.Kr.T:Scer\GAL4,T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes kni202-358.T:Scer\GAL4 in vitro construct - coding region fusion 0 Yes kni22FKE.eve FLPase 0 Yes kni22FKT.eve FLPase 0 Yes kni255-429.twi.T:Scer\GAL4 in vitro construct - coding region fusion in vitro construct - regulatory fusion 0 Yes kni2FKE.eve FLPase 0 Yes kni2FKT.eve FLPase 0 Yes kni330.hs.T:Zzzz\His6,T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes kni52-93.MtnA.T:Ecol\lacZ in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes kni64-81.MtnA.T:Ecol\lacZ in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes kni71-93.MtnA.T:Ecol\lacZ in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes kni75-189,254-429.T:Scer\GAL4,T:Zzzz\FLAG,T:Zzzz\His6 in vitro construct - deletion 0 Yes kni75-189.T:Scer\GAL4,T:Zzzz\FLAG,T:Zzzz\His6 in vitro construct - site directed mutagenesis 0 Yes kni75-254.T:Scer\GAL4,T:Zzzz\FLAG,T:Zzzz\His6 in vitro construct - site directed mutagenesis 0 Yes kni75-276.T:Scer\GAL4,T:Zzzz\FLAG in vitro construct - coding region fusion 0 Yes kni75-330.hs.T:Zzzz\His6,T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes kni75-330.Kr.T:Scer\GAL4,T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes kni75-330.T:Scer\GAL4,T:Zzzz\FLAG in vitro construct - coding region fusion 0 Yes kni75-332.T:Scer\GAL4,T:Zzzz\FLAG,T:Zzzz\His6 in vitro construct - site directed mutagenesis 0 Yes kni75-364mut.T:Scer\GAL4 in vitro construct - coding region fusion in vitro construct - deletion in vitro construct - site directed mutagenesis 0 Yes kni75-394mut.T:Scer\GAL4 in vitro construct - coding region fusion in vitro construct - deletion in vitro construct - site directed mutagenesis 0 Yes kni75-429.hs.T:Zzzz\His6,T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes kni75-429.Kr.T:Scer\GAL4,T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes kni75-429.T:Scer\GAL4,T:Zzzz\FLAG,T:Zzzz\His6 in vitro construct - coding region fusion 0 Yes kni75-429.T:Scer\GAL4 in vitro construct - coding region fusion 0 Yes kni75-429.ΔPMDL.Kr.T:Scer\GAL4,T:Zzzz\FLAG in vitro construct - amino acid replacement 0 Yes kni75-429mut.T:Scer\GAL4 in vitro construct - coding region fusion in vitro construct - deletion in vitro construct - site directed mutagenesis 0 Yes kni94-330.T:Scer\GAL4,T:Zzzz\FLAG in vitro construct - deletion 0 Yes kniAct5C.PH in vitro construct - regulatory fusion 0 Yes kniAct5C.T:Tn10\tetR in vitro construct - coding region fusion in vitro construct - regulatory fusion 0 Yes kniC.Act5C.T:Tn10\tetR in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes kniCmut.Act5C.T:Tn10\tetR in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes knieve.P in vitro construct - regulatory fusion 0 Yes knihs.PH in vitro construct - regulatory fusion 0 Yes knihs.PR in vitro construct - regulatory fusion 0 Yes knihs.T:Zzzz\His6,T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes kniM42.Act5C in vitro construct - regulatory fusion in vitro construct - site directed mutagenesis 0 Yes kniN.Act5C.T:Tn10\tetR in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes kniNmut.Act5C.T:Tn10\tetR in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes kniP-DLS-K.eve FLPase 0 Yes kniScer\FRT.22FKE.eve in vitro construct - regulatory fusion 0 Yes kniScer\FRT.22FKT.eve in vitro construct - regulatory fusion 0 Yes kniScer\FRT.2FKE.eve in vitro construct - regulatory fusion 0 Yes kniScer\FRT.2FKT.eve in vitro construct - regulatory fusion 0 Yes kniScer\FRT.P-DLS-K.eve in vitro construct - site directed mutagenesis 0 Yes kniScer\FRT.sna in vitro construct - regulatory fusion 0 Yes kniScer\UAS.cCa in vitro construct - regulatory fusion 0 Yes kniScer\UAS.cLa in vitro construct - regulatory fusion 0 Yes knisna.PC FLPase 0 Yes knitCH322-25A12 in vitro construct - genomic fragment 0 Yes knitRa in vitro construct - genomic fragment in vitro construct 0 Yes kniΔ159-164.Act5C in vitro construct - regulatory fusion in vitro construct - site directed mutagenesis 0 Yes kniΔ187-199.Act5C in vitro construct - regulatory fusion in vitro construct - site directed mutagenesis 0 Yes kniΔ75-93.Act5C in vitro construct - regulatory fusion in vitro construct - site directed mutagenesis 0 Yes kniΔA.T:Scer\GAL4 in vitro construct - deletion 0 Yes kniΔB.T:Scer\GAL4 in vitro construct - deletion 0 Yes kniΔC.T:Scer\GAL4 in vitro construct - deletion 0 Yes kniΔD.T:Scer\GAL4 in vitro construct - deletion 0 Yes kniΔE.T:Scer\GAL4 in vitro construct - deletion 0 Yes kniΔF.T:Scer\GAL4 in vitro construct - deletion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3L)A81 (Jurgens et al., 1984) Df(3L)BSC448 (Christensen et al., 2008.4.15) Df(3L)BSC452 (Christensen et al., 2008.4.15) Df(3L)BSC563 (Cook et al., 2008.9.3) Df(3L)BSC796 (Christensen et al., 2009.5.6) Df(3L)BSC797 (Christensen et al., 2009.5.6) Df(3L)FA12 (Muller et al., 1999, Jurgens et al., 1984) Df(3L)J158 (Muller et al., 1999, Jurgens et al., 1984) Df(3L)kni-FC82 (Lunde et al., 1998) Df(3L)N2-27 (Muller et al., 1999) Df(3L)ri-79c (Grosshans and Wieschaus, 2000, Jurgens et al., 1984, Smith et al., 1993, Adler et al., 1994, Harbecke and Lengyel, 1995) Df(3L)riXT106 (Tearle and Nusslein-Volhard, 1987, Oro et al., 1989) Df(3L)ri-XT1 (Chen et al., 1998, Boube et al., 2001, Tearle and Nusslein-Volhard, 1987, Oro et al., 1989, Tremml and Bienz, 1989, Rothe et al., 1992, Gonzalez-Gaitan et al., 1994, Ruden and Jaeckle, 1995) In(3L)riXT101 (Lunde et al., 1998) Tp(3;2)kni-FC82 (Nauber et al., 1988)
Duplicated in	Dp(3;2)N2-27 (Puro, 1982)
Transgenic Constructs & Insertions
Transgenic Constructs
heat-shock construct	Name Expression Data P{hs-kni.75-330.6His.FLAG} NA P{hs-kni.75-429.6His.FLAG} NA P{hs-kni.330.6His.FLAG} NA P{hs-kni.429.6His.FLAG} NA P{hsp70-kni} NA P{kni-hsp70} NA
reporter construct	Name Expression Data P{2bcd} No P{2cad} No P{3x2bcd} No P{4bcd} No P{5x4bcd} No P{5xbcd} No P{kni64.SH} No P{kni64.SN} No P{kni64} No P{kni223/kni64.RH} No P{kni223/kni64} No P{kni223.SN} No P{kni223} No P{kni.KBg} No P{kni.KC} No P{kni.KD} No P{kni.KFn} No P{kni.KN/CR} No P{kni.KP/NR} No P{kni.KP/RBg} No P{kni.KR} No P{kni.KT} No P{kni.KX} No P{kni.PN} No P{kni.RR} No P{kni.SN} No P{kni.XK} No P{kni(4.4)-lacZ} No P{kni-hkb-lacZ.VAE} No P{kni-hkb-lacZ.VE.45} No P{kni-hkb-lacZ.VE} No P{kni-hkb-lacZ.VRE} No P{kni-lacZ.2R} No P{kni-lacZ.-5} No P{kni-lacZ.+1} No P{kni-lacZ.AE19} No P{kni-lacZ.AE20} No P{kni-lacZ.AE20BtM} No P{kni-lacZ.AE20d} No P{kni-lacZ.AE20NASE} No P{kni-lacZ.E} No P{kni-lacZ.EC-3Sdmut} No P{kni-lacZ.EC} No P{kni-lacZ.ES} No P{kni-lacZ.EX(ri53j)} No P{kni-lacZ.EX} No P{kni-lacZ.EΔri1} No P{kni-lacZ.W} No P{kni-lacZ.Z} No P{kni-lacZ.Ψ} No P{lacZkni.6bcd} No P{lacZkni.PX} No P{Δhbkni223/kni64} No
GAL4 construct	Name Expression Data P{Gal4-kni.75-189,254-429} No P{Gal4-kni.75-189} No P{Gal4-kni.75-254} No P{Gal4-kni.75-276} No P{Gal4-kni.75-330} No P{Gal4-kni.75-332} No P{Gal4-kni.75-364mut} No P{Gal4-kni.75-394mut} No P{GAL4-kni.75-429} No P{Gal4-kni.75-429} No P{Gal4-kni.75-429mut} No P{Gal4-kni.94-330} No P{Gal4-kni.139-330} No P{Gal4-kni.169-330} No P{Gal4-kni.188-429} No P{GAL4-kni.189-254} No P{Gal4-kni.189-254} No P{Gal4-kni.189-330} No P{Gal4-kni.202-358} No P{Gal4-kni.ΔA} No P{Gal4-kni.ΔB} No P{Gal4-kni.ΔC} No P{Gal4-kni.ΔD} No P{Gal4-kni.ΔE} No P{Gal4-kni.ΔF} No P{Kr-GAL4-kni.75-330} No P{Kr-GAL4-kni.75-429.ΔPMDL} No P{Kr-GAL4-kni.75-429} No P{Kr-GAL4-kni.139-330} No P{Kr-GAL4-kni.189-330} No P{Kr-GAL4-kni.202-358} No P{twi-GAL4-kni.255-429} No
UAS construct	Name Expression Data P{GD1470} NA P{TRiP.HMS01184} NA P{TRiP.JF02544} NA P{UAS-kni.C} NA P{UAS-kni.L} NA
characterization construct	Name Expression Data P{hb-h::kni.J} NA P{kni.eve.2FKE} NA P{kni.eve.2FKT} NA P{kni.eve.22FKE} NA P{kni.eve.22FKT} NA P{kni.eve.P-DLS-K} NA P{kni.FRT.2FKE} NA P{kni.FRT.2FKT} NA P{kni.FRT.22FKE} NA P{kni.FRT.22FKT} NA P{kni.FRT.P-DLS-K} NA P{kni.PX} NA P{kni(0.5)-lacZ} NA P{kni(1.8)-lacZ} NA P{kni(3.6)-lacZ} NA P{knicLa} NA P{knieve.P} NA P{kni-GAL4.L2} NA P{kniknrlfing} NA P{kniSH} NA P{sna(FRT.STOP)kni.C} NA P{sna(-FRT)kni.C} NA PBac{CH322-25A12} NA
Insertions
	Type of insertions Name Expression data insertion of mobile activating element P{XP}knid10922 NA miscellaneous insertions P{}kniP5 NA P{UAS-kni.L}EP NA insertion of enhancer trap P{lacZ}kniSchuh No
Gene Ontology: Function, Process & Cellular Component ( 20 unique terms )
Terms Based on Experimental Evidence ( 7 terms )
Molecular Function
CV term Evidence References
repressing transcription factor binding inferred from physical interaction with CtBP (Keller et al., 2000) RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription inferred from direct assay (Keller et al., 2000) sequence-specific DNA binding transcription factor activity inferred from direct assay (Li et al., 2008)
Biological Process
CV term Evidence References
dendrite morphogenesis inferred from mutant phenotype (Parrish et al., 2006) epidermis development inferred from mutant phenotype (Parrish et al., 2006) muscle organ development inferred from mutant phenotype (Parrish et al., 2006) regulation of mitosis inferred from mutant phenotype (Fuss et al., 2001)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 14 terms )
Molecular Function
CV term Evidence References
ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity inferred from sequence or structural similarity with UniProtKB:Q60674 (FlyBase, 1992-) non-traceable author statement (Swiss-Prot Project Members, 1989.7.1, Maglich et al., 2001) sequence-specific DNA binding inferred from electronic annotation with InterPro:IPR001628 (FlyBase Curators et al., 2004-) sequence-specific DNA binding transcription factor activity inferred from sequence or structural similarity with UniProtKB:Q60674 (FlyBase, 1992-) zinc ion binding inferred from electronic annotation with InterPro:IPR001628, InterPro:IPR013088 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
branched duct epithelial cell fate determination, open tracheal system traceable author statement (Zelzer and Shilo, 2000, Affolter and Shilo, 2000, Uv et al., 2003) epithelial cell migration, open tracheal system traceable author statement (Affolter, 2000) negative regulation of transcription, DNA-dependent non-traceable author statement (Swiss-Prot Project Members, 1989.7.1) negative regulation of transcription from RNA polymerase II promoter traceable author statement (Courey and Jia, 2001) open tracheal system development traceable author statement (Ghabrial et al., 2003) regulation of transcription, DNA-dependent inferred from electronic annotation with InterPro:IPR001628, InterPro:IPR008946, InterPro:IPR013088 (FlyBase Curators et al., 2004-) regulation of tube size, open tracheal system traceable author statement (Affolter and Shilo, 2000) trunk segmentation traceable author statement (Peel, 2004) zygotic determination of anterior/posterior axis, embryo non-traceable author statement (Swiss-Prot Project Members, 1989.7.1, Courey and Jia, 2001) traceable author statement (Peel, 2004)
Cellular Component
CV term Evidence References
nucleus inferred from sequence or structural similarity with UniProtKB:Q60674 (FlyBase, 1992-) non-traceable author statement (Swiss-Prot Project Members, 1989.7.1)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
kni - CG14480 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) kni - CG3224 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) kni - CG34132 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) kni - CG5746 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) kni - Cad88C anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) kni - CtBP anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) kni - REG anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) kni - SC35 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) kni - SmG anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) kni - Tim8 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) kni - ric8a anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) kni - snRNP-U1-70K 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 kni allele Gene References kni2FKE.eve hb (Wu et al., 2001) kni3 Res (Ruden and Jaeckle, 1995) kni8 Res (Ruden and Jaeckle, 1995) kniri-1 eg (Lunde et al., 2003) knrl (Lunde et al., 2003) rho (Lunde et al., 2003) salm (Lunde et al., 1998) kniScer\UAS.cCa knrl (Fuss et al., 2001) kniunspecified Egfr (Diaz-Benjumea and Garcia-Bellido, 1990) God (Ruden et al., 1997) neb (Ruden et al., 1997) Res (Ruden and Jaeckle, 1994) unspecified btl (Myat et al., 2005) CtBP (Nibu et al., 1998) God (Ruden and Jaeckle, 1995, Carthew et al., 1994) nej (Anderson et al., 2005) pnt (Myat et al., 2005) rho (Sturtevant and Bier, 1995) Rpd3 (Struffi and Arnosti, 2005) RpII140 (Parkhurst and Ish-Horowicz, 1991) RpL36 (Duffy et al., 1996)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 65544 DPiM - DPiM, Drosophila Protein interaction Map • FBgn0001320 DroID - A comprehensive database of gene and protein interactions. • FBgn0001320 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 40287 SignaLink - A protein-protein and protein-miRNA interaction database with multi-layered structure and multiple confidence scores. • P10734
Orthologs
OrthoDB Orthologs (61) - 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 EOG6JHD10 Dipteran inclusive ortholog search EOG6JWVNH Insect inclusive ortholog search EOG6JHB9J Arthropod inclusive ortholog search EOG6DR7T6 Metazoa inclusive ortholog search EOG6NWBC0
Orthologs in Drosophila Species (EOG6JHD10)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\kni     Drosophila melanogaster fruit fly  Dmel\CG6498     Drosophila simulans   Dsim\GD14555   Y Drosophila sechellia   Dsec\GM25540   Y Drosophila erecta   Dere\GG15910   Y Drosophila yakuba   Dyak\GE22251   Y Drosophila yakuba   Dyak\GE22255   Y Drosophila ananassae   Dana\GF24080   Y Drosophila pseudoobscura pseudoobscura   Dpse\GA22590   Y Drosophila pseudoobscura pseudoobscura   Dpse\GA19640   Y Drosophila persimilis   Dper\GL24910   Y Drosophila willistoni   Dwil\GK17419   Y Drosophila virilis   Dvir\GJ13868   Y Drosophila mojavensis   Dmoj\GI13121   Y Drosophila grimshawi   Dgri\GH14743   Y
Orthologs in non-Drosophila Dipterans (EOG6JWVNH)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL006330 Y Anopheles gambiae Malaria mosquito  Agam\AGAP011030 Y Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ011012 Y Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ018765 Y
Orthologs in non-Dipteran Insects (EOG6JHB9J)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\GB47422 Y Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG008926 Y Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH14595 Y Atta cephalotes Leafcutter ant  Acep\ACEP19084 Y Camponotus floridanus Florida carpenter ant  Cflo\CFLO12554 Y Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL13562 Y Linepithema humile Argentine ant  Lhum\LH11697 Y Pogonomyrmex barbatus Red harvester ant  Pbar\PB11053 Y Solenopsis invicta Red fire ant  Sinv\SINV10125 Y Acyrthosiphon pisum Pea aphid  Apim\ACYPI000329 Y Bombyx mori Silkmoth  Bmor\BGIBMGA013400 Y Pediculus humanus Human body louse  Phum\PHUM291260 Y Tribolium castaneum Red flour beetle  Tcas\TC004792 Y
Orthologs in non-Insect Arthropods (EOG6DR7T6)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\TRIM62 Y Ixodes scapularis Deer tick  Isca\ISCW023226 Y
Orthologs in non-Arthropod Metazoa (EOG6NWBC0)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Caenorhabditis elegans Nematode  Cele\kin-4 Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_022164gn Y Danio rerio Zebrafish  Drer\ENSDARG00000088789 Y Danio rerio Zebrafish  Drer\ENSDARG00000074311 Y Danio rerio Zebrafish  Drer\ENSDARG00000061725 Y Danio rerio Zebrafish  Drer\BX004890.2 Y Danio rerio Zebrafish  Drer\mast4 Y Danio rerio Zebrafish  Drer\BX547996.1 Y Xenopus tropicalis Western clawed frog  Xtro\mast2 Y Xenopus tropicalis Western clawed frog  Xtro\mast3 Y Xenopus tropicalis Western clawed frog  Xtro\mast1 Y Xenopus tropicalis Western clawed frog  Xtro\mast4 Y Gallus gallus Domestic chicken  Ggal\MAST3 Y Gallus gallus Domestic chicken  Ggal\MAST1 Y Gallus gallus Domestic chicken  Ggal\MAST4 Y Mus musculus House mouse  Mmus\Mast2 Y Mus musculus House mouse  Mmus\Mast1 Y Mus musculus House mouse  Mmus\Mast3 Y Mus musculus House mouse  Mmus\Mast4 Y Rattus norvegicus Norway rat  Rnor\Mast2 Y Rattus norvegicus Norway rat  Rnor\Mast4 Y Rattus norvegicus Norway rat  Rnor\Mast1 Y Rattus norvegicus Norway rat  Rnor\Mast3 Y Homo sapiens Human  Hsap\MAST2 Y Homo sapiens Human  Hsap\ENSG00000069020 Y Homo sapiens Human  Hsap\MAST3 Y Homo sapiens Human  Hsap\MAST1 Y
Human Orthologs (4)
Gene OMIM HGNC Hsap\MAST2     Hsap\ENSG00000069020     Hsap\MAST3     Hsap\MAST1
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\kni Drosophila sechellia Dsec\kni Drosophila erecta Dere\GG13292 Drosophila yakuba Dyak\GE22389 Drosophila ananassae Dana\GF24121 Drosophila pseudoobscura pseudoobscura Dpse\GA18381 Drosophila persimilis Dper\GL12762 Drosophila willistoni Dwil\GK10545 Drosophila virilis Dvir\kni Drosophila mojavensis Dmoj\GI11896 Drosophila grimshawi Dgri\GH16981
Stocks & Reagents
Stocks Listed in FlyBase ( 340 )
Bloomington	566 kniri-1 738 kniri-1 e1 19340 w1118; P{XP}knid10922 718 C(3L)RM-P3, kniri-1; C(3R)RM-P3 704 Df(3R)M35, kniri-1/TM3, Sb1 6178 kD es/TM2, kniri-1 27259 y1 v1; P{TRiP.JF02544}attP2
Harvard	- P{XP}knid10922
Kyoto	101731 kniri-1 ss1 106041 Df(3R)M35, kniri-1/TM3, Sb1
VDRC	v2980 w1118; P{GD1470}v2980 v2981 w1118; P{GD1470}v2981
	More stocks available...
Genomic Clones ( 2 )
	BACR21J02 BACR48C13 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 11 )
	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	GH19318
Other clones	DPiM_GH19318
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	LD19841
Other clones	190776 CK01.26A.E6 CK01.26A.F6 CK01.91D.F7 CK01.105D.D1 CK01.144C.C3 EK071824 EK293038
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0001320 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 40287
Antibody Information
	polyclonal (Dubuis et al., 2013, Li et al., 2008)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: kni ri (Lunde et al., 1998)
Additional comments
Other Comments
	DNA-protein interactions: genome-wide binding profile assayed for kni protein in 2-3 hr embryos; see BDTNP1_TFBS_kni collection report. (Li et al., 2008) dsRNA has been made from templates generated with primers directed against this gene. RNAi of kni causes dorsal overextension of primary dendrites in ddaD and ddaE neurons. For such neurons, the most distal branchpoint is located 25 microns or further from the distal tip of the primary dendrite. However, branching of these dendrites is almost completely blocked. RNAi also causes defects in muscle, defects in the epidermis and defects in dendrite morphogenesis. (Parrish et al., 2006) Both Dpp and FGF signalling pathways control kni expression. (Myat et al., 2005) kni and knrl appear to be important in spatially restricting endoreduplication domains. (Fuss et al., 2001) knrl and kni possess multiple and redundant functions during tracheal development. knrl/ kni activity is necessary to mediate dpp signalling (which is required for tracheal cell migration and formation of dorsal and ventral branches). knrl/ kni activity in dorsal tracheal cells is essential for secondary and terminal branch formation, via repression of salm. The border between dorsal trunk and branch identity is established by the direct interaction of kni with a salm cis-regulatory element. (Chen et al., 1998) Zygotic activation of h stripe 6 expression is preceded by activation in response to maternal cad activity, activation does not depend exclusively on the zygotic activity of kni as thought previously. cad and kni activities cooperate in a non-synergistic manner to activate h stripe 6 transcription. Absence of kni does not cause lack of h stripe 6 activation but delays the appearance of the stripe. Activation of the stripe depends on a minimal number of activator binding sites that are scattered throughout the stripe 6 element. (Hader et al., 1998) In a sample of 79 genes with multiple introns, 33 showed significant heterogeneity in G+C content among introns of the same gene and significant positive correspondence between the intron and the third codon position G+C content within genes. These results are consistent with selection adding against preferred codons at the start of genes. (Kliman and Eyre-Walker, 1998) Mutations in kni fail to complement ri, when rearranged with respect to each other, while complementing without rearrangement, suggesting ri-kni transvection. A kni cDNA transgene can rescue the ri phenotype. Genomic Southern data reveals that transheterozygosity of overlapping deficiencies resulting in an ri phenotype creates a small synthetic deletion in the kni upstream region. (Lunde et al., 1998) Mutants are isolated in an EMS mutagenesis screen to identify zygotic mutations affecting germ cell migration at discrete points during embryogenesis: mutants exhibit gap pattern defects. (Moore et al., 1998) In vitro binding assays, gene dosage studies and transgenic repression assays suggest that CtBP is essential for kni-mediated repression in the early embryo. sna may also require CtBP. (Nibu et al., 1998) CtBP mediates transcriptional repression by the kni, Kr and sna products in the Drosophila embryo. (Nibu et al., 1998) The eve stripe 2 enhancer and yeast Scer\FLP1-Scer\FRT system have been used to create a domain of ectopic kni expression in the blastoderm embryo. Specific disruptions of pair-rule patterning are correlated with the level and timing of ectopic expression. This suggests that the ectopic kni domain acts as a source for morphogenetic activity that specifies regions in the embryo where pair-rule genes can be activated or repressed. (Kosman and Small, 1997) The kni gene product mediates both transcriptional quenching and direct repression. The range of kni repression at upstream activators is ~50-100bp, leaving neighboring enhancers free to interact with the transcription complex. kni can also act in promoter-proximal positions, as a dominant repressor, where it can block multiple enhancers. (Arnosti et al., 1996) Gene product is known to regulate Kr CD (cis acting control element) expression. (Carrera and Jaeckle, 1995) Two independent and redundant elements in the kni upstream region depend upon bcd and cad activity. Ecol\lacZ reporter gene analysis demonstrates bcd and cad are necessary to activate kni. (Hader et al., 1995) Rescue of the kni- embryonic abdominal segmentation phenotype by Res requires another gene, it is likely this is knrl. (Ruden and Jaeckle, 1995) Transcription factors hb and kni can associate with Kr in vitro and they interact functionally with Kr-dependent target gene expression mediated by a single Kr-binding site close to an heterologous promoter in Schneider cells. (Sauer and Jaeckle, 1995) The abdominal cad domain is required to activate the gap genes kni and gt. (Schulz and Tautz, 1995) Misexpression of kniby the eve stripe 2 enhancer demonstrates that kni can function as an homeotic gene outside its normal domain. (Small and Kosman, 1995) Loss of vein mutations cause suppression of rhohs.PSt ectopic vein phenotype and enhancement of the rhove-1 loss of vein phenotype. (Sturtevant and Bier, 1995) The biochemically equivalent gene products of kni and knrl are both functional in the head anlage and lack of one gene can be overcome by the activity of the other. kni is also required for abdominal segmentation and knrl is nonfunctional in its posterior expression domain. Therefore the kni/knrl pair of genes provides a region-specific buffering system, rather than global functional redundancy. (Gonzalez-Gaitan et al., 1994) h stripe 6 is critically dependent upon kni for activation. (Langeland et al., 1994) E(z) is required to maintain the expression domain of kni and gt initiated by the maternal hb gradient. A small region of the kni promoter mediates regulation by E(z) and hb. (Pelegri and Lehmann, 1994) Regulation of kni and knrl in their common anterior expression domain requires the same trans-acting factors. Both genes fail to be activated by bcd or dl. (Rothe et al., 1994) Expression of prd depends on activation by gap gene hb, Kr, kni and gt products. Primary pair rule gene products act primarily in subsequent modulation rather than activation of prd stripes. Factors activating prd expression in the pair rule mode interact with those activating it along the dorso-ventral axis. (Gutjahr et al., 1993) The role of kni in the regulation of run mRNA expression in the early embryo has been investigated. (Klingler and Gergen, 1993) DNaseI footprinting analysis reveals core histones His2A, His2B, His3 and His4 (but not His1) bind to the kni minimal enhancer element in a periodic manner. (Kerrigan and Kadonaga, 1992) Evolutionary history for nuclear receptor genes, in which gene duplication events and swapping between domains of different origins took place, is studied. (Laudet et al., 1992) 4.4kb upstream sequence of kni directs Ecol\lacZ reporter gene constructs in a region corresponding to the endogenous kni transcripts. Deletion constructs were made to determine how kni is spatially regulated. (Pankratz et al., 1992) Males of an isogenic line with a mutation at the ri locus were treated with a standard light heat shock and by a heavy heat shock. Mass transposition of the copia-like element 412 occurred at five transposition "hot-spots" (43B, 49CD, 56A, 56E and 66A) when the F1 generation of males were crossed with untreated females of the same isogenic line. The probabilities of transposition were two orders of magnitude higher than in the control sample. Stepwise temperature treatment shows the induction depends on the intensity of the temperature than any other stress action. (Ratner et al., 1992) kni is required to establish abdominal segmentation. knrl differs from kni with respect to transcription unit size, kni contains 1kb and knrl contains 19kb intron sequences. The consequence of the intron difference is that knrl cannot substitute for kni segmentation function. The length of the mitotic cycle provides physiological barrier to transcript size and could be a significant factor in controlling developmental gene activity during short phenocritical periods. (Rothe et al., 1992) kni was included in a study to determine how gap genes influence gt expression. (Eldon and Pirrotta, 1991) kni is a dual regulator of gt in the embryo: represses in the head regions and maintains high levels of gt in the tail. (Kraut and Levine, 1991) Mutations in zygotic cardinal gene kni interact with RpII140wimp. (Parkhurst and Ish-Horowicz, 1991) Mutant kni embryos do not alter the expression of the Ubx bx region enhancer element, BRE. (Qian et al., 1991) Zygotically active locus involved in the terminal developmental program in the embryo. (Strecker et al., 1991) Mutations in ri affect individual longitudinal veins: vein specific effects. (Diaz-Benjumea and Garcia-Bellido, 1990) kni mutants exhibit deletion of the abdomen. (Gaul and Jaeckle, 1990) The effect of hb protein concentration on the expression of kni and Kr in the embryo has been studied. (Hulskamp et al., 1990) The expression patterns of Kr and kni demonstrate the proteins form overlapping concentration gradients that generate the periodic pair-rule expression pattern. (Pankratz et al., 1990) ri, tg, tt, ab, cv, cv-2, cv-c and cv-d belong to the radius incompletus phenotypic group within the 'lack-of-vein' mutant class. Loss-of-function alleles at these loci remove stretches of veins in two or more longitudinal veins. Double mutants of this group have additive phenotypes suggesting the genes are vein-specific, and have small lanceolate wings. Genes are involved in whole vein region-specification rather than vein differentiation. (Diaz-Benjumea et al., 1989) An investigation of the role of gap genes in expression from Ubx and Antp promoters in the blastoderm embryo reveals that a unique combination of gap genes and pair rule genes is required for their initial activation. (Irish et al., 1989) Mutations in kni alter gt expression in the posterior of the embryo. (Mohler et al., 1989) Expression of kni-Ecol\lacZ regulatory fusion constructs in mutant embryos shows that kni expression is repressed by tll activity, but enhanced by Kr activity. (Pankratz et al., 1989) Genetic analysis demonstrates that the effect of the gap gene product kni on homeotic gene expression in the visceral mesoderm is indirect and mediated by the genes that establish parasegment borders, eve and ftz. (Tremml and Bienz, 1989) kni activity exerts a negative effect on Antp expression. This negative regulation is indirect and mediated by an alteration of Kr expression, this can be seen when comparing Antp expression in kni- embryos and Kr-/kni- embryos. kni is involved in restricting Abd-B products within the A8--A9 domain. (Harding and Levine, 1988) Mutant embryos exhibit normal Dfd expression. (Jack et al., 1988) Molecular characterisation of kni. (Nauber et al., 1988) kni mutants display denticle bands of A1 to A7 fused. (Jurgens et al., 1984) Mutant individuals display interruptions of wing vein L2. (Duncan and Kaufman, 1975) Zygotic gap gene whose mutants are homozygous lethal; their denticle belts in segments one through seven are fused into a single field (Nusslein-Volhard and Wieschaus, 1980), but the head, thorax, eighth abdominal segment and tail region appear normal. Embryos homozygous for a strong kni mutant show a wide band of ftz staining instead of the normal number of ftz stripes (Carroll and Scott, 1986).
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_079463 RefSeq (Proteins) • NP_524187 DDBJ / EMBL / GenBank • AAF51629 AAM50658 AI388412 AY118798 CAA31709 X13331 Entrez Gene - A searchable database of RefSeq genes. • 40287 UniProtKB/Swiss-Prot • P10734
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Zinc finger, nuclear hormone receptor-type (IPR001628) Zinc finger, NHR/GATA-type (IPR013088) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • GH19318
Linkouts
	BioGRID - A database of protein and genetic interactions • 65544 DPiM - DPiM, Drosophila Protein interaction Map • FBgn0001320 DroID - A comprehensive database of gene and protein interactions. • FBgn0001320 DRSC - Results from RNAi screens. • FBgn0001320 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0001320 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG4717-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0001320 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 40287 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /segment/knirps1.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 40287 modMine - Data generated by the modENCODE project. • FBgn0001320 REDfly - A database of transcriptional regulatory elements. • FBgn0001320 SignaLink - A protein-protein and protein-miRNA interaction database with multi-layered structure and multiple confidence scores. • P10734
Synonyms & Secondary IDs ( 11 )
Reported As
Symbol Synonym	CG4717 (Zhang et al., 2002, Kreiman, 2004, Mohammad et al., 2009, Ni et al., 2010.12.1) kn (Jack et al., 1988) Kni (Petit et al., 2002, Hou et al., 2002, Fuss et al., 2001, Parrish et al., 2006, Sutrias-Grau and Arnosti, 2004, Papatsenko and Levine, 2011, Papatsenko et al., 2009, Noyes et al., 2008, He et al., 2009, He et al., 2010, Bauer et al., 2010, Fakhouri et al., 2010, The modENCODE Consortium, 2010, The modENCODE Consortium, 2010, Letizia et al., 2011, Gursky et al., 2011, Nikulova et al., 2012) KNI (Boube et al., 2000, Li et al., 2008, Ho et al., 2009, Bradley et al., 2010, Dilão and Muraro, 2010, Dilão and Muraro, 2010, modENCODE Consortium et al., 2010) kni (Peel et al., 2005, Struffi and Arnosti, 2005, Jaeger and Reinitz, 2006, Chen et al., 1998, Wang et al., 2006, Bangi and Wharton, 2006, Arbouzova et al., 2006, Jiang and Crews, 2006, Cela and Llimargas, 2006, Daulny et al., 2003, Zeitlinger et al., 2007, Sandmann et al., 2007, Kreiman, 2004, Sotillos and de Celis, 2006, Stathopoulos and Levine, 2005, Zeremski et al., 2003, Aerts et al., 2007, Turki-Judeh and Courey, 2012, Brody et al., 2012, Segal et al., 2008, Fu et al., 2003, Jennings et al., 2006, Venken et al., 2009, Cook et al., 2008, Christensen et al., 2008.4.15, Christensen et al., 2008.4.15, Jaeger et al., 2007, Azevedo et al., 2006, Cook et al., 2008.9.3, Kim et al., 2011, Kaplan et al., 2011, Fomekong-Nanfack et al., 2009, Moran and Jimenez, 2006, Xing et al., 2007, Aswani et al., 2010, Chung et al., 2011, Hare et al., 2008, Fowlkes et al., 2008, Fomekong-Nanfack et al., 2009, Nègre et al., 2011, Li et al., 2011, Perry et al., 2011, Liang et al., 2012, Clyde et al., 2003, Araujo et al., 2007, Haecker et al., 2007, Cinnamon et al., 2008, Haecker et al., 2008, Surkova et al., 2008, Yu and Small, 2008, Kim et al., 2009, Ochoa-Espinosa et al., 2009, Manu et al., 2009, Christensen et al., 2009.5.6, Christensen et al., 2009.5.6, Angulo et al., 2004, Akdemir et al., 2007, Terriente-Félix and de Celis, 2009, Pisarev et al., 2009, Jennings et al., 2008, Butler et al., 2009, Perkins et al., 2009.8.10, MacArthur et al., 2009, Janssens et al., 2006, Otsuna and Ito, 2006, Löhr et al., 2009, Payankaulam and Arnosti, 2009, Ashyraliyev et al., 2009, Surkova et al., 2008, Venken et al., 2009, Manu et al., 2009, Luengo Hendriks et al., 2006, Grad et al., 2004, Tran et al., 2010, Blanco and Gehring, 2008, Gurunathan et al., 2004, Sánchez et al., 2010, Guichard et al., 2006, Rendina et al., 2010, Marco et al., 2009, Liu and Ma, 2011, Sung et al., 2013, Pilgram et al., 2011, Weiss et al., 2010, Ajuria et al., 2011, Zhang et al., 2011, Dworkin et al., 2011, Kazemian et al., 2010, Tchuraev and Galimzyanov, 2009, Fowlkes et al., 2011, Ashyraliyev et al., 2008, Kim et al., 2011, Kozlov et al., 2012, Kim et al., 2012, Sokolowski et al., 2012, Aswani et al., 2012, Kvon et al., 2012, Nikulova et al., 2012) KNIRPS (Kim et al., 2010) NR0A1 (Nuclear Receptors Nomenclature Committee, 1999) ri (Vasil'eva and Ratner, 2000, de Celis, 1998, Lunde et al., 1998, Sturtevant and Bier, 1995, Meyer, 1952, Ratner et al., 1992, Diaz-Benjumea and Garcia-Bellido, 1990, Diaz-Benjumea and Garcia-Bellido, 1990, Diaz-Benjumea et al., 1989, Reuter et al., 1986, Kokoza et al., 1982, Puro and Nygren, 1975, Duncan and Kaufman, 1975, Kalisch and Rasmuson, 1974, Arajarvi and Hannah-Alava, 1969, Hannah-Alava, 1964, )
Name Synonym	Knirps (Arnosti et al., 2002, Arnosti et al., 2000, Payankaulam and Arnosti, 2007, Arnosti et al., 2007, Hallikas et al., 2006, Veitia, 2006, Halfon and Arnosti, 2007, Arnosti et al., 2008, Sutrias-Grau and Arnosti, 2004, Kulkarni and Arnosti, 2005, Hare et al., 2008, Crocker and Erives, 2008, MacArthur et al., 2009, Janssens et al., 2006, Payankaulam and Arnosti, 2009, Dilão and Muraro, 2010, Dilão and Muraro, 2010, Fakhouri et al., 2010, Weiss et al., 2010, Letizia et al., 2011, Li and Arnosti, 2010, Nikulova et al., 2012) knirps (Nauber, 1988.10.24, Payankaulam and Arnosti, 2007, Payankaulam et al., 2006, Jaeger and Reinitz, 2006, Chen et al., 1998, McGregor, 2006, Jiang and Crews, 2006, King-Jones and Thummel, 2005, Kreiman, 2004, Sotillos and de Celis, 2006, Zeremski et al., 2003, Cook et al., 2008, Jaeger et al., 2007, Turner et al., 2011, Moran and Jimenez, 2006, Xing et al., 2007, Saunders and Howard, 2009, Papatsenko and Levine, 2011, Chung et al., 2011, Papatsenko et al., 2009, Nègre et al., 2011, Perry et al., 2011, Ishihara and Shibata, 2008, Liang et al., 2012, Sosinsky et al., 2007, Haecker et al., 2007, Cinnamon et al., 2008, Bosveld et al., 2008, Yu and Small, 2008, Ochoa-Espinosa et al., 2009, Manu et al., 2009, Haecker et al., 2008, Terriente-Félix and de Celis, 2009, Pisarev et al., 2009, Jennings et al., 2008, Butler et al., 2009, Iovino et al., 2009, Löhr et al., 2009, Surkova et al., 2008, Manu et al., 2009, Blanco and Gehring, 2008, Zamparo and Perkins, 2009, Abnizova et al., 2005, Sánchez et al., 2010, Liu and Ma, 2011, Li and Arnosti, 2011, Zhang et al., 2011, Bieler et al., 2011, Gursky et al., 2011) KNIRPS (Ho et al., 2009) radius incompletus (Protsenko et al., 2005, )
Secondary FlyBase IDs
	FBgn0003253 FBgn0017615
References ( 587 )
Generate a list of	All references relating to this gene ( 587 )
List References by type	Research paper  ( 384 ) Supplementary material  ( 7 ) Review  ( 86 ) Personal communication to FlyBase  ( 19 ) Abstract  ( 77 ) FlyBase analysis  ( 1 ) DNA/RNA sequence record  ( 1 ) Conference report  ( 2 ) Stock list  ( 2 ) Letter  ( 2 ) Protein sequence record  ( 1 ) Website  ( 1 ) Curated genome annotation  ( 2 ) Book  ( 1 )
Recent research papers ( 43 )
	Dubuis et al., 2013, Mol. Syst. Biol. 9: 639 Accurate measurements of dynamics and reproducibility in small genetic networks. [FBrf0220617] Rockel et al., 2013, Nucleic Acids Res. 41(4): e52 iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks. [FBrf0220859] Shu and Li, 2013, Theor. Biol. Med. Model. 10(1): 11 A statistical thin-tail test of predicting regulatory regions in the Drosophila genome. [FBrf0221021] Staller et al., 2013, Genetics 193(1): 51--61 Depleting Gene Activities in Early Drosophila Embryos with the "Maternal-Gal4-shRNA" System. [FBrf0220341] Sung et al., 2013, Curr. Biol. 23(2): 133--138 Number of nuclear divisions in the Drosophila blastoderm controlled by onset of zygotic transcription. [FBrf0220648] Aswani et al., 2012, Methods Cell Biol. 110: 243--261 Nonparametric variable selection and modeling for spatial and temporal regulatory networks. [FBrf0217971] Brody et al., 2012, Dev. Dyn. 241(1): 169--189 Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers. [FBrf0216969] Crombach et al., 2012, PLoS Comput. Biol. 8(7): e1002589 Efficient reverse-engineering of a developmental gene regulatory network. [FBrf0218873] Fisher et al., 2012, Proc. Natl. Acad. Sci. U.S.A. 109(52): 21330--21335 DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. [FBrf0220344] 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] Kozlov et al., 2012, PLoS Comput. Biol. 8(8): e1002635 Modeling of gap gene expression in Drosophila kruppel mutants. [FBrf0219301] Kvon et al., 2012, Genes Dev. 26(9): 908--913 HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. [FBrf0218184] Liang et al., 2012, Development 139(11): 1956--1964 Response to the BMP gradient requires highly combinatorial inputs from multiple patterning systems in the Drosophila embryo. [FBrf0218213] Nikulova et al., 2012, Nucleic Acids Res. 40(12): e93 CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation. [FBrf0218757] Shu and Li, 2012, Comput. Biol. Med. 42(9): 935--941 A statistical fat-tail test of predicting regulatory regions in the Drosophila genome. [FBrf0219304] Sokolowski et al., 2012, PLoS Comput. Biol. 8(8): e1002654 Mutual repression enhances the steepness and precision of gene expression boundaries. [FBrf0219378] Spirov et al., 2012, ScientificWorldJournal 2012: 560101 In silico evolution of gene cooption in pattern-forming gene networks. [FBrf0220710] Turki-Judeh and Courey, 2012, PLoS ONE 7(2): e30610 The unconserved groucho central region is essential for viability and modulates target gene specificity. [FBrf0217447] Wells and Johnston, 2012, Dev. Biol. 361(2): 263--276 Maintenance of imaginal disc plasticity and regenerative potential in Drosophila by p53. [FBrf0217050] Ajuria et al., 2011, Development 138(5): 915--924 Capicua DNA-binding sites are general response elements for RTK signaling in Drosophila. [FBrf0212975] Bieler et al., 2011, Biophys. J. 101(2): 287--296 Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains. [FBrf0214381] Chung et al., 2011, Dev. Biol. 360(1): 160--172 Trachealess (Trh) regulates all tracheal genes during Drosophila embryogenesis. [FBrf0216563] Dworkin et al., 2011, Genetics 187(4): 1171--1184 The effects of weak genetic perturbations on the transcriptome of the wing imaginal disc and its association with wing shape in Drosophila melanogaster. [FBrf0214376] Fowlkes et al., 2011, PLoS Genet. 7(10): e1002346 A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila. [FBrf0216666] 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] Gursky et al., 2011, BMC Syst. Biol. 5(1): 118 Mechanisms of gap gene expression canalization in the Drosophila blastoderm. [FBrf0217946] Hengenius et al., 2011, PLoS ONE 6(11): e26797 Analysis of Gap Gene Regulation in a 3D Organism-Scale Model of the Drosophila melanogaster Embryo. [FBrf0216698] Kaplan et al., 2011, PLoS Genet. 7(2): e1001290 Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development. [FBrf0213025] Kim et al., 2011, Dev. Cell 20(6): 880--887 Gene regulation by MAPK substrate competition. [FBrf0213872] Kim et al., 2011, Mol. Cells 32(6): 549--554 The pleiohomeotic functions as a negative regulator of Drosophila even-skipped gene during embryogenesis. [FBrf0217062] Letizia et al., 2011, J. Cell Sci. 124(2): 240--251 Regulated Crb accumulation controls apical constriction and invagination in Drosophila tracheal cells. [FBrf0212559] Li et al., 2011, Genome Biol. 12(4): R34 The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. [FBrf0216471] Li and Arnosti, 2011, Curr. Biol. 21(5): 406--412 Long- and short-range transcriptional repressors induce distinct chromatin States on repressed genes. [FBrf0213170] Liu and Ma, 2011, Nat. Cell Biol. 13(1): 22--29 Fates-shifted is an F-box protein that targets Bicoid for degradation and regulates developmental fate determination in Drosophila embryos. [FBrf0212612] McHale et al., 2011, Dev. Biol. 360(1): 230--240 Gene length may contribute to graded transcriptional responses in the Drosophila embryo. [FBrf0216627] Nègre et al., 2011, Nature 471(7339): 527--531 A cis-regulatory map of the Drosophila genome. [FBrf0213303] Papatsenko and Levine, 2011, PLoS ONE 6(7): e21145 The Drosophila gap gene network is composed of two parallel toggle switches. [FBrf0214233] Perry et al., 2011, Proc. Natl. Acad. Sci. U.S.A. 108(33): 13570--13575 Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. [FBrf0214713] Pilgram et al., 2011, J. Neurosci. 31(2): 492--500 The RhoGAP crossveinless-c Interacts with Dystrophin and Is Required for Synaptic Homeostasis at the Drosophila Neuromuscular Junction. [FBrf0212767] Sayal et al., 2011, Fly 5(1): 47--52 Optimization of reporter gene architecture for quantitative measurements of gene expression in the Drosophila embryo. [FBrf0213005] Struffi et al., 2011, Development 138(19): 4291--4299 Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer. [FBrf0215233] Turner et al., 2011, PLoS Genet. 7(3): e1001336 Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster. [FBrf0213327] Zhang et al., 2011, Dev. Biol. 353(2): 259--265 Drosophila long-chain acyl-CoA synthetase acts like a gap gene in embryonic segmentation. [FBrf0213522] Show all research papers ...
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