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Gene Dmel\phm

General Information
Symbol	Dmel\phm	Species	D. melanogaster
Name	phantom	Annotation symbol	CG6578
Feature type	protein_coding_gene	FlyBase ID	FBgn0004959
Created / Updated	2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)	X	Recombination map	1-64
Cytogenetic map	17D1-17D1	Sequence location	X:18,579,802..18,582,257 [+]
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 phantom is referred to in FlyBase by the symbol phm (CG6578, FBgn0004959). It has the cytological map location 17D1. Its sequence location is X:18579802..18582257. Its molecular function is described as: electron carrier activity; ecdysteroid 25-hydroxylase activity; heme binding; iron ion binding. It is involved in the biological processes: ecdysone biosynthetic process; embryonic development via the syncytial blastoderm; insecticide metabolic process; oogenesis. 18 alleles are reported. The phenotypes of these alleles are annotated with 12 unique terms, many of which group under: anatomical structure; organ system; organism; embryonic nervous system; nervous system; integumentary system; embryonic head; primordium; commissure; cuticle; embryonic peripheral nervous system; embryonic tagma; portion of tissue. 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	exo: exocephalon Sex-linked recessive lethal; variably differentiated cuticle; complete failure of head involution with well developed head structures on exterior of the embryo. Many embryos slightly twisted with defective ventral denticle patterns. phm: phantom Male lethal. Cuticle of lethal embryos not well differentiated and contracted posteriorly.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 17D1-17D1   Limits computationally determined from genome sequence between P{EP}EP443EP443&P{EP}BxEP1383 and P{EP}Pk17EEP438
Experimentally Determined Cytological Location
Cytogenetic map Notes References 17C-17C   (Dunkov, 2000.6.29)
Experimentally Determined Recombination Data
Location	1-64 (Tearle and Nusslein-Volhard, 1987)
Left of (cM)
Right of (cM)
Notes	Map location of 1-64 is based on mapping of original phm alleles; map location of 1-58 corresponds to mapping based on phm alleles of the exocephalon class.
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\phm for information on other features
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) phm-RA FBtr0074603  NM_133091   1991   574
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 phm-PA   FBpp0074374   65.2   574   6.11     NP_573319   AAF48873
Additional Polypeptide Data & Comments
Reported size (kD)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Cytochrome P450 (IPR001128) Cytochrome P450, E-class, group I (IPR002401)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE003509 AAF48873   AF484413 AAQ05971   AY070930 AAL48552   BI163061   BI163691   BI166172   BI232033   CO270692   CO326677   EC082734   EC225444   EC251814   EC254427
UniProtKB/Swiss-Prot	Q9VWR5
UniProtKB/TrEMBL
Maps to
Does NOT map to
Identified with	RE03155 (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 phm[E7] X:18,581,315..18,581,315 evidence=experimental pr_change=Q286@|phm-PA reported_na_change=C1049T reported_pr_change=Q286@ na_change=C18581315T (Niwa et al., 2004, Warren et al., 2004)
External Data
Linkouts	DEDB - Drosophila exon database: splicing graphs • 3277
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
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0004959 FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for phm 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 lethal | maternal effect phmEH162b lethal | recessive phmE7 phmT112 phmexo-1 lethal | embryonic stage | recessive phm15D phm16C phm29N phmE7 phmEH162b phmEH320 phmEH603b phmEH740b phmR32 phmexo-1 Phenotype manifest in Allele embryonic/first instar larval cuticle phm15D phm16C phm29N phmE7 phmEH162b phmEH320 phmEH603b phmEH740b phmR32 phmT112 phmexo-1 embryonic head phm15D phm16C phm29N phmE7 phmEH162b phmEH320 phmEH603b phmEH740b phmR32 phmT112 phmexo-1 ovary phm16C phmE7 phmEH603b phmEH740b stage 14 embryo phmE7 dorsal closure embryo phmE7 embryonic digestive system phmE7 midgut primordium phmE7 embryo phmE7 larval hindgut & embryo phmexo-1 embryonic central nervous system phmunspecified commissure phmunspecified embryonic epidermis phmunspecified embryonic peripheral nervous system phmunspecified sensory neuron & embryo phmunspecified
Classical Alleles ( 13 )
For All Classical Alleles Show
Allele of phm Class Mutagen Stocks Known lesion phm15D ethyl methanesulfonate 0 -- phm16C ethyl methanesulfonate 0 -- phm29N ethyl methanesulfonate 0 -- phmE7 ethyl methanesulfonate 2 Yes phmEH162b ethyl methanesulfonate 0 -- phmEH320 ethyl methanesulfonate 0 -- phmEH603b ethyl methanesulfonate 0 -- phmEH740b ethyl methanesulfonate 0 -- phmR32 ethyl methanesulfonate 0 -- phmT112 ethyl methanesulfonate 0 -- phmexo-1 ethyl methanesulfonate 0 -- phmexo-2 ethyl methanesulfonate 0 -- phmunspecified 0 --
Alleles Carried on Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Allele of phm Class Mutagen Stocks Known lesion phmAct5C.PW in vitro construct | regulatory fusion 0 Yes phmAct5C.T:Ivir\HA1 in vitro construct | regulatory fusion in vitro construct | coding region fusion 0 Yes phmGD3430 in vitro construct | RNAi in vitro construct | regulatory fusion 2 Yes phmScer\UAS.T:Ivir\HA1 in vitro construct | regulatory fusion in vitro construct | coding region fusion 0 Yes phmScer\UAS.cNa in vitro construct | regulatory fusion 0 Yes
Aneuploid Aberrations
Useful deficiency	Df(1)E128
Useful duplication	Dp(1;1)BSTAG
Disrupted in	Df(1)E128 (Eberl et al., 1992) Df(1)Exel7463 (Ryder, 2004.4.26) Df(1)N19 (Tearle and Nusslein-Volhard, 1987, Eberl et al., 1992, Harbecke and Lengyel, 1995) Df(1)fu-E5 (Eberl et al., 1992) Df(1)fu-H4 (Eberl et al., 1992) Df(1)fu-S4 (Eberl et al., 1992)
Not duplicated in	Dp(1;3)f+71b (Eberl and Hilliker, 1988) Dp(1;4)r+l (Eberl and Hilliker, 1988) Ts(1Rt;YLt)B50 (Eberl and Hilliker, 1988)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD3430} NA P{UAS-phm.N} NA
Insertions
	Type of insertions Name Expression data
Related Comments
	Please look at the allele reports for the complete phenotype data phm mutants display a posterior contraction and poorly differentiated cuticle. (Wieschaus et al., 1984) A screen for X-linked genes that affect embryo morphology revealed phm. (Eberl and Hilliker, 1988) Muscle phenotype of mutants studied using polarised light microscopy and antibody staining to detect Mhc-lacZ reporter gene expression in muscles. (Drysdale et al., 1993) Six EMS induced alleles have been identified in a screen for mutations affecting commissure formation in the CNS of the embryo. (Hummel et al., 1999)
Gene Ontology: Function, Process & Cellular Component ( 11 )
Molecular Function
CV term Evidence References
ecdysteroid 25-hydroxylase activity inferred from direct assay (Warren et al., 2004)
electron carrier activity non-traceable author statement (Dunkov, 2000.6.29) inferred from sequence or structural similarity (Dunkov, 1999.11) non-traceable author statement (Swiss-Prot Project Members, 2000.5.1) inferred from electronic annotation with InterPro:IPR001128 (FlyBase Curators et al., 2004-)
heme binding inferred from electronic annotation with InterPro:IPR001128, InterPro:IPR002401 (FlyBase Curators et al., 2004-)
iron ion binding inferred from electronic annotation with InterPro:IPR001128, InterPro:IPR002401 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
ecdysone biosynthetic process inferred from direct assay (Warren et al., 2004)
embryonic development via the syncytial blastoderm inferred from mutant phenotype (Eberl et al., 1992)
insecticide metabolic process non-traceable author statement (Swiss-Prot Project Members, 2000.5.1)
oogenesis inferred from mutant phenotype (Eberl et al., 1992)
Cellular Component
CV term Evidence References
endoplasmic reticulum inferred from direct assay (Warren et al., 2004)
membrane non-traceable author statement (Swiss-Prot Project Members, 2000.5.1)
microsome non-traceable author statement (FlyBase, 1992-)
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 phm allele Gene References
External Data
Linkouts	BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions • 59169
Orthologs
Genome-wide drosophilid orthologs	Dana\GF22543 Dere\GG19180 Dgri\GH12529 Dmoj\GI11185 Dper\GL26991 Dpse\GA19697 Dsim\GD24859 Dvir\GJ19547 Dwil\GK10191 Dyak\GE17743
Curated drosophilid orthologs	Dmir\CG6578 (Bachtrog and Andolfatto, 2006) Dpse\GA19697
Linkouts	InParanoid orthologs - Eukaryotic orthologs • ENSANGP00000001701 Anopheles gambiae (Ensembl) Q69NF4 Oryza sativa (Gramene) DDB0232976 Dictyostelium discoideum (Dictybase)
Functional Complementation between Species
Partially functionally complemented by	Bmor\Cyp306a1 (Niwa et al., 2004)
Inter-Species Misexpression Data
Produces phenotype in
Produces NO phenotype in
Stocks & Reagents
Stocks Listed in FlyBase ( 4 )
VDRC	v6169 w1118; P{GD3430}v6169 v6170 w1118; P{GD3430}v6170
Bloomington	2208 y1 phmE7/FM7c
Kyoto	106740 y1 phmE7/FM7c
Genomic Clones ( 2 )
	BACR14D22 BACR17H16
cDNA Clones ( 6 )
	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	RE03155
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	RE28030 RE06214 RE02363
Other clones	EP04431 EK099820
RNAi & Array Information
Affy Oligo
Linkouts	DRSC - RNAi screening (Harvard): high-throughput cell culture data and design • FBgn0004959
Antibody Information
Other Information
Discoverer
Etymology
Identification
Position Effect Variegation Data
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: phm Cyp306a1 Source for merge of phm Cyp306a1 was sequence comparison (date:040503). (FlyBase, 1996-)
Additional comments	Existence of five alleles stated but no individual designations given. (Wieschaus et al., 1984)
Comments About Role
Comments About Molecular Function
	phm encodes a ecdysteroid 25-hydroxylase that catalyzes the conversion of 2,22,25-trideoxyecdysone (3-beta,5-beta-ketodiol) to 2,22-dideoxyecdysone (3-beta-5-beta-ketotriol) in S2 cells. (Warren et al., 2004)
Other Comments
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_133091 RefSeq (Proteins) • NP_573319 DDBJ / EMBL / GenBank • AE003509 AAF48873 AF484413 AAQ05971 AY070930 AAL48552 BI163691 UniProtKB/Swiss-Prot • Q9VWR5
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Cytochrome P450 (IPR001128) Cytochrome P450, E-class, group I (IPR002401)
Linkouts
	BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions • 59169 DEDB - Drosophila exon database: splicing graphs • 3277 DRSC - RNAi screening (Harvard): high-throughput cell culture data and design • FBgn0004959 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0004959 FlyExpress - Embryonic expression images (BDGP data) • FBgn0004959 FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0004959 InParanoid orthologs - Eukaryotic orthologs • ENSANGP00000001701 Anopheles gambiae (Ensembl) Q69NF4 Oryza sativa (Gramene) DDB0232976 Dictyostelium discoideum (Dictybase)
Synonyms & Secondary IDs ( 8 )
Reported As
Symbol Synonym	306a1 (Nelson, 2001.2.5) CG6578   Cyp306a1 (Tijet et al., 2001, ) Cyp306a1-Dm (Niwa et al., 2004) exo (Harbecke and Lengyel, 1995, Eberl and Hilliker, 1988, ) phm (Sandmann et al., 2007, Ono et al., 2006, Stathopoulos and Levine, 2005)
Name Synonym	exocephalon   phantom (Hummel et al., 1999, Serpe and O'Connor, 2006)
Secondary FlyBase IDs
	FBgn0000613 FBgn0003080 FBgn0030948
References ( 40 )
Generate a list of	All references relating to this gene ( 40 )
List References by type	Research paper  ( 18 ) Supplementary material  ( 1 ) Review  ( 4 ) Personal communication to FlyBase  ( 5 ) Abstract  ( 3 ) FlyBase analysis  ( 2 ) Stock list  ( 1 ) Curated genome annotation  ( 1 ) Protein sequence record  ( 1 ) Computer file  ( 1 ) Automatic genome annotation  ( 1 ) Book  ( 1 ) DNA/RNA sequence record  ( 1 )
Recent research papers ( 4 )
	Sandmann et al., 2007, Genes Dev. 21(4): 436--449 A core transcriptional network for early mesoderm development in Drosophila melanogaster. [FBrf0195237] Bachtrog and Andolfatto, 2006, Genetics 174(4): 2045--2059 Selection, recombination and demographic history in Drosophila miranda. [FBrf0193451] Ono et al., 2006, Dev. Biol. 298(2): 555--570 Spook and Spookier code for stage-specific components of the ecdysone biosynthetic pathway in Diptera. [FBrf0200145] Serpe and O'Connor, 2006, Development 133(24): 4969--4979 The metalloprotease tolloid-related and its TGF-beta-like substrate Dawdle regulate Drosophila motoneuron axon guidance. [FBrf0194328] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2006 Show reviews ...