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Gene Dmel\kn

General Information
Symbol	Dmel\kn	Species	D. melanogaster
Name	knot	Annotation symbol	CG10197
Feature type	protein_coding_gene	FlyBase ID	FBgn0001319
Created / Updated	2003-12-02/2007-03-20
Genomic Location
Chromosome (arm)	2R	Recombination map	2-72.3
Cytogenetic map	51C2-51C3	Sequence location	2R:10,660,152..10,694,566 [-]
Map ( GBrowse )	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene knot is referred to in FlyBase by the symbol kn (CG10197, FBgn0001319). It has the cytological map location 51C2-51C3. Its sequence location is 2R:10660152..10694566. Its molecular function is described as: specific RNA polymerase II transcription factor activity; transcription regulator activity; DNA binding. It is involved in the biological processes described with 14 unique terms, many of which group under: head segmentation; embryonic pattern specification; anatomical structure development; regionalization; regulation of metabolic process; embryonic development; organ morphogenesis; regulation of biological process; immune response; embryonic development via the syncytial blastoderm; segment specification; organ development; response to symbiont. 21 alleles are reported. The phenotypes of these alleles are annotated with 44 unique terms, many of which group under: adult segment; organ system; adult mesothoracic segment; hypodermal muscle of larval abdomen; abdominal oblique muscle; thoracic segment; cephalopharyngeal skeleton; wing cell; embryonic/larval hemocoel; larval abdominal segment 5. It has 3 annotated transcripts and 3 annotated polypeptides.
External Summaries
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	kn: knot Veins L3 and L4 shifted closer together in region of anterior crossvein, which is either extremely thick or eliminated by regional fusion of L3 and L4. Frequently, extra crossvein between L3 and L4 near end of wing. Shift in positions of sensilla and extra chaetae accompanies shift in vein positions. Wing narrowed. Head narrowed and flattened, so the long axis of eye is at oblique angle. May overlap wild type at high temperatures and in late counts. Best at 19. RK2.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 51C2-51C3   Limits computationally determined from genome sequence between P{lacW}Rpn6k00103 and P{PZ}chn02064
Experimentally Determined Cytological Location
Cytogenetic map Notes References 51C1-51C2 (determined by in situ hybridisation)   (Crozatier et al., 1999) 51B10-51C1 Placed in 51B10--51C1 by deficiency mapping (details unspecified).   (Crozatier et al., 1996) 51E-51F (determined by in situ hybridisation)   (Kania et al., 1995) 51C1-51C2 (determined by in situ hybridisation)   (Vincent, 1995)
Experimentally Determined Recombination Data
Location	2-72.3
Left of (cM)
Right of (cM)	L (Nestoras et al., 1997)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology) References Gene Order (overall orientation not stated) References
Gene Model & Products
Please see the GBrowse view of Dmel\kn for information on other features
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) kn-RA FBtr0087465  NM_080074   3461   557 kn-RB FBtr0112809  NM_166070   3927   575 kn-RC FBtr0112810  NM_001103847   3342   689
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein kn-PA   FBpp0086595   60.5   557   8.69     NP_524813   AAF58204 kn-PB   FBpp0111721   62.5   575   8.53     NP_725419   AAM68551 kn-PC   FBpp0111722   74.8   689   8.41     NP_001097317   ABV53800
Additional Polypeptide Data & Comments
Reported size (kD)
Comments
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0001319
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Cell surface receptor IPT/TIG (IPR002909) Transcription factor COE (IPR003523) Basic helix-loop-helix dimerisation region bHLH (IPR001092) Immunoglobulin E-set (IPR014756)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE003813 AAF58204   AI258364   AY119102 AAM50962   BI164134   BI234222   BI240518   BI577611   BI577655   BI592030   CL526130   CO179589   CO179722   CO266449   CO285735   CO288277   CO289739   CO311535   EC057056   EC058463   EC067982   EC069932   EC087092   EC196710   EC207762   EC213599   EC218811   EC218974   EC244867   X97803
UniProtKB/Swiss-Prot	P56721
UniProtKB/TrEMBL
Maps to
Does NOT map to
Identified with	RE03728 (BDGP Project Members, 2000-)
Mapped Features & Mutations
Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here Type Symbol & Location Additional Notes References
External Data
Linkouts	DEDB - Drosophila exon database: splicing graphs • 12499
Crossreferences
Expression Data
FlyBase-Curated Data
Transcript and Protein data	Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
Summary of Transcript Expression
Stage Tissue/Position Reference  embryonic stage  embryonic mandibular segment (Seecoomar et al., 2000)  larval stage | third instar  anterior/posterior compartment boundary | anterior to <of> dorsal mesothoracic disc (Glise et al., 2002)  embryonic stage  procephalic mesoderm (Seecoomar et al., 2000)
Marker for
Subcellular Localization
CV Term
Summary of Polypeptide Expression
Stage Tissue/Position Reference  larval stage | third instar  anterior/posterior compartment boundary | anterior to <of> dorsal mesothoracic disc (Glise et al., 2002)
Marker for
	eo neuron
Subcellular Localization
CV Term
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0001319 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0001319 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0001319 BDGP expression data • Show all BDGP original images, annotations and embryonic microarray data for kn FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for kn Stage(s) 4-6 Stage(s) 9-10 Stage(s) 11-12 Stage(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele viable knSA2 lethal | recessive kncol-1 kncol-2 kncol-3 lethal | embryonic stage knSA1 lethal | embryonic stage | recessive knKN1 knKN2 knKN3 knKN4 knunspecified lethal | embryonic stage | conditional - heat sensitive knhs.PS lethal | embryonic stage | conditional - heat sensitive, with Scer\GAL4srp.D.cCa knScer\UAS.cVa Other Phenotypes Allele wild-type kn+m5 visible kn+m5 kn1 knunspecified visible (with kn1) kncol-1 visible (with kncol-1) kn1 visible | cell non-autonomous | recessive | somatic clone knKN4 visible | recessive kn1 knSA1 visible | somatic clone knKN1 knKN2 knKN3 knKN4 kncol-1 knunspecified visible, with Scer\GAL4Bx-MS1096 knScer\UAS.cMa visible, with Scer\GAL4dpp.blk1 knScer\UAS.cMa visible, with kncol-1 kn+m5 visible, with kn+m5 kncol-1 olfaction defective kncol-85 immune response defective, with kncol-1 kn+m5 immune response defective, with kn+m5 kncol-1 Phenotype manifest in Allele wing vein L3, with Scer\GAL4ap-md544 kndsRNA.Scer\UAS wing vein L4, with Scer\GAL4ap-md544 kndsRNA.Scer\UAS 1st posterior cell, with kncol-1 kn+m5 wing vein L3, with kncol-1 kn+m5 wing vein L4, with kncol-1 kn+m5 wing, with kncol-1 kn+m5 submarginal cell, with kncol-1 kn+m5 2nd posterior cell, with kncol-1 kn+m5 3rd posterior cell, with kncol-1 kn+m5 wing & pupa, with kncol-1 kn+m5 wing vein kn+m5 kncol-1 knunspecified wing vein L3 kn+m5 kn1 knSA1 kncol-1 wing vein L4 kn+m5 kn1 knSA1 kncol-1 posterior crossvein kn+m5 kncol-1 anterior crossvein kn+m5 kn1 kncol-1 1st posterior cell kn+m5 kn1 knSA1 kncol-1 1st posterior cell (with kncol-1) kn1 2nd posterior cell (with kncol-1) kn1 3rd posterior cell (with kncol-1) kn1 wing & pupa (with kncol-1) kn1 wing cell & wing vein L3 & wing vein L4 kn1 wing basal cell 1 kn1 knSA1 wing vein | ectopic knKN1 knKN2 knKN3 knKN4 sensillum campaniformium of dorsal radius | ectopic knKN1 knKN2 knKN3 knKN4 wing cell & wing vein L3 & wing vein L4 | somatic clone knKN1 knKN2 knKN3 knKN4 wing | anterior compartment | somatic clone knKN1 knKN2 knKN3 knKN4 wing vein | ectopic | somatic clone knKN1 knKN2 knKN3 knKN4 knunspecified wing vein L4 | cell non-autonomous | somatic clone knKN1 knKN2 knKN3 knKN4 wing margin bristle | somatic clone knKN1 knKN2 knKN3 knKN4 macrochaeta | ectopic | somatic clone knKN1 knKN2 knKN3 knKN4 cephalopharyngeal skeleton knKN2 knKN4 kncol-1 kncol-2 kncol-3 lateral process knKN2 knKN4 kna.hs kncol-1 kncol-2 kncol-3 ventral wing knKN2 knKN4 wing | cell non-autonomous | somatic clone knKN4 wing vein | cell non-autonomous | ectopic | somatic clone knKN4 hypopharyngeal lobe knKN4 wing cell knSA2 wing knSA2 knunspecified wing vein L3, with Scer\GAL4Bx-MS1096 knScer\UAS.cMa wing vein L4 | distal, with Scer\GAL4Bx-MS1096 knScer\UAS.cMa wing vein L5 | proximal, with Scer\GAL4Bx-MS1096 knScer\UAS.cMa wing vein L2, with Scer\GAL4Bx-MS1096 knScer\UAS.cMa wing vein L4 | proximal, with Scer\GAL4Bx-MS1096 knScer\UAS.cMa wing vein L5 | distal, with Scer\GAL4Bx-MS1096 knScer\UAS.cMa wing vein L3 | distal, with Scer\GAL4dpp.blk1 knScer\UAS.cMa lamellocyte | supernumerary, with Scer\GAL4srp.D.cCa knScer\UAS.cVa melanotic mass | ectopic, with Scer\GAL4srp.D.cCa knScer\UAS.cVa crystal cell, with Scer\GAL4srp.D.cCa knScer\UAS.cVa wing vein L5, with Scer\GAL4en-e16E knScer\UAS.cVa lymph gland, with Scer\GAL4dome-PG125 knScer\UAS.cVa 1st posterior cell, with kn+m5 kncol-1 wing vein L3, with kn+m5 kncol-1 wing vein L4, with kn+m5 kncol-1 wing, with kn+m5 kncol-1 submarginal cell, with kn+m5 kncol-1 2nd posterior cell, with kn+m5 kncol-1 3rd posterior cell, with kn+m5 kncol-1 wing & pupa, with kn+m5 kncol-1 1st posterior cell (with kn1) kncol-1 2nd posterior cell (with kn1) kncol-1 3rd posterior cell (with kn1) kncol-1 wing & pupa (with kn1) kncol-1 embryonic head kncol-1 kncol-2 kncol-3 embryonic/larval somatic muscle kncol-1 kncol-2 kncol-3 abdominal 1 dorsal acute muscle 3 kncol-1 kncol-2 kncol-3 knhs.PS abdominal 2 dorsal acute muscle 3 kncol-1 kncol-2 kncol-3 knhs.PS abdominal 3 dorsal acute muscle 3 kncol-1 kncol-2 kncol-3 knhs.PS abdominal 4 dorsal acute muscle 3 kncol-1 kncol-2 kncol-3 knhs.PS abdominal 5 dorsal acute muscle 3 kncol-1 kncol-2 kncol-3 knhs.PS abdominal 6 dorsal acute muscle 3 kncol-1 kncol-2 kncol-3 knhs.PS abdominal 7 dorsal acute muscle 3 kncol-1 kncol-2 kncol-3 knhs.PS mesothoracic dorsal acute muscle 4 kncol-1 kncol-2 kncol-3 metathoracic dorsal acute muscle 4 kncol-1 kncol-2 kncol-3 wing vein L4 | somatic clone kncol-1 knunspecified lymph gland kncol-1 abdominal 1 dorsal oblique muscle 5 knhs.PS abdominal 2 dorsal oblique muscle 5 knhs.PS abdominal 3 dorsal oblique muscle 5 knhs.PS abdominal 4 dorsal oblique muscle 5 knhs.PS abdominal 5 dorsal oblique muscle 5 knhs.PS abdominal 6 dorsal oblique muscle 5 knhs.PS abdominal 7 dorsal oblique muscle 5 knhs.PS hypostomal sclerite | conditional - heat sensitive knhs.PS lateral process | conditional - heat sensitive knhs.PS cephalopharyngeal skeleton | conditional - heat sensitive knhs.PS wing vein L3 | somatic clone knunspecified
Classical Alleles ( 13 )
For All Classical Alleles Show
Allele of kn Class Mutagen Stocks Known lesion kn1 2 -- knEY09641 P-element activity 1 -- knKN1 ethyl methanesulfonate 0 -- knKN2 ethyl methanesulfonate 0 -- knKN3 ethyl methanesulfonate 0 -- knKN4 ethyl methanesulfonate 1 -- knSA1 X ray 1 -- knSA2 γ ray 1 Yes kncol-1 amorph, loss of function ethyl methanesulfonate 2 -- kncol-2 loss of function ethyl methanesulfonate 0 -- kncol-3 loss of function ethyl methanesulfonate 0 -- kncol-85 P-element activity 0 -- knunspecified 0 --
Alleles Carried on Transgenic Constructs ( 8 )
For All Alleles Carried on Transgenic Constructs Show
Allele of kn Class Mutagen Stocks Known lesion kn+m5 in vitro construct | regulatory fusion 0 Yes knGD4730 in vitro construct | RNAi in vitro construct | regulatory fusion 0 Yes knScer\UAS.cMa in vitro construct | regulatory fusion 1 Yes knScer\UAS.cVa in vitro construct | regulatory fusion 0 Yes kna.hs in vitro construct | regulatory fusion 0 Yes kndsRNA.Scer\UAS in vitro construct | regulatory fusion in vitro construct | RNAi 0 Yes knhs.PS in vitro construct | regulatory fusion 0 Yes knt5 in vitro construct | genomic fragment 0 Yes
Aneuploid Aberrations
Useful deficiency	Df(2R)L4   Df(2R)knSA3
Useful duplication	Dp(2;2)SMG45
Disrupted in	Df(2R)BSC429 (Christensen et al., 2008.4.15) Df(2R)knSA3 (Mohler, 1997.8.7) In(2R)knSA1 (Nestoras et al., 1997) T(1;2)knSA2 (Seecoomar et al., 2000)
Not disrupted in	Df(2R)Jp1 (Nestoras et al., 1997) Df(2R)trix (Nestoras et al., 1997)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data reporter construct P{col5-lacZ.C} No P{kn-lacZ.-20} No P{kn-lacZ.1-2330} No P{kn-lacZ.1599-1991} No P{kn-lacZ.224-1426} No P{kn-lacZ.701-1835} No P{kn-lacZ.701-1991.Ci1047} No P{kn-lacZ.701-1991.Ci1341} No P{kn-lacZ.701-1991.Ci1680} No P{kn-lacZ.701-1991.KOmut} No P{kn-lacZ.701-1991.KO} No P{kn-lacZ.701-1991.UBX1KO} No P{kn-lacZ.701-1991.UBX2KO} No P{kn-lacZ.701-1991.UBX3KO} No P{kn-lacZ.701-1991.UBX4KO} No P{kn-lacZ.701-1991.mut} No P{kn-lacZ.701-1991} No P{kn-lacZ.compositeKO} No P{kn-lacZ.composite} No UAS construct P{GD17582} NA P{GD4730} NA P{GD7846} NA P{UAS-col.dsRNA} NA P{UAS-kn.M} NA P{UAS-kn.V} NA characterization construct P{C4-gBF} NA P{col5-cDNA.C} N