• Home
• Tools
  • Tools Overview
  • Query Tools

    
    • QuickSearch
    • QueryBuilder
    • TermLink
    • CytoSearch
    • Interactions Browser
    • ImageBrowse
    • Find A Person
    • Google™ FlyBase
  • Genomic/Map Tools

    
    • BLAST
    • GBrowse
    • CytoSearch
    • Aberrations Maps
    • Chromosome Maps
    • Coordinates Converter
  • Retrieve/Convert

    
    • Batch Download
    • Coordinates Converter
    • ID Converter
  • Data Submission

    
    • Fast-Track Your Paper
    • Submit Personal Comm
    • Add A New Person
    • Update Person Info
  • People

    
    • Find A Person
    • Add A New Person
    • Update Person Info
• Files
  • Files Overview
  • Downloads:
  • Precomputed files
  • Archived data
  • Releases (FTP)
  • Genomes (FTP)
  • AAA data (FTP)
  • Lists:
  • Transposons (Dmel)
  • Transposons (other)
  • Vectors & Constructs
  • Anatomical Terms
  • Map Conversion
• Species
  • Phylogeny
  • Sequenced Species
  • Synteny Table
  • Color Illustrations
  • Abbreviations
• Documents
  • About FlyBase
  • Reference Manual:
  • Sections
  • Contents
  • Nomenclature
  • Release Notes
• Resources
  • All Resources
  • Model Organisms
  • Stock Collections
  • Other links:
  • BDGP
  • DGRC
  • FlyExpress
  • Interactive Fly
  • modENCODE
  • Textpresso for Fly
• News
  • News
  • FlyBase Forum
  • FlyBase Positions
  • Meetings
  • Courses
  • Fly Board
  • White papers
  • Funding
  • bionet.dros
• Help
  • Google™ FlyBase
  • Site Map
  • FAQs
  • FlyBase Guides
  • Video Tutorials
  • Report help
  • New to Flies
  • Pers. comm.
  • Author guidelines
  • Contact FlyBase
• Archives
  • Prior Release
  • Other Archives
  • Coordinate Converter

Gene Dmel\cnc

General Information
Symbol	Dmel\cnc	Species	D. melanogaster
Name	cap-n-collar	Annotation symbol	CG43286
Feature type	protein_coding_gene	FlyBase ID	FBgn0262975
Gene Model Status	Current	Stock availability	25 publicly available
Also Known As	CG17894, CG4566, CG13826
Genomic Location
Chromosome (arm)	3R	Recombination map	3-81.2
Cytogenetic map	94E4-94E7	Sequence location	3R:19,011,302..19,052,430 [-]
Genomic Maps Select View:Gene Models/EvidenceExpression/RegulationMegaViewGene Disruptions, Stocks and Reagents modENCODE 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 cap-n-collar is referred to in FlyBase by the symbol Dmel\cnc (CG43286, FBgn0262975). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: sequence-specific DNA binding transcription factor activity; protein heterodimerization activity. There is experimental evidence for 13 unique biological process terms, many of which group under: biological regulation; cellular component organization or biogenesis; localization; anterior/posterior axis specification; regulation of developmental process; dorsal/ventral axis specification; response to stress; determination of adult lifespan; digestive tract development; regulation of embryonic development. 63 alleles are reported. The phenotypes of these alleles are annotated with: organ system; cephalopharyngeal skeleton; multicellular structure; organ system subdivision; pharyngeal sclerite; acellular anatomical structure; external compound sense organ; embryonic labral segment; embryonic mandibular segment; larval head segment. It has 14 annotated transcripts and 14 annotated polypeptides. Protein features are: Basic-leucine zipper (bZIP) transcription factor; Eukaryotic transcription factor, Skn-1-like, DNA-binding; bZIP transcription factor, bZIP-1. Gene sequence location is 3R:19011302..19052430.
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2012_01	Controlled Vocabulary Terms pharynx development head development positive regulation of transcription from RNA polymerase II promoter Sequence features BKN24936 HFA15601 HFA15289 HFA14676 HFA15600 BKN21690 References Misra et al., 2011, Genes Dev. 25(17): 1796--1806
FB2011_10	Transgenic Constructs P{UAS-cnc.C} P{UAS-cnc.C.RNAi} References Gurunathan et al., 2004, BMC Bioinformatics 5: 202
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 94E4-94E7   Limits computationally determined from genome sequence between P{EP}hhEP3521 and P{PZ}cnc03921; Limits computationally determined from genome sequence between P{PZ}cnc03921 and P{PZ}l(3)0690606906
Experimentally Determined Cytological Location
Cytogenetic map Notes References 94E3-94E7   (determined by in situ hybridisation)   (Spradling et al., 1999) 94E3-94E7   (determined by in situ hybridisation)   (Perrimon et al., 1996) 93E4-93E5   94E3--7   (BDGP Project Members, 1994-1999) 94E3-94E4   (determined by in situ hybridisation)   (Mohler et al., 1991)
Experimentally Determined Recombination Data
Location	3-81.2
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\cnc for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
	Gene merge based on RNA-seq data.
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) cnc-RA FBtr0306747     3477   533 cnc-RB FBtr0306749     5130   805 cnc-RC FBtr0306748     6701   1383 cnc-RD FBtr0306746     3570   533 cnc-RE FBtr0306745     3550   533 cnc-RF FBtr0306744     4073   533 cnc-RG FBtr0306750     3792   533 cnc-RH FBtr0306751     3552   533 cnc-RI FBtr0306752     4747   1133 cnc-RJ FBtr0306753     6785   1383 cnc-RK FBtr0306754     6954   1383 cnc-RL FBtr0306755     5119   1046 cnc-RM FBtr0308226     4734   1133 cnc-RN FBtr0308227     4743   1133
Additional Transcript Data & Comments
Reported size (kB)	6.6, 5.4, 3.3 (northern blot) (McGinnis et al., 1998) 2.722 (longest cDNA) (Mohler et al., 1991)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein cnc-PA   FBpp0297670   56.5   533   9.06       cnc-PB   FBpp0297672   85.2   805   7.66       cnc-PC   FBpp0297671   147.4   1383   5.30       cnc-PD   FBpp0297669   56.5   533   9.06       cnc-PE   FBpp0297668   56.5   533   9.06       cnc-PF   FBpp0297667   56.5   533   9.06       cnc-PG   FBpp0297673   56.5   533   9.06       cnc-PH   FBpp0297674   56.5   533   9.06       cnc-PI   FBpp0297675   121.0   1133   6.35       cnc-PJ   FBpp0297676   147.4   1383   5.30       cnc-PK   FBpp0297677   147.4   1383   5.30       cnc-PL   FBpp0297678   111.6   1046   6.11       cnc-PM   FBpp0300546   121.0   1133   6.35       cnc-PN   FBpp0300547   121.0   1133   6.35
Additional Polypeptide Data & Comments
Reported size (kDa)	1296, 805, 533 (aa) (McGinnis et al., 1998) 533 (aa) (Mohler et al., 1991)
Comments	cnc protein shows the strongest resemblance to the jun subclass of bZIP proteins in the basic binding domain but is very divergent from this class in the leucine-repeat region. (Mohler et al., 1991)
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • bZIP transcription factor, bZIP-1 (IPR011616) Basic-leucine zipper (bZIP) transcription factor (IPR004827) Eukaryotic transcription factor, Skn-1-like, DNA-binding (IPR008917)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA201619   AA392043   AF070062 AAC72896   AF070063 AAC72897   AF070064 AAC72898   AI259806   AI259953   AI293880   AI387817   AI404840   AI532261   AI944811   AQ026326   AQ073076   AQ073861   AW942234   AX201622   AX201623   AY061154 AAL28702   AY070954 AAL48576   BE977755   BE979052   BF489960   BF506049   BI165628   BI166575   BI232454   BI355414   BI373494   BI483469   BI485365   BI611479   BP540931   BP540932   BP548578   BP549836   BP549837   BQ102759   BQ102966   BT024968   BT099672   CA804581   CK657647   CK658906   CO154702   CO178122   CO187318   CO189503   CO190432   CO265411   CO271773   CO272371   CO280014   CO280140   CO282726   CO285465   CO287289   CO294589   CO295642   CO296603   CO308191   CO314357   CO318690   CO318708   CO320308   CO343051   CO343463   CO344251   CZ466274   CZ469011   CZ469059   CZ470641   CZ470642   CZ473972   CZ479585   CZ479613   CZ483013   CZ488373   DN154470   EC060336   EC064169   EC066846   EC069072   EC071575   EC077647   EC080463   EC084902   EC089753   EC090025   EC195526   EC207200   EC207201   EC210277   EC213919   EC215504   EC220600   EC223067   EC224394   EC224534   EC229769   EC233735   EC234942   EC237552   EC239711   EC243646   EC245146   EC245372   EC245480   EC247665   EC253673   EC254952   EC255078   EC257380   EC264667   EL875340   EL875341   EL880444   EL884071   EL884072   EL884186   EV575649   EV586865   EV587255   EV587428   EV587708   EV587784   EV588016   EV589276   EV590009   EV590559   EV591707   G00591   GH748389   GH759560   GH771636   GH773233   GH773351   GH791774   GH810240   GH810881   GH812873   GH818142   GH826355   GH836018   GH859356   GH875264   GH912825   GH931452   M37495 AAB59246
UniProtKB/Swiss-Prot	P20482
UniProtKB/TrEMBL	Q9VCP5
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
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
No Assay Recorded Stage Tissue/Position (including subcellular localization) Reference embryonic stage   mandibular segment   (Mohler et al., 1991) blastoderm stage   organism | 70% egg length   (Mohler et al., 1991) in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage   intercalary segment   (Mohler et al., 1991) embryonic stage | early -- embryonic stage | mid   labral segment   (Mohler et al., 1991) embryonic stage 1 -- 4   organism | ubiquitous   (McGinnis et al., 1998) Comment:reference states 0-2 hr AEL blastoderm stage   organism | 90-100% egg length   (Mohler et al., 1991) Comment:90-98% egg length northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage   embryonic labral segment   (McGinnis et al., 1998) embryonic mandibular segment   (McGinnis et al., 1998)   (McGinnis et al., 1998) embryonic stage 1 -- 4     (McGinnis et al., 1998) Comment:reference states 0-2 hr AEL embryonic stage 5 -- 17     (McGinnis et al., 1998) Comment:reference states >2 hr AEL embryonic stage 14 -- 17   organism | ubiquitous   (McGinnis et al., 1998) embryonic stage 15 -- 17   organism | ubiquitous   (McGinnis et al., 1998)   (McGinnis et al., 1998) Comment:reference states 12-24 hr AEL
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Notes
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage | early   organism | ubiquitous   (McGinnis et al., 1998) embryonic stage 6 -- 17   embryonic mandibular segment   (McGinnis et al., 1998) embryonic labral segment   (McGinnis et al., 1998) embryonic stage 15 -- 17   organism | ubiquitous   (McGinnis et al., 1998)
Additional Descriptive Data
	cnc antiserum detects a low level ubiquitous staining in syncytial embryos. From stage 6-14, staining is localized to the mandibular and labral segments. After stage 14 a low level ubiquitous staining is observed in addition to the strong staining in the mandibular and labral cells. The antibody recognizes all cnc isoforms. (McGinnis et al., 1998) Strong cnc staining is observed in the mandibular and labral segments from stage 6 on. This is presumed to be isoform B since only the mRNA for isoform B is expressed in these cells. (McGinnis et al., 1998)
Marker for
Subcellular Localization
CV Term	nucleus (McGinnis et al., 1998)
Notes
High-Throughput Expression Data
or
See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes. [an error occurred while processing this directive] modENCODE Temporal Expression Data (Graveley et al., 2011) FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
Expression Clusters
External Data & Images
Linkouts
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal cncB.hs lethal (with cncK6) cncVL110 lethal (with cncVL110) cncK6 lethal | embryonic stage | recessive cnc03921 cnc05561 cncVL70 cncVL110 lethal | heat sensitive cncB.hs lethal | recessive cnc03921 cnc05134 semi-lethal | pupal stage, with Scer\GAL4pnr-MD237 cncGD4437 viable cncA.hs cncPL00139 Sterility Allele female sterile cnc03921 fertile cncPL00139 Other Phenotypes Allele oxidative stress response defective, with Scer\GAL4αTub84B.Switch.PK cncdsRNA.Scer\UAS cncScer\UAS.cSa visible, with Scer\GAL4GMR.PF cncScer\UAS.cVa visible, with Scer\GAL4sev.EP cncScer\UAS.cSa Phenotype manifest in Allele abdominal 1 ventral denticle belt | heat sensitive cncB.hs abdominal 2 ventral denticle belt | heat sensitive cncB.hs abdominal 3 ventral denticle belt | heat sensitive cncB.hs abdominal 4 ventral denticle belt | heat sensitive cncB.hs abdominal 5 ventral denticle belt | heat sensitive cncB.hs abdominal 6 ventral denticle belt | heat sensitive cncB.hs abdominal 7 ventral denticle belt | heat sensitive cncB.hs cephalopharyngeal skeleton | larval stage cncVL110 cnc05561 cncEB6 cncVL70 chorion | dorsal | germline clone cnc05561 cnc03921 chorion | maternal effect cncunspecified cirri cncC.hs cirri | ectopic cncVL110 cncC7 cnc2E16 cirri | heat sensitive cncB.hs cirri | larval stage cncVL110 cnc05561 cncEB6 cncVL70 dorsal appendage cnc05561 cnc03921 dorsal bridge cncC.hs dorsal bridge | heat sensitive cncB.hs dorsal pouch | larval stage cncVL110 cnc05561 cncEB6 cncVL70 embryonic/larval pharynx | ectopic, with Scer\GAL469B cncA.Scer\UAS.T:Hsim\VP16 cncScer\UAS.cVa embryonic/larval pharynx | embryonic stage cncVL110 embryonic intercalary segment cncVL110 cnc05561 cncEB6 cncVL70 embryonic labral segment cncVL110 cnc05561 cncEB6 cncVL70 embryonic mandibular segment cncVL110 cnc05561 cncEB6 cncVL70 eye, with Scer\GAL4GMR.PF cncScer\UAS.cVa head cnc03921 hypostomal sclerite | heat sensitive cncB.hs labrum cnc03921 labrum | larval stage cncVL110 cnc05561 cncEB6 cncVL70 larval head, with Scer\GAL469B cncA.Scer\UAS.T:Hsim\VP16 lateral process cncVL110 cncC15 cncdsRNA.B cncC5 cnc2E16 cncC.hs cncJ26 cncC29 cncK22 cncG15 cnc03921 lateral process | anterior | heat sensitive cncB.hs lateral process | larval stage cncVL110 cnc05561 cncEB6 cncVL70 maxillary segment, with Scer\GAL469B cncA.Scer\UAS.T:Hsim\VP16 median tooth cncVL110 cncdsRNA.B cncC5 cncC.hs cncC29 cncK22 cncG15 mouth hooks cncC15 cncC.hs cncJ26 cnc03921 mouth hooks | ectopic cncVL110 cncC7 cnc2E16 cnc03921 mouth hooks | heat sensitive cncB.hs mouth hooks | larval stage cncVL110 cnc05561 cncEB6 cncVL70 mouth hooks | supernumerary cncdsRNA.B cncC5 cncC29 cncK22 cncG15 ommatidium, with Scer\GAL4GMR.PF cncScer\UAS.cVa ommatidium, with Scer\GAL4sev.EP cncScer\UAS.cSa oocyte | germline clone cnc03921 oocyte nucleus | germline clone cnc05561 cnc03921 ovariole | germline clone cnc03921
Classical Alleles ( 46 )
For All Classical Alleles Show
Allele of cnc Class Mutagen Stocks Known lesion cnc03921 P-element activity 1 -- cncc00210 piggyBac transposase 1 -- cncc04133 piggyBac transposase 1 -- cncc06374 piggyBac transposase 1 -- cncd04513 P-element activity 1 -- cncDG04108 P-element activity 1 -- cnce01770 piggyBac transposase 1 -- cnce01792 piggyBac transposase 1 -- cncf00553 piggyBac transposase 1 -- cncf05381 1 -- cncf05746 piggyBac transposase 1 -- cncGS8035 1 Yes cncMB10127 1 -- cncNP0386 1 -- cncNP0916 1 -- cncNP2146 1 -- cncNP2187 1 -- cncPL00139 P-element activity 1 -- cncUM-8235-3 1 -- cnc05561 amorphic allele - genetic evidence P-element activity 0 Yes cncEB6 amorphic allele - genetic evidence gamma ray 0 Yes cncVL110 amorphic allele - genetic evidence P-element activity 0 Yes cncVL70 amorphic allele - genetic evidence P-element activity 0 Yes cnc03871 P-element activity 0 -- cnc05134 P-element activity 0 -- cnc2E16 ethyl methanesulfonate 0 Yes cnc5F8-5 ethyl methanesulfonate 0 -- cnc7G2-10 ethyl methanesulfonate 0 -- cnc8A1-14 ethyl methanesulfonate 0 -- cncc04192 piggyBac transposase 0 -- cncC14 ethyl methanesulfonate 0 -- cncC15 hypomorphic allele - genetic evidence ethyl methanesulfonate 0 -- cncC29 loss of function allele ethyl methanesulfonate 0 Yes cncC5 loss of function allele ethyl methanesulfonate 0 Yes cncC7 ethyl methanesulfonate 0 Yes cncDG05305 P-element activity 0 -- cncEP3258 P-element activity 0 Yes cncEP3633 P-element activity 0 Yes cncG15 loss of function allele ethyl methanesulfonate 0 -- cncgcgt 0 Yes cncJ26 hypomorphic allele - genetic evidence ethyl methanesulfonate 0 Yes cncj5E7 0 -- cncK22 loss of function allele ethyl methanesulfonate 0 -- cncK6 ethyl methanesulfonate 0 Yes cncP2 0 -- cncunspecified 0 --
Alleles Carried on Transgenic Constructs ( 17 )
For All Alleles Carried on Transgenic Constructs Show
Allele of cnc Class Mutagen Stocks Known lesion cncGD4437 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes cncHMS00650 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes cncJF02006 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes cncKK101639 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes cncKK103976 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes cncA.hs in vitro construct - regulatory fusion 0 Yes cncA.Scer\UAS.T:Hsim\VP16 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes cncB.Ala.hs in vitro construct - amino acid replacement in vitro construct - regulatory fusion 0 Yes cncB.hs in vitro construct - regulatory fusion 0 Yes cncC.hs in vitro construct - regulatory fusion 0 Yes cncdsRNA.A in vitro construct - RNAi 0 Yes cncdsRNA.B in vitro construct - RNAi 0 Yes cncdsRNA.C in vitro construct - RNAi 0 Yes cncdsRNA.Scer\UAS in vitro construct - regulatory fusion in vitro construct - RNAi 0 Yes cncGD8127 in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes cncScer\UAS.cSa in vitro construct - regulatory fusion 0 Yes cncScer\UAS.cVa in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3R)BSC56 (Andrade et al., 2004.9.20) Df(3R)BSC619 (Christensen et al., 2008.9.29) Df(3R)BSC803 (Christensen et al., 2009.5.6) Df(3R)EB6 (Mohler et al., 1995) Df(3R)ED6096 (Ryder and Roote, 2004.11.10) Df(3R)ED6103 (Ryder and Roote, 2004.11.10) Df(3R)Exel6274 (Ryder, 2004.4.26) Df(3R)Exel6280 (Ryder, 2004.4.26) Df(3R)P2O (Hales and Fuller, 1997)
Not disrupted in	Df(3R)e-N19 (BDGP Project Members, 1994-1999) Df(3R)hhE23 (BDGP Project Members, 1994-1999, Spradling et al., 1999)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD4437} NA P{KK101639} NA P{TRiP.HMS00650} NA P{TRiP.JF02006} NA P{UAS-cnc.B} NA P{UAS-cnc.C.RNAi} NA P{UAS-cnc.C} NA P{UAS-cnc.T:VP16} NA heat-shock construct P{hs-cnc.A} NA P{hs-cnc.B.Ala} NA P{hs-cnc.B} NA P{hs-cnc.C} NA reporter construct P{cnc-lacZ.+10} No
Insertions
	Type of insertions Name Expression data insertion of enhancer trap P{lacW}cncj5E7 No P{luc-sniffer}4-16 No P{PZ}cnc03871 No P{PZ}cnc03921 No P{PZ}cnc05134 No P{PZ}cnc05561 No insertion of mobile activating element P{EP}cncEP3258 NA P{EP}cncEP3633 NA P{GSV1}EP-J63.2EP-J63.2 NA P{GSV3}cncGS8035 NA P{XP}cncd04513 NA miscellaneous insertions P{RS3}cncUM-8235-3 NA P{SUPor-P}KG00646 NA P{wHy}cncDG04108 NA P{wHy}cncDG05305 NA PBac{PB}cncc00210 NA PBac{PB}cncc04133 NA PBac{PB}cncc04192 NA PBac{PB}cncc06374 NA PBac{RB}cnce01770 NA PBac{RB}cnce01792 NA PBac{WH}cncf00553 NA PBac{WH}cncf05381 NA PBac{WH}cncf05746 NA insertion of enhancer trap binary system Mi{ET1}cncMB10127 No P{GawB}cncNP0386 No P{GawB}cncNP0916 No P{GawB}cncNP2146 No P{GawB}cncNP2187 No PBac{GAL4D,EYFP}cncPL00139 No
Gene Ontology: Function, Process & Cellular Component ( 17 unique terms )
Terms Based on Experimental Evidence ( 16 terms )
Molecular Function
CV term Evidence References
protein heterodimerization activity inferred from physical interaction with maf-S (Veraksa et al., 2000) contributes_to sequence-specific DNA binding transcription factor activity inferred from direct assay (Veraksa et al., 2000)
Biological Process
CV term Evidence References
bicoid mRNA localization inferred from mutant phenotype (Martin et al., 2003) blastoderm segmentation inferred from mutant phenotype (Veraksa et al., 2000) determination of adult lifespan inferred from mutant phenotype (Sykiotis and Bohmann, 2008) head development inferred from mutant phenotype (Veraksa et al., 2000) maintenance of oocyte nucleus location involved in oocyte dorsal/ventral axis specification inferred from mutant phenotype (Guichet et al., 2001, Guichet et al., 2002) oocyte dorsal/ventral axis specification inferred from mutant phenotype (Guichet et al., 2001) oocyte microtubule cytoskeleton polarization inferred from mutant phenotype (Guichet et al., 2001) pharynx development inferred from mutant phenotype (Veraksa et al., 2000) pole plasm oskar mRNA localization inferred from mutant phenotype (Martin et al., 2003) positive regulation of transcription from RNA polymerase II promoter inferred from direct assay (Veraksa et al., 2000) regulation of bicoid mRNA localization inferred from mutant phenotype (Guichet et al., 2001) regulation of pole plasm oskar mRNA localization inferred from mutant phenotype (Guichet et al., 2001) response to oxidative stress inferred from mutant phenotype (Sykiotis and Bohmann, 2008)
Cellular Component
CV term Evidence References
nucleus inferred from direct assay (Veraksa et al., 2000, Guichet et al., 2001)
Terms Based on Predictions or Assertions ( 4 terms )
Molecular Function
CV term Evidence References
protein heterodimerization activity inferred from sequence or structural similarity (Fassler et al., 2002) sequence-specific DNA binding inferred from electronic annotation with InterPro:IPR004827, InterPro:IPR011616 (FlyBase Curators et al., 2004-) sequence-specific DNA binding transcription factor activity traceable author statement (Guichet et al., 2001)
Biological Process ( 0 terms)
Cellular Component
CV term Evidence References
nucleus non-traceable author statement (Swiss-Prot Project Members, 1991.2.1)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Protein-protein
Interacting group Assay References
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions cnc allele Gene References cncA.hs Dfd (McGinnis et al., 1998) cncB.hs Dfd (McGinnis et al., 1998, Veraksa et al., 2000) hth (Veraksa et al., 2000) cncVL110 Dfd (Harding et al., 1995) unspecified D1 (Sun et al., 2006) Dfd (Gellon et al., 1997) lap (Sun et al., 2006)
External Data
Linkouts	DroID - A comprehensive database of gene and protein interactions. • FBgn0262975
Orthologs
Genome-wide drosophilid orthologs	Dana\GF18024 Dana\GF18025 Dere\GG12452 Dere\GG12453 Dgri\GH21427 Dgri\GH21438 Dmoj\GI10507 Dmoj\GI10508 Dper\GL23040 Dper\GL23043 Dpse\GA12552 Dpse\GA14711 Dsec\GM23583 Dsim\GD18398 Dsim\fzo Dvir\GJ23188 Dvir\GJ23189 Dwil\GK13230 Dwil\GK13231 Dyak\GE23975 Dyak\GE23976
Curated drosophilid orthologs	Dpse\GA12552   Dpse\GA14711
Linkouts
Stocks & Reagents
Stocks Listed in FlyBase ( 25 )
Harvard	- P{XP}cncd04513 - PBac{PB}cncc00210 - PBac{PB}cncc04133 - PBac{PB}cncc06374 - PBac{RB}cnce01770 - PBac{RB}cnce01792 - PBac{WH}cncf00553 - PBac{WH}cncf05381 - PBac{WH}cncf05746
VDRC	v101235 P{KK103976}VIE-260B v108127 P{KK101639}VIE-260B v37673 w1118; P{GD4437}v37673
	More stocks available...
Genomic Clones ( 3 )
	BACR01E13 BACR03N12 BACR17P04 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 121 )
	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	IP15234 LD12407 RE05559 SD04321
Other clones	DPiM_RE05559
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	AT08413 AT26211 GH18478 GH24678 GM30690 LD04714 LP03307 LP03485 LP07130 LP16195 LP24116 RE06745 RE28523 RE60795 RE66371 RE68678 RH17728 SD03690
Other clones	2190 8203 33549 39110 39297 42851 43800 45342 56632 61635 75336 77733 79164 81317 105972 119855 153541 164567 172739 172751 178445 214213.2 214343.8 214417.72 214513.10 274804 524026 bs05g02 bs68f09 bs86b02 CK01.32D.H9 CK01.33C.G6 CK01.54D.F5 CK01.59B.F10 CK01.69B.F10 CK01.168A.G12 Dmel_dig_005694_0701_1852 Dmel_neb_006239_0189_0373 Dmel_neb_006431_0128_2664 Dmel_neb_009700_0363_2405 Dmel_neb_010542_0091_0443 Dmel_neb_010956_0129_3450 Dmel_neb_011977_0381_1853 Dmel_neb_012267_0150_2361 Dmel_neb_013166_0069_2857 Dmel_neb_014667_0378_2597 Dmel_neb_015775_0324_2893 EK028129 EK029945 EK044423 EK048153 EK055355 EK065441 EK104545 EK106926 EK142607 EK152229 EK152720 EK161046 EK169038 EK207244 EK211147 EK214412 EK235916 EK256946 EK273433 EK273457 EK283661 EN04628 EP16018 EP16825 EP18931 ESG0114b.B21_C07 FGA009B03 FGH129C07 FGM103G07 IP10270 IP15334 IP15434 IP15534 RP003019459 RP003048652 RP003093806 RP003097463 RP003101608 RP003106783 RP003137853 RP003202041 RP003202599 RP003237049 RP003300131 RP003323186 RP003329894 RP003447062 RP003472545 RP003503175 UUGC0143 UUGC0360
RNAi & Array Information
Linkouts	GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 42743 50063
Antibody Information
	polyclonal (McGinnis et al., 1998)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: CG13826 BcDNA:RE05559 (FlyBase, 1996-) Source for merge of: cnc anon-WO0153538.6 anon-WO0153538.7 (FlyBase, 1996-) Source for merge of: cnc CG13826 (FlyBase Genome Annotators, 2011) Source for merge of: cnc CG17894 (FlyBase, 1996-)
Additional comments	Annotations CG17894 and CG13826 merged as CG43286 in release 5.35 of the genome annotation. (FlyBase Genome Annotators, 2011) Annotations CG4566, CG4578 and CG17894 merged as CG17894 (which corresponds to cnc) in release 3 of the genome annotation. (FlyBase Genome Annotators, 2002-2003) Source for merge of cnc anon-WO0153538.6 anon-WO0153538.7 was sequence comparison (date:051113). (FlyBase, 1996-) Source for merge of cnc CG17894 was a shared cDNA (date:010720). (FlyBase, 1996-) Source for merge of CG13826 BcDNA:RE05559 was a shared cDNA (date:030728). (FlyBase, 1996-)
Other Comments
	Identification: in a germline clone screen for mutants that are defective in localisation of an Avic\GFP-stau marker in living oocytes. 3 alleles of cnc have been identified in the screen. (Martin et al., 2003) cnc has diverse functions in anterior-posterior patterning in the embryonic head. (Veraksa et al., 2000) Identification: Enhancer trap expression pattern survey for loci expressed in the ring gland. (Harvie et al., 1998) The autosomal "FLP-DFS" technique (using the P{ovoD1-18} P{FRT(whs)} P{hsFLP} chromosomes) has been used to identify the specific maternal effect phenotype for the zygotic lethal mutation. cnc is required for germ cell viability or early oogenesis. (Perrimon et al., 1996) cnc interacts with Dfd, hh and shd. Null mutations delete both labral and mandibular structures. (Gellon et al., 1995) Mutations of cnc interact with Dfd to reduce the viability of the Dfd3/Dfd13 combination. (Harding et al., 1995) cnc functions in combination with Dfd to specify mandibular development and is also required for labral segment identity. fkh and cnc homeotic genes are required for the maintenance of segment polarity gene expression in the foregut. cnc is required for the continued expression of the dorsal pharyngeal domains of wg and hh expression past stage 10 and the labral domain of wg expression past the middle stage 11. (Mohler et al., 1995) In its anterior domain (labral primordia) cnc is activated by bcd and tor maternal pathways, but activation in intercalary and mandibular primordia requires zygotic gap gene products, activation by btd and repression by oc (anteriorly) or sna (ventrally). (Mohler, 1993) Expression pattern and DNA sequence data suggest a role of cnc in cephalic patterning during embryogenesis. (Mohler et al., 1991) In situ hybridization reveals cnc transcripts are localised to the mandibular segment and the hypopharyngeal and labial primordia, first detectable in late blastoderm stages. Sequence analysis of cnc gene product reveals similarities to transcription factors of the leucine zipper (bZIP) class. (Mohler et al., 1991)
External Crossreferences & Linkouts
Sequence Crossreferences
	DDBJ / EMBL / GenBank • AA201619 AA392043 AAB59246 AAC72896 AAC72897 AAC72898 AAF56108 AAF56109 AAF56111 AAF56112 AAL28702 AAL48576 AAN13930 AAN13931 AAN13932 AAN13933 AF070062 AF070063 AF070064 AI293880 AI944811 AQ026326 AQ073076 AQ073861 AW942234 AX201622 AX201623 AY061154 AY070954 BI165628 CZ466274 CZ469011 CZ469059 CZ470641 CZ470642 CZ473972 CZ479585 CZ479613 CZ483013 CZ488373 G00591 M37495 Entrez Gene - A searchable database of RefSeq genes. • 42743 50063 UniProtKB/Swiss-Prot • P20482 UniProtKB/TrEMBL • Q9VCP5
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • bZIP transcription factor, bZIP-1 (IPR011616) Basic-leucine zipper (bZIP) transcription factor (IPR004827) Eukaryotic transcription factor, Skn-1-like, DNA-binding (IPR008917)
Linkouts
	DroID - A comprehensive database of gene and protein interactions. • FBgn0262975 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 42743 50063
Synonyms & Secondary IDs ( 21 )
Reported As
Symbol Synonym	5134 (Harvie et al., 1998) anon-WO0153538.6   anon-WO0153538.7   BcDNA:RE05559   CG4566 (Luschnig, 2003.12.17, Wang et al., 2004) CG4578 (Ruden, 2002.1.7, ) CG13826 (Nechaev et al., 2010, Keleman et al., 2009.8.5) CG17894 (Laviolette et al., 2005, Mohit et al., 2006, Molnar et al., 2006, Perkins et al., 1.15.2009, Keleman et al., 2009.8.5, Ni et al., 2010.12.1) CG43286 (FlyBase Genome Annotators, 2011) cnc (Gurunathan et al., 2004, Bantignies et al., 2011, Laviolette et al., 2005, Garcia-Lopez et al., 2008, Segal et al., 2008, Molnar et al., 2006, Geng and MacDonald, 2007, Christensen et al., 2008.9.29, Shravage et al., 2007, Sykiotis and Bohmann, 2008, Economou and Telford, 2009, Christensen et al., 2009.5.6, Löhr et al., 2009, Platts et al., 2009, Mourikis et al., 2010, Zsindely et al., 2009, Hazelett et al., 2009, The modENCODE Consortium, 2010, The modENCODE Consortium, 2010) Cnc (Veraksa et al., 2000) CNC (Mohler, 1993.6.22) CNC_DROME (Bornberg-Bauer et al., 1998) l(3)03921 (Perrimon et al., 1996, ) l(3)j5E7 (Spradling et al., 1999)
Name Synonym	Cap 'n' collar (Veraksa et al., 2000, Veraksa et al., 2000) cap'n'collar (Seecoomar et al., 2000, Shravage et al., 2007) cap 'n' collar (Gellon et al., 1995) cap "n" collar (Economou and Telford, 2009) cap and collar (Dubois and Vincent, 2001, Zsindely et al., 2009) cap-n-collar (Garcia-Lopez et al., 2008, Coiffier et al., 2008, Löhr et al., 2009)
Secondary FlyBase IDs
	FBgn0000338 FBgn0010824 FBgn0039062 FBgn0039063 FBgn0040590 FBgn0045881 FBgn0045892 FBgn0047182
References ( 107 )
Generate a list of	All references relating to this gene ( 107 )
List References by type	Research paper  ( 53 ) Supplementary material  ( 5 ) Review  ( 4 ) Personal communication to FlyBase  ( 19 ) Abstract  ( 11 ) FlyBase analysis  ( 5 ) DNA/RNA sequence record  ( 1 ) Computer file  ( 4 ) Protein sequence record  ( 1 ) Automatic genome annotation  ( 1 ) Patent  ( 1 ) Curated genome annotation  ( 2 )
Recent research papers ( 4 )
	Bantignies et al., 2011, Cell 144(2): 214--226 Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila. [FBrf0212775] Misra et al., 2011, Genes Dev. 25(17): 1796--1806 Transcriptional regulation of xenobiotic detoxification in Drosophila. [FBrf0215251] Mourikis et al., 2010, BMC Dev. Biol. 10: 107 Modifiers of notch transcriptional activity identified by genome-wide RNAi. [FBrf0212287] Nechaev et al., 2010, Science 327(5963): 335--338 Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. [FBrf0209722] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2010 Show reviews ...