A Database of Drosophila Genes & Genomes

FB2008_07, released August 8, 2008
 

Gene Dmel\ct

General Information
SymbolDmel\ctSpeciesD. melanogaster
NamecutAnnotation symbolCG11387
Feature typeprotein_coding_geneFlyBase IDFBgn0004198
Created / Updated2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)XRecombination map1-20.0
Cytogenetic map7B4-7B6Sequence locationX:7,503,181..7,570,056 [+]
Map ( GBrowse ) detailed view
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Automatically generated summary

See sections below for more information
The gene cut is referred to in FlyBase by the symbol ct (CG11387, FBgn0004198). It has the cytological map location 7B4-7B6. Its sequence location is X:7503181..7570056. Its molecular function is described as: DNA binding; specific RNA polymerase II transcription factor activity; sequence-specific DNA binding; transcription factor activity. It is involved in the biological processes described with 21 unique terms, many of which group under: anatomical structure development; organ morphogenesis; gamete generation; ovarian follicle cell development; antennal development; sensory organ development; open tracheal system development; regulation of biological process; sexual reproduction; immune response; cell cycle; regulation of metabolic process; sensory perception of mechanical stimulus; negative regulation of Notch signaling pathway. 319 alleles are reported. The phenotypes of these alleles are annotated with 57 unique terms, many of which group under: peripheral nervous system; adult segment; nervous system; adult mesothoracic segment; spiracle; organ system; spiracular plate; appendage segment; germarium; larval abdominal segment 5; dorsal thoracic disc; antennal segment. It has 3 annotated transcripts and 3 annotated polypeptides.

External Summaries
hide Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage
ct: cut
ct mutations fall into three nonoverlapping phenotypic classes: kinked femur, cut wings, and lethal. Kinked- femur mutants are small with slightly dark, dull, red eye color; femurs kinked; wings seldom expand following eclosion, or when they do expand they are opaque and abnormal in shape; flies seem unable to move normally and die on the food soon after eclosion. Cut-wing mutants variably affect wing shape and head capsule development; phenotypic effects include incised wing margins with the tips usually cut to points, missing or ventrally displaced vibrissae, deformed antennae, e.g., flattened and embedded with aristae concave forward, smaller kidney-shaped eyes, warped abdominal bands, and fine bristles. Most lethal alleles survive as clones of homozygous epidermal cells (Demerec). Developmental study of ct6 by Waddington [1939, Proc. Nat. Acad. Sci. USA 25: 299-308; 1940, J. Genet. 41: 75-139 (fig.)] shows wing bud narrower than wild type as early as just after eversion of wing in early pupa. Cell death observed in prepupal wing bud (D. Fristrom, 1969, Mol. Gen. Genet. 103: 363-79). Clones of ct6 cells in internal areas of wing blade normal in size; marginal clones much reduced in size indicating cell death. Homozygous clones in either dorsal or ventral membrane must reach margin in order to produce incision, 100/127 marginal clones unassociated with gaps; when gaps are produced, they affect both wing surfaces even though clone confined to a single surface. Both dorsal and ventral chaetal elements at the edges of such gaps may show the markers of such clones (Santamaria and Garc'a-Bellido, 1975, Wilhelm Roux's Arch. Entwicklungsmech. Org. 178: 233-45). Lethal alleles fall into three groups, based on their complementation characteristics: cutless, group I, and group II. Lethal alleles ctC145, ctJA124, and ctl49 exhibit polyphasic lethality from late embryo to pharate adult (Johnson and Judd, 1979). Lethal embryos characterized by posterior defects in spiracles; no Keilin's organs, and abnormal maxillary complex (Wieschaus, Nusslein-Volhard, and Jurgens, 1984, Wilhelm Roux's Arch. Dev. Biol. 193: 296-307). Group II and to a slightly lesser degree group I lethals fail to differentiate external sensory neurons in the peripheral nervous system; the presumptive external sensory neurons of the embryonic peripheral nervous system and their support cells are transformed into chordotonal neurons with their support cells; the transformed organs are chordotonal both in morphology and antigenic specificity. Same effect seen in the adult sensory organs in mosaics; embryonic effect differs from that seen in adults in that embryos lack peripheral sensory structures, e.g., Keilin's organs, whereas such structures persist, though reduced in size, in adult tissue. The numbers and positions of peripheral neurons is normal. CNS structure and function appear normal. No discernable effect of absence of ct function in the maternal germ line. Effect of ct mutations on PNS differentiation cell autonomous. [Bodmer, Barbel, Sheperd, Jack, Jan, and Jan, 1987, Cell 51: 293-307 (fig.).] Antibodies to ct protein specifically bind to nuclei of presumptive external sensory organ cells including those of the antennamaxillary organ and external sensory organs in spiracles, but not to nuclei of chordotonal organs; antibody staining also seen in some neurons with multiple dendritic arborizations and in cells lining the Malpighian tubules (Blochlinger, Bodmer, Jack, Jan, and Jan, 1988, Nature 333: 629-35). Kinked-femur, cut-wing, and cutless alleles are mutually complementing: group I lethals complement kinked-femur but not cut-wing alleles; and group II lethals are noncomplementing; all combinations of lethal alleles are lethal. The different phenotypic classes of alleles occupy discrete and separate regions of the complex, with the order from left to right being, kinked femur, cut wing, group I lethals, and group II lethals; cutless alleles have not been mapped. Kinked femur, cut, and group-I-lethal mutations are associated with chromosome aberrations or insertions of transposable elements, whereas group II lethals appear to be point mutations. ct6, ct68E (= ct67s?), ct78a, and ctK suppressed by su(Hw)2; dvr2 enhances ct6 and inhibits its complete suppression by su(Hw)2; su(Hw)2/+ shows slight dominant suppression of wing phenotype of ctK (Lee, 1973, Aust. J. Biol. Sci. 26: 903-09). ct6 and ctK strongly enhanced by su(s); su(s) ctK lethal (Johnson) but rescued by su(Hw)2/+ (Craymer). ct6 the most commonly used allele.
           
                                                               ct
kf2   ctnct6                           ctK                lethals
_________________________________________________________________

|       | |                             |                       |
|  -0.04- |           -0.16-            |     - ~0.07-          |
         Genetic fine structure map of the cut locus

           
ct71g
ctJC20
ctk
Classified as a group-I lethal because homozygotes show reduced viability, and only 10% of fewer heterozygotes with other lethal alleles survive; survivors have weakly cut wings, as well as fine bristles, and enlarged and deformed humeral callus, not seen in other cut-wing mutants.
ctcl: cut-cutless
Acts as a lethal allele in combination with deficiencies for ct; phenotype normal in combination with viable ct alleles. Homozygotes have reduced viability and show thoracic protuberances (Schalet). Heterozygotes of ctcl with lethal alleles of ct die or eclose in small numbers; an exception is ctcl/ctHA46, which exhibits normal survival.
ctlS1 (A. Schalet)
Lethal; a member of cut Lethal II group, maps proximal to ctC145 (Jack, 1985). Not suppressed by su(Hw)2 (Schalet). ctlS1/+ males, frequently show thoracic protuberances (Schalet).
ctlS2 (A. Schalet)
Almost complete lethal; survival less than 1%. Not suppressed by su(Hw)2; cut-cutless type of mutant in that ctlS2 fails to complement lethal alleles, e.g. ctlS1, but complements kf2, ct6 and ctS. Rare surviving males and females are fertile with normal wings, but usually show thoracic protuberances in the region of the presutural and notoplural bristles as are also seen in heterozygotes of ctlS1, Df(1)ctJ4 or Df(1)ctJ6.
kf2
hide Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
7B4-7B6  
Limits computationally determined from genome sequence between P{EP}CBPEP1643&P{EP}EP1523EP1523 and P{EP}CHES-1-likeEP1453  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
7B1-7B2
7B3-7B4
(determined by in situ hybridisation)  
7B-7B
(determined by in situ hybridisation)  
7B1-7B2
(determined by in situ hybridisation)  
7B3-7B3
(determined by in situ hybridisation)  
7B-7B
(determined by in situ hybridisation)  
7B1-7B4
(determined by in situ hybridisation)  
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
The interval between ct and cm or ct and sn is that between ct6 and either cm or sn. ctkf-2 (the most distal locus in this study) maps 0.04 units to the left of ct6. ctn maps 0.007 units to the left of ct6, and ctK maps 0.16 units to the right of ct6. The lethal ct alleles used in this study map as a cluster approximately 0.07 units to the right of ctK.
ct14-95-1D and ct20-135 map to the right of ct6.
Molecular Map Data
Gene Order (in direction of increasing cytology)
References
Gene Order (overall orientation not stated)
References
hide Gene Model & Products
Please see the GBrowse view of Dmel\ct for information on other features
detailed view FBtr0114613 FBtr0071068 FBtr0071069 FBpp0071026 FBpp0113105 FBpp0071027 FBti0055426
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
FBtr0071068
  8202
  2175
FBtr0071069
  2533
  257
FBtr0114613
 
  8826
  2383
Additional Transcript Data & Comments
Reported size (kB)
8.2 (compiled cDNA)
Comments
Fragments of the 8.2 kb sequence hybridize to at least two transcripts of 8.5 and 9.5 kb on Northern blots of early and late embryos. A 2175 amino acid protein is predicted from the 8.2 kb sequence.
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kD)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
ct-PA  
FBpp0071026  
233.6  
2175  
5.31  
ct-PB  
FBpp0071027  
27.3  
257  
3.81  
ct-PC  
FBpp0113105  
256.6  
2383  
5.17  
 
 
Additional Polypeptide Data & Comments
Reported size (kD)
2175 (aa); 240 (kD predicted)
320, 280 (kD observed)
Comments
g1345461 contains only the homeodomain.
When the complete ct coding sequence is expressed under the control of a heat shock promoter, 320 kD and 280 kD bands are observed on a Western blot. The same two protein sizes are detected in Western blots of wild type embryos.
ct protein positively regulates its own expression.
External Data
Linkouts
PANTHER - Protein classification by function, families, and pathways
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
TRANSFAC - Eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles
  • T02004
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
 
 
 
 
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
Maps to
Does NOT map to
Identified with
hide 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
protein binding site
ct-protein_bind-1
X:7,424,494..7,424,520
bound_moiety=sd-XP
evidence=experimental
protein binding site
ct-protein_bind-2
X:7,424,594..7,424,610
bound_moiety=sd-XP
evidence=experimental
protein binding site
ct-protein_bind-3
X:7,424,390..7,424,403
bound_moiety=sd-XP
evidence=experimental
protein binding site
ct-protein_bind-4
X:7,424,473..7,424,487
bound_moiety=sd-XP
evidence=experimental
protein binding site
ct-protein_bind-5
X:7,424,692..7,424,701
bound_moiety=sd-XP
evidence=experimental
protein binding site
ct-protein_bind-6
X:7,424,821..7,424,843
bound_moiety=sd-XP
evidence=experimental
protein binding site
ct-protein_bind-7
X:7,424,422..7,424,433
bound_moiety=sd-XP
evidence=experimental
hide External Data
Linkouts
Crossreferences
hide Expression Data
FlyBase-Curated Data
Transcript and
Protein data
Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
hide Summary of Transcript Expression
Stage
Tissue/Position
Reference
 embryonic stage | >5-6 hr
 embryonic/larval posterior spiracle | surrounding
 pupal stage
 pupal stage
 pupal stage
 embryonic stage | >5-6 hr
 embryonic/larval anterior spiracle | surrounding
(