• Home
• Tools
  • BLAST
  • GBrowse
  • QueryBuilder
  • TermLink
  • ImageBrowse
  • Interactions Browser
  • Apollo
  • CytoSearch
  • QuickSearch
  • Batch Download
  • Coordinate Converter
  • Google™ FlyBase
  • Find A Person
  • Update An Address
  • Add A New Person
• Files
  • Downloads:
  • Precomputed files
  • Archived data
  • Releases FTP
  • Genomes FTP
  • Lists:
  • Transposons (Dmel)
  • Transposons (other)
  • Vectors & Constructs
  • Anatomical Terms
  • Map Conversion
• Species
  • Phylogeny
  • Synteny Table
  • Drosophilidae
  • Abbreviations
• Documents
  • About FlyBase
  • Reference Manual:
  • Sections
  • Contents
  • Nomenclature
  • Release Notes
• Resources
  • All resources
  • Interactive Fly
  • Textpresso for Fly
  • AAA site
  • BDGP
  • DHGP
  • DGRC
  • Model Organisms
  • Stock Collections:
  • Bloomington
  • DrosDel
  • Ehime
  • Exelixis (Harvard)
  • GDP (Baylor)
  • Kyoto
  • NIG-Fly
  • Szeged
  • Tucson
  • VDRC
• News
  • News
  • FlyBase Forum
  • FlyBase Positions
  • Meetings
  • Courses
  • Fly Board
  • White papers
  • Funding
  • bionet.dros
• Help
  • Google™ FlyBase
  • Site Map
  • FAQs
  • Report help
  • New to Flies
  • Pers. comm.
  • Author guidelines
  • Known Problems
  • Contact FlyBase
• Archives
  • Prior Home Page
  • R4.3 BLAST
  • R4.3 GBrowse
  • Older Archives

Gene Dmel\car

General Information
Symbol	Dmel\car	Species	D. melanogaster
Name	carnation	Annotation symbol	CG12230
Feature type	protein_coding_gene	FlyBase ID	FBgn0000257
Created / Updated	2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)	X	Recombination map	1-62.5
Cytogenetic map	18D1-18D1	Sequence location	X:19,460,052..19,463,440 [+]
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 carnation is referred to in FlyBase by the symbol car (CG12230, FBgn0000257). It has the cytological map location 18D1. Its sequence location is X:19460052..19463440. Its molecular function is described as: protein binding; SNARE binding. It is involved in the biological processes described with 12 unique terms, many of which group under: transport; organelle organization and biogenesis; vacuolar transport; cellular localization; eye pigmentation; compound eye pigmentation; determination of adult life span; biopolymer modification; cellular pigmentation; ocellus pigmentation; exocytosis; endosome organization and biogenesis. 9 alleles are reported. The phenotypes of these alleles are annotated with: late endosome; eye; pigment cell; Malpighian tubule; larval brain. It has 2 annotated transcripts and 2 annotated polypeptides.
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	car: carnation Eye color dark ruby. Body shape and proportions seem rounded. With st, eye color is yellow-brown; with bw, brownish yellow to brown (Mainx, 1938, Z. Indukt. Abstamm. Vererbungsl. 75: 256-76). Malpighian tubes pale yellow in mature larva (Beadle, 1937, Genetics 22: 587-611) but hard to distinguish from wild type before third instar. Eye color autonomous in transplant into wild-type host (Beadle and Ephrussi, 1936, Genetics 21: 230). car dor is pupal lethal and shows reduced recovery in gynandromorphs with male parts car dor (Nash, 1971, DIS 47: 73). car lt also lethal, dies as larva when mother car;lt/+ or car/+;lt and as pupa when mother car/+;lt/+ (Nickla, 1977, Nature 268: 638-39); lethal focus domineering; fate maps to ventral nervous system (Nickla, Lilly, and McCarthy, 1980, Experientia 36: 402-05). Brain histology abnormal [McCarthy and Nickla, 1980, Experientia 36: 1361-63 (fig.)].
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 18D1-18D1   Limits computationally determined from genome sequence between P{EP}EP1526&P{EP}PfrxEP1150 and P{EP}Tao-1EP1455
Experimentally Determined Cytological Location
Cytogenetic map Notes References 18D1-18D4 (determined by in situ hybridisation)   (Peter et al., 2002) 18D1-18D4 (determined by in situ hybridisation)   (Schaefer et al., 1999.12.2) 18D1-18D2   (Lindsley and Grell, 1968)
Experimentally Determined Recombination Data
Location	1-62.5
Left of (cM)	sol (Fischbach and Lyly-Hunerberg, 1983) l(1)adl13 l(1)adl15 l(1)adl14 (Homyk et al., 1986)
Right of (cM)	l(1)adl8 l(1)adl9 l(1)adl7 l(1)adl6 l(1)adl10 l(1)adl12 l(1)adl11 l(1)adl3 (Homyk et al., 1986)
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\car for information on other features
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) car-RA FBtr0074728  NM_078686   3086   617 car-RB FBtr0074727  NM_167664   3179   617
Additional Transcript Data & Comments
Reported size (kB)	3.022 (longest cDNA) (Sevrioukov et al., 1999)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein car-PA   FBpp0074497   68.8   617   6.74     NP_523410   AAF48972 car-PB   FBpp0074496   68.8   617   6.74     NP_728266   AAN09503
Additional Polypeptide Data & Comments
Reported size (kD)	617 (aa) (Sevrioukov et al., 1999)
Comments
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0000257
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Sec1-like protein (IPR001619)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA264748   AA817218   AA940832   AE003512 AAF48972   AE003512 AAN09503   AF133260 AAD38513   AI258414   AI389000   AI514335   AI519211   AJ426996   AW942637   AY069498 AAL39643   BF490882   BF492272   BI235432   BI236587   BI483836   CL526132   CO154770   CO155380   CO157081   CO278201   CO289355   CO299898   CO304833   CO345293   EC070276   EC218019   EC233134   EC254010   EC261016   EC263864
UniProtKB/Swiss-Prot	Q9Y1I2
UniProtKB/TrEMBL
Maps to	DS00611 (Sevrioukov et al., 1999)
Does NOT map to
Identified with	LD08438 (Sevrioukov et al., 1999) LD22396 (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 point mutation car[1]-1 X:19,460,450..19,460,450 comment=One of two amino acid substitutions observed in car[1] mutant. Site of nucleotide substitution in mutant inferred by FlyBase based on reported amino acid change. evidence=experimental pr_change=L26V|car-PA,L26V|car-PB reported_pr_change=L26V na_change=C19460450G (Sevrioukov et al., 1999) point mutation car[1]-2 X:19,461,120..19,461,120 comment=One of two amino acid substitutions observed in car[1] mutant. Site of nucleotide substitution in mutant inferred by FlyBase based on reported amino acid change. evidence=experimental pr_change=G249V|car-PA,G249V|car-PB reported_pr_change=G249V na_change=G19461120T (Sevrioukov et al., 1999)
External Data
Linkouts	DEDB - Drosophila exon database: splicing graphs • 3378
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
Marker for
Subcellular Localization
CV Term
Summary of Polypeptide Expression
Stage Tissue/Position Reference
Marker for
Subcellular Localization
CV Term
Microarray Data
	Developmental timecourse, Costello et al., 2008 (Original data from Arbeitman et al., 2002) AI389000
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0000257 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0000257 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0000257 BDGP expression data • Show all BDGP original images, annotations and embryonic microarray data for car FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for car Stage(s) 4-6 Stage(s) 7-8 Stage(s) 9-10 Stage(s) 11-12 Stage(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele viable car1 carEY09656 semi-lethal | recessive carG0447 Other Phenotypes Allele wild-type carGMR.PS visible | recessive car1 car26-48 car2 eye color defective car1 car26-48 car2 carunspecified short lived | male car1 Sterility Allele fertile carEY09656 Phenotype manifest in Allele late endosome car1 eye car1 pigment cell car1 car2 car26-48 carunspecified Malpighian tubule car1 larval brain car1
Classical Alleles ( 7 )
For All Classical Alleles Show
Allele of car Class Mutagen Stocks Known lesion car1 X ray 59 Yes car26-48 sulfur mustard 0 -- car2 0 -- carEY09656 P-element activity 1 -- carG0447 P-element activity 1 -- carunspecified 0 -- carΔ146 loss of function 0 --
Alleles Carried on Transgenic Constructs ( 2 )
For All Alleles Carried on Transgenic Constructs Show
Allele of car Class Mutagen Stocks Known lesion carGD1397 in vitro construct | RNAi in vitro construct | regulatory fusion 2 Yes carGMR.PS in vitro construct | regulatory fusion 0 Yes
Aneuploid Aberrations
Useful deficiency	Df(1)S4010
Useful duplication	Dp(1;1)BSTAG
Disrupted in	Df(1)268 (Patterson, 1932) Df(1)BSC275 (Christensen and Cook, 2007.3.22) In(1)ClLbbDfR   In(1)y4Lsc4R   In(1)y4Lsc8R   Tp(1;2)26 (Pontecorvo, 1942)
Duplicated in	Dp(1;f)100 (Morgan, 1938) Dp(1;f)3 (Schalet and Finnerty, 1968) Dp(1;f)52 (Schalet and Finnerty, 1968) In(1)bbDfLClR   In(1)bbDfLy4R   In(1)sc4Ly4R   In(1)sc8Ly4R   In(1)y3PLsc9R
Not disrupted in	Df(1)244 (Patterson, 1932) Df(1)267 (Patterson, 1932) Df(1)274 (Patterson, 1932) Df(1)D43L1 (Schalet and Finnerty, 1968) Df(1)DCB1-35c (Schalet and Finnerty, 1968) Df(1)JA27 (Craymer and Roy, 1980) Df(1)O4 (Oliver, 1937) Df(1)mal10 (Schalet and Finnerty, 1968) Df(1)mal13 (Schalet and Finnerty, 1968) Df(1)mal6 (Schalet and Finnerty, 1968) Df(1)mal8 (Schalet and Finnerty, 1968) In(1)ClLy4R
Not duplicated in	Dp(1;Y)mal+   Dp(1;f)65 (Gethmann, 1967) Dp(1;f)65XC2 (Gethmann, 1967) Dp(1;f)sc7.2   Ts(1Rt;3Lt)102
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD1397} NA characterization construct P{GMR-car.S} NA
Insertions
	Type of insertions Name Expression data insertion of enhancer trap P{lacW}carG0447 No P{lacW}l(1)G0041G0041 No insertion of mobile activating element P{EPgy2}carEY09656 NA
Related Comments
	Please look at the allele reports for the complete phenotype data Lesions in car reduce eye and ocelli pigmentation and cause excretion of pigment from the tubules. (Tearle, 1991)
Gene Ontology: Function, Process & Cellular Component ( 17 )
Molecular Function
CV term Evidence References
SNARE binding inferred from sequence or structural similarity (Littleton, 2000)
protein binding inferred from physical interaction with FLYBASE:dor; FB:FBgn0000482 (Sevrioukov et al., 1999)
Biological Process
CV term Evidence References
compound eye pigmentation traceable author statement (Toonen and Verhage, 2003) inferred from mutant phenotype (Falcon-Perez et al., 2007)
determination of adult life span inferred from mutant phenotype (Simonsen et al., 2007)
endosome organization and biogenesis inferred from mutant phenotype (Sriram et al., 2003)
endosome to lysosome transport traceable author statement (Toonen and Verhage, 2003) traceable author statement (Luzio et al., 2000)
eye pigment granule organization and biogenesis inferred from mutant phenotype (Sevrioukov et al., 1999)
intracellular transport traceable author statement (Narayanan and Ramaswami, 2001)
lysosome organization and biogenesis non-traceable author statement (Kramer, 1999.3.5)
ommochrome biosynthetic process inferred from mutant phenotype (Tearle, 1991)
protein targeting to lysosome inferred from mutant phenotype (Sevrioukov et al., 1999)
regulation of protein ubiquitination inferred from mutant phenotype (Simonsen et al., 2007)
vesicle docking during exocytosis inferred from electronic annotation with InterPro:IPR001619 (FlyBase Curators et al., 2004-)
vesicle-mediated transport inferred from sequence or structural similarity (Littleton, 2000)
Cellular Component
CV term Evidence References
cytosol traceable author statement (Toonen and Verhage, 2003)
lysosome inferred from direct assay (Sevrioukov et al., 1999)
membrane traceable author statement (Toonen and Verhage, 2003)
Sequence Ontology: Class of Gene
	protein_coding_gene   nuclear_gene
Interactions & Pathways
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions car allele Gene References car1 dor (Sriram et al., 2003) lt (Nickla et al., 1980, Warner et al., 1998) carunspecified w (Lloyd et al., 2002) unspecified g (Lindsley and Grell, 1968) bchs (Simonsen et al., 2007)
External Data
Linkouts	BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions • 59247
Orthologs
Genome-wide drosophilid orthologs	Dana\GF20198 Dere\GG19231 Dgri\GH12312 Dmoj\GI21456 Dpse\GA11493 Dsec\GM22966 Dsim\GD17447 Dvir\GJ16477 Dwil\GK10350 Dyak\GE15849
Curated drosophilid orthologs	Dpse\GA11493
Linkouts	InParanoid orthologs - Eukaryotic orthologs • ENSANGP00000014711 Anopheles gambiae (Ensembl) ENSBTAP00000005508 Bos taurus (Ensembl) ENSCAFP00000011731 Canis familiaris (Ensembl) ENSCINP00000019308 Ciona intestinalis (Ensembl) NEWSINFRUP00000142336 Takifugu rubripes (Ensembl) ENSGALP00000007052 Gallus gallus (Ensembl) ENSP00000267199 Homo sapiens (Ensembl) ENSMMUP00000023702 Macaca mulatta (Ensembl) ENSMODP00000015299 Monodelphis domestica (Ensembl) ENSPTRP00000009469 Pan troglodytes (Ensembl) ENSRNOP00000011458 Rattus norvegicus (Ensembl) GSTENP00009601001 Tetraodon nigroviridis (Ensembl) ENSXETP00000008197 Xenopus tropicalis (Ensembl) Q7XQY9 Oryza sativa (Gramene) AT3G54860.1 Arabidopsis thaliana (Arabidopsis) WBGene00035639 Caenorhabditis briggsae (Wormbase) WBGene00016960 Caenorhabditis elegans (Wormbase) ZDB-CDNA-050327-73 Danio rerio (Zfin) ZDB-GENE-050327-73 Danio rerio (Zfin) DDB0189239 Dictyostelium discoideum (Dictybase) MGI:1924823 Mus musculus (Informatics) YLR396C Saccharomyces cerevisiae (Yeastgenome) SPBC1703.15c Schizosaccharomyces pombe (Sanger)
Functional Complementation between Species
Inter-Species Misexpression Data
Produces phenotype in
Produces NO phenotype in
Stocks & Reagents
Stocks Listed in FlyBase ( 64 )
Bloomington	19 car1 20 car1 su(f)8 579 Df(1)JF5, f1 car1/FM7a 788 In(1)rst3, y1 car1 12257 w67c23 P{lacW}carG0447/FM7c 11895 w67c23 P{lacW}l(1)G0041G0041/FM7c
Kyoto	105680 car1 101065 car1 su(f)8 101194 v1 f3N car1 105990 Df(1)JF5, f1 car1/FM7a
VDRC	v4548 w1118; P{GD1397}v4548 v4547 w1118; P{GD1397}v4547/CyO
	More stocks available...
Genomic Clones ( 2 )
	BACR10M08 BACR27L16
cDNA Clones ( 20 )
	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	LD22396
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	AT27510 LP01613 LD08438 LD23088 RE31274 RE32658 LD40135 RE66786 AT29179 GH20069 LD38724
Other clones	EK129323 EP21750 EN04753 EK176856 EK070843 EK246504 EN09909 EN05938
RNAi & Array Information
Affy Oligo
Linkouts	DRSC - RNAi screening (Harvard): high-throughput cell culture data and design • FBgn0000257 GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data • FBgn0000257
Antibody Information
	polyclonal (Sevrioukov et al., 1999)
Other Information
Discoverer
	Patterson, 20th March 1928.