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Gene Dmel\cm

General Information
Symbol	Dmel\cm	Species	D. melanogaster
Name	carmine	Annotation symbol	CG3035
Feature type	protein_coding_gene	FlyBase ID	FBgn0000330
Created / Updated	2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)	X	Recombination map	1-18.9
Cytogenetic map	6E4-6E4	Sequence location	X:6,903,333..6,905,168 [-]
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 carmine is referred to in FlyBase by the symbol cm (CG3035, FBgn0000330). It has the cytological map location 6E4. Its sequence location is X:6903333..6905168. Its molecular function is described as protein binding. It is involved in the biological processes: determination of adult life span; ommochrome biosynthetic process; neurotransmitter secretion; synaptic vesicle coating; vesicle coating; lysosome organization and biogenesis; intracellular transport; regulation of alternative nuclear mRNA splicing, via spliceosome; intracellular protein transport; vesicle-mediated transport. 13 alleles are reported. The phenotypes of these alleles are annotated with: pigment cell; secondary pigment cell pigment granule; tertiary pigment cell pigment granule; rhabdomere; Malpighian tubule; wing; eye. It has one annotated transcript and one annotated polypeptide.
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	cm: carmine Eye color translucent dark ruby. With st, eye color deep orange; with brown, slightly lighter than bw alone. Larval Malpighian tubes very pale yellow. RK1.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 6E4-6E4   Limits computationally determined from genome sequence between P{EP}inx7EP1641 and P{EP}CG9650EP1340&P{EP}CG9650EP1617
Experimentally Determined Cytological Location
Cytogenetic map Notes References 6E-6E Determined by comparing Celera genomic sequence with sequence from BDGP BAC and P1 clones.   (Lloyd et al., 2000) 6E-6E   (Zhang, 1998.7.17) 6E1-6E4 (determined by in situ hybridisation)   (Zhang and Broadie, 1999)
Experimentally Determined Recombination Data
Location	1-18.9 (Nicklas and Cline, 1983) 1-18.8 (Neel, 1942)
Left of (cM)	ct sn (Johnson and Judd, 1979)
Right of (cM)	stout (Nicklas and Cline, 1983)
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\cm for information on other features
Comments on Gene Model
	This gene model; overlaps 5'UTR of downstream gene CG2977 (transcript CG2977-RB)
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) cm-RA FBtr0071033  NM_176700   1470   415
Additional Transcript Data & Comments
Reported size (kB)	1.476 (sequence analysis) (Zhang and Broadie, 1999) 1.455 (sequence analysis) (Mullins 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 cm-PA   FBpp0070992   46.8   415   8.19     NP_788873   AAF46231
Additional Polypeptide Data & Comments
Reported size (kD)	415 (aa) (Mullins et al., 1999, Zhang and Broadie, 1999)
Comments
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0000330
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Clathrin adaptor, mu subunit (IPR001392) Clathrin adaptor, mu subunit, C-terminal (IPR008968) Longin-like (IPR011012)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA390968   AE003439 AAF46231   AF110233 AAF14249   AI403995   AJ009657 CAA08768   AW942086   AY051561   AY069388 AAL39533   BF486873   BI214681   CA807360   CO317021   CO336059   CZ490188   CZ490189   EC089481   EC240360   EC265039
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	O76928
Maps to
Does NOT map to
Identified with	LD09732 (Zhang and Broadie, 1999, Mullins et al., 1999, 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 • 736
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-adult stage   (Mullins et al., 1999)
Marker for
Subcellular Localization
CV Term
Summary of Polypeptide Expression
Stage Tissue/Position Reference
Marker for
Subcellular Localization
CV Term
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0000330 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0000330 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0000330
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele viable cmf05774 lethal | larval stage | recessive cm5 lethal, with Scer\GAL4Act5C cmGD10049 Other Phenotypes Allele visible | recessive cm1 eye color defective cmunspecified eye color defective | recessive cm1 cm2 short lived | male cm1 Sterility Allele fertile cmf05774 Phenotype manifest in Allele pigment cell cm1 cm2 cmunspecified secondary pigment cell pigment granule cm1 tertiary pigment cell pigment granule cm1 rhabdomere cm1 Malpighian tubule cm1 wing, with Scer\GAL4Bx-MS1096 cmGD10049 eye, with Scer\GAL4GMR.PF, Scer\GAL4ey.PH cmGD10049
Classical Alleles ( 12 )
For All Classical Alleles Show
Allele of cm Class Mutagen Stocks Known lesion cm1 spontaneous 26 Yes cm2 sulfur mustard 0 -- cm3 X ray 0 -- cm41c27 spontaneous 0 -- cm4 spontaneous 0 Yes cm5 ethyl methanesulfonate 0 -- cmMR17 0 -- cmMR19 0 -- cmMR8 0 -- cmf05774 piggyBac transposase 2 -- cmf07380 piggyBac transposase 1 -- cmunspecified 0 --
Alleles Carried on Transgenic Constructs ( 1 )
For All Alleles Carried on Transgenic Constructs Show
Allele of cm Class Mutagen Stocks Known lesion cmGD10049 in vitro construct | RNAi in vitro construct | regulatory fusion 1 Yes
Aneuploid Aberrations
Useful deficiency	Df(1)HA32
Useful duplication	Dp(1;1)GH65
Disrupted in	Df(1)GCF (Nicklas and Cline, 1983) Df(1)HA32 (Craymer and Roy, 1980, Nicklas and Cline, 1983, Simpson and Wieschaus, 1990, Watanabe and Kankel, 1990) Df(1)LIMDF (Simpson and Wieschaus, 1990, Rose and Wieschaus, 1992) Df(1)LIMWO (Simpson and Wieschaus, 1990) Df(1)Sxl-bt (Nicklas and Cline, 1983, Watanabe and Kankel, 1990) Df(1)Sxl-nl (Simpson and Wieschaus, 1990) Df(1)cm-R8 (Valencia, 1966) Df(1)cm10a (Simpson and Wieschaus, 1990) Df(1)cm13a (Simpson and Wieschaus, 1990) Df(1)cm14a (Simpson and Wieschaus, 1990) Df(1)cm2a (Simpson and Wieschaus, 1990) Df(1)cm7c (Simpson and Wieschaus, 1990) Df(1)cmD15 (Simpson and Wieschaus, 1990) Df(1)ct-J6 (Nicklas and Cline, 1983) Df(1)ct268-37
Duplicated in	Dp(1;3)ct11a   Dp(1;3)ct268-37 (Demerec, 1940) Dp(1;3)sn13a1 (Lefevre and Johnson, 1973, Lefevre, 1981, Cline, 1983) Dp(1;Y)ct+y+ (Johnson and Judd, 1979, Nicklas and Cline, 1983) Tp(1;2)sn+72d (Lefevre, 1981)
Not duplicated in	Dp(1;2)ct7c1   Dp(1;2)sn+72d (Nicklas and Cline, 1983) Dp(1;f)q2
Not disrupted in	Df(1)6F1-2 (Simpson and Wieschaus, 1990, Rose and Wieschaus, 1992) Df(1)L-1-18 (Simpson and Wieschaus, 1990) Df(1)L-1-2 (Simpson and Wieschaus, 1990, Rose and Wieschaus, 1992) Df(1)LV16 (Simpson and Wieschaus, 1990, Rose and Wieschaus, 1992) Df(1)RF19 (Nicklas and Cline, 1983) Df(1)Sp8A (Schalet, 1986) Df(1)Sxl-ra (Nicklas and Cline, 1983, Simpson and Wieschaus, 1990) Df(1)ct-J4 (Nicklas and Cline, 1983) Df(1)ct78 (Simpson and Wieschaus, 1990, Rose and Wieschaus, 1992) Df(1)ogre18-183 (Watanabe and Kankel, 1990) Dp(1;f)A12 (Mackensen, 1935) In(1)F10h1 (Simpson and Wieschaus, 1990)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD10049} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions ?{}cm1 NA ?{}cm4 NA PBac{WH}cmf05774 NA PBac{WH}cmf07380 NA
Related Comments
	Please look at the allele reports for the complete phenotype data Lesions in cm reduce or eliminate pigmentation in the eyes and ocelli and block pigmentation of the fat body and tubules: cm is required for normal pigmentation of all four tissues. (Tearle, 1991) hobo dysgenesis causes instability at the cm locus, in progeny derived from the unstable chromosome U-7 line. Once cm mutations are produced they are genetically stable and do not revert. Cytological analysis suggests that the mutations involve minute structural aberrations, and molecular analysis revealed that many result from the deletion of DNA between two hobos. (Sheen et al., 1993)
Gene Ontology: Function, Process & Cellular Component ( 15 )
Molecular Function
CV term Evidence References
protein binding inferred from electronic annotation with InterPro:IPR001392, InterPro:IPR008968 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
determination of adult life span inferred from mutant phenotype (Simonsen et al., 2007)
intracellular protein transport inferred from electronic annotation with InterPro:IPR001392, InterPro:IPR008968 (FlyBase Curators et al., 2004-)
intracellular transport traceable author statement (Narayanan and Ramaswami, 2001)
lysosome organization and biogenesis inferred from sequence or structural similarity (Mullins and Bonifacino, 2001)
neurotransmitter secretion non-traceable author statement (Stimson and Ramaswami, 1999)
ommochrome biosynthetic process inferred from mutant phenotype (Tearle, 1991)
regulation of alternative nuclear mRNA splicing, via spliceosome inferred from mutant phenotype (Park et al., 2004)
synaptic vesicle coating traceable author statement (Stimson and Ramaswami, 1999)
vesicle coating traceable author statement (Stimson and Ramaswami, 1999)
vesicle-mediated transport inferred from electronic annotation with InterPro:IPR001392, InterPro:IPR008968 (FlyBase Curators et al., 2004-)
Cellular Component
CV term Evidence References
clathrin adaptor complex non-traceable author statement (Zhang, 1998.7.17) inferred from sequence or structural similarity with UniProtKB:P53678 (FlyBase, 1992-)
coated vesicle traceable author statement (Stimson and Ramaswami, 1999)
nucleus inferred by curator from GO:0000381 (Park et al., 2004)
synaptic vesicle traceable author statement (Stimson and Ramaswami, 1999)
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 cm allele Gene References cmunspecified w (Lloyd et al., 2002) unspecified bchs (Simonsen et al., 2007)
External Data
Linkouts	BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions • 58125
Orthologs
Genome-wide drosophilid orthologs	Dana\GF20328 Dere\GG17643 Dgri\GH24272 Dmoj\GI21579 Dper\GL26809 Dpse\GA15778 Dsec\GM17484 Dsim\GD16169 Dvir\GJ15801 Dwil\GK25293 Dyak\GE17549
Curated drosophilid orthologs	Dpse\GA15778
Linkouts	InParanoid orthologs - Eukaryotic orthologs • ENSANGP00000011636 Anopheles gambiae (Ensembl) ENSBTAP00000001640 Bos taurus (Ensembl) ENSCAFP00000008348 Canis familiaris (Ensembl) ENSCINP00000009835 Ciona intestinalis (Ensembl) NEWSINFRUP00000142492 Takifugu rubripes (Ensembl) ENSGALP00000005789 Gallus gallus (Ensembl) ENSP00000174653 Homo sapiens (Ensembl) ENSMMUP00000018954 Macaca mulatta (Ensembl) ENSMODP00000012861 Monodelphis domestica (Ensembl) ENSPTRP00000034595 Pan troglodytes (Ensembl) ENSRNOP00000025675 Rattus norvegicus (Ensembl) GSTENP00030655001 Tetraodon nigroviridis (Ensembl) ENSXETP00000036627 Xenopus tropicalis (Ensembl) Q6AV18 Oryza sativa (Gramene) AT1G56590.1 Arabidopsis thaliana (Arabidopsis) WBGene00029947 Caenorhabditis briggsae (Wormbase) WBGene00000164 Caenorhabditis elegans (Wormbase) ZDB-CDNA-040625-245 Danio rerio (Zfin) ZDB-GENE-040625-169 Danio rerio (Zfin) DDB0214930 Dictyostelium discoideum (Dictybase) MGI:1929212 Mus musculus (Informatics)
Functional Complementation between Species
Inter-Species Misexpression Data
Produces phenotype in
Produces NO phenotype in
Stocks & Reagents
Stocks Listed in FlyBase ( 30 )
Kyoto	105681 cm1 105682 cm1 ct6 106890 cm1 ct6 mysts1 106261 cm1 m74f sd1 oss
Bloomington	21 cm1 22 cm1 ct6 4679 cm1 l(1)7Dd4/FM7a 18905 w1118 PBac{WH}cmf05774 3169 cm1 ct6 mysts1
Harvard	- PBac{WH}cmf05774 - PBac{WH}cmf07380
VDRC	v21139 w1118; P{GD10049}v21139
	More stocks available...
Genomic Clones ( 1 )
	BACR17C09
cDNA Clones ( 8 )
	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	GH21056 LD09732
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	RE20674 AT21424 GH23560
Other clones	ESG017c.E21.3_E01 EK266736 EN11736
RNAi & Array Information
Affy Oligo
Linkouts	DRSC - RNAi screening (Harvard): high-throughput cell culture data and design • FBgn0000330 GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data • FBgn0000330
Antibody Information
Other Information
Discoverer
	Mohr, 27th April 1927.
Etymology
Identification
Position Effect Variegation Data
No PEV in	Tp(1;3)ct268-37
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: cm Mu3 (Mullins et al., 1999) Source for merge of: cm AP-3 Source for merge of cm AP-3 was sequence comparison (date:991227). (FlyBase, 1996-)
Additional comments
Comments About Role
Comments About Molecular Function
Other Comments
	dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology. (Kiger et al., 2003)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_176700 RefSeq (Proteins) • NP_788873 DDBJ / EMBL / GenBank • AA390968 AE003439 AAF46231 AF110233 AAF14249 AJ009657 CAA08768 AW942086 AY069388 AAL39533 CZ490188 CZ490189 UniProtKB/TrEMBL • O76928
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Clathrin adaptor, mu subunit (IPR001392) Clathrin adaptor, mu subunit, C-terminal (IPR008968) Longin-like (IPR011012)
Linkouts
	BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions • 58125 DEDB - Drosophila exon database: splicing graphs • 736 DRSC - RNAi screening (Harvard): high-throughput cell culture data and design • FBgn0000330 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0000330 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0000330 FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0000330 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0000330 GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data • FBgn0000330 InParanoid orthologs - Eukaryotic orthologs •