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Gene Dmel\rap

General Information
Symbol	Dmel\rap	Species	D. melanogaster
Name	retina aberrant in pattern	Annotation symbol	CG3000
Feature type	protein_coding_gene	FlyBase ID	FBgn0003200
Created / Updated	2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)	X	Recombination map	1-
Cytogenetic map	4C11-4C12	Sequence location	X:4,561,315..4,573,619 [-]
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 retina aberrant in pattern is referred to in FlyBase by the symbol rap (CG3000, FBgn0003200). It has the cytological map location 4C11-4C12. Its sequence location is X:4561315..4573619. Its molecular function is unknown. It is involved in the biological processes: glial cell migration; cyclin catabolic process; protein catabolic process; compound eye morphogenesis; eye-antennal disc morphogenesis; positive regulation of exit from mitosis. 21 alleles are reported. The phenotypes of these alleles are annotated with 18 unique terms, many of which group under: peripheral nervous system; organ system; nervous system; adult; embryonic pericardial cell; morphogenetic furrow; primordium; extended germ band embryo; imaginal precursor; portion of tissue. It has 2 annotated transcripts and 2 annotated polypeptides.
External Summaries
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	rap: retina aberrant in pattern (J.C. Hall) Eyes grossly abnormal: rough surface texture, and deep pseudopupil (DPP) has anomalous appearance; finer level observations show ommatidia to be aberrant in size, shape, and alignment; in sections, numbers of photoreceptor cells per ommatidium vary greatly, and positions of such cells plus rhabdomere arrangements are altered. Developmentally, recruitment of presumptive photoreceptors behind morphogenetic furrow in third larval instar eye disc is abnormal: e.g., arrangement of five-cell preclusters is very disorganized, and the normal increase in numbers of cells within clusters does not occur, so that, in regions where eight-cell clusters are found in wild-type, there are small clusters in rap, intermingled with others than can have >8 cells; cell bodies of developing photoreceptor cells do not become apically positioned in the disc, as in wild-type. Temperature-shift experiments on rap4 show a temperature-sensitive period for roughened eye is in third larval instar. Mosaic experiments, involving induced mitotic recombination in rap1/+ larvae, showed that normal adult ommatidia always had a rap+ R8 cell, whereas R1-7 could readily be genotypically rap1 in such facets; also, certain phenotypically mutant ommatidia, near borders separating mutant and wild-type tissue, contained all rap+ cells (in clusters of 3, 4, 6, or 8 photoreceptor cells).
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 4C11-4C12   Limits computationally determined from genome sequence between P{EP}CG2930EP1352 and P{EP}EP425
Experimentally Determined Cytological Location
Cytogenetic map Notes References 4C11-4C16 (determined by in situ hybridisation) 4C7--8 (determined by in situ hybridisation)   (Peter et al., 2002) 4C7-4C8 (determined by in situ hybridisation)   (Schaefer et al., 1999.12.2)
Experimentally Determined Recombination Data
Location	1- (Lehner, 1997.7.4)
Left of (cM)
Right of (cM)
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\rap for information on other features
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) rap-RA FBtr0070686  NM_080113   2667   478 rap-RB FBtr0070687  NM_167013   2522   478
Additional Transcript Data & Comments
Reported size (kB)	2.6 (longest cDNA) (Sigrist and Lehner, 1997)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein rap-PA   FBpp0070654   53.5   478   9.24     NP_524852   AAF45973 rap-PB   FBpp0070655   53.5   478   9.24     NP_726941   AAN09125
Additional Polypeptide Data & Comments
Reported size (kD)	478 (aa) (Sigrist and Lehner, 1997)
Comments
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0003200
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • WD40/YVTN repeat-like (IPR015943) Cdc20/Fizzy (IPR000002) WD40 repeat (IPR001680) WD40 repeat-like (IPR011046)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA567442   AA698344   AA735416   AE003431 AAF45973   AE003431 AAN09125   AI106696   AI260863   AI386532   AI387581   AI402555   AI455119   AI946472   AX777339   BI162575   BI162576   BI166588   BI169831   BI212328   BI214802   BI215202   BI229236   BI232995   BI233032   BI239843   BI363790   BI365354   BI368866   BI370008   BI482526   BI482758   BI485945   BP552146   BT001403 AAN71158   BT010011 AAQ22480   CK659374   CK661063   CO177002   CO178789   CO180497   CO185898   CO265279   CO272435   CO278048   CO279552   CO280241   CO280627   CO281232   CO284619   CO284653   CO285681   CO286977   CO294425   CO294768   CO295617   CO295828   CO300578   CO301709   CO309182   CO311999   CO317601   CO317603   CO317671   CO323245   CO325472   CO329398   CO330649   CZ482300   CZ482334   EC057250   EC061346   EC062422   EC063761   EC067500   EC072576   EC075412   EC077215   EC078908   EC079420   EC081262   EC084813   EC085639   EC085717   EC086136   EC087724   EC089019   EC198874   EC200712   EC204173   EC207158   EC210643   EC211459   EC212041   EC225280   EC227268   EC232779   EC233814   EC233855   EC235970   EC236934   EC238076   EC239338   EC240346   EC241561   EC247450   EC249064   EC249659   EC251953   LD21270   RE01858   Y14162 CAA74575
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	O18402 Q9W4H9
Maps to
Does NOT map to
Identified with	bs26f10 LP04853 (Oliver, 2001.8.16) GH07620 RE20929 (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 • 480
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  adult stage  spermatocyte (Jacobs et al., 2002)  embryonic stage | stage 11  posterior midgut primordium (Sigrist and Lehner, 1997)  embryonic stage | stage 11  anterior midgut primordium (Sigrist and Lehner, 1997)  embryonic stage | syncytial blastoderm   (Sigrist and Lehner, 1997)  embryonic stage | stage 11  salivary gland placode (Sigrist and Lehner, 1997)
Marker for
Subcellular Localization
CV Term
Summary of Polypeptide Expression
Stage Tissue/Position Reference  embryonic stage  salivary gland body specific anlage (Jacobs et al., 2002)
Marker for
Subcellular Localization
CV Term
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0003200 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0003200 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0003200
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal rapP2241 lethal | recessive rapG0326 rapG0418 rapie28 lethal | embryonic stage rapG0326 lethal | larval stage rapG0418 lethal | prepupal stage rapG0418 lethal | pupal stage rapG0418 lethal | pupal stage, with Scer\GAL4ptc-559.1 rapScer\UAS.cSa lethal | pupal stage, with Scer\GAL4en-e16E rapScer\UAS.cSa Other Phenotypes Allele visible | recessive rapx-3 mitotic cell cycle defective rapdsRNA.cJa rapie28 rapx-3 mitotic cell cycle defective | somatic clone, with Scer\GAL4Act5C.PP rapScer\UAS.cSa mitotic cell cycle defective | embryonic stage rapie28 mitotic cell cycle defective | embryonic stage, with Scer\GAL4prd.RG1 rapScer\UAS.cSa rappsm.Scer\UAS mitotic cell cycle defective, with Scer\GAL4prd.RG1 rapScer\UAS.cSa tumorigenic, with Scer\GAL4ey.PH rapScer\UAS.cSa Phenotype manifest in Allele eye | conditional - heat sensitive rap4 eye, with Scer\GAL4ey.PH rapScer\UAS.cSa antenna | ectopic, with Scer\GAL4ey.PH rapScer\UAS.cSa antennal primordium, with Scer\GAL4ey.PH rapScer\UAS.cSa adult head, with Scer\GAL4ey.PH rapScer\UAS.cSa embryonic pericardial cell, with Scer\GAL4twi.PG rapScer\UAS.cSa cardioblast, with Scer\GAL4twi.PG rapScer\UAS.cSa cycle 16 embryo, with Scer\GAL4prd.RG1 rapScer\UAS.cSa embryonic epidermis, with Scer\GAL4prd.RG1 rapScer\UAS.cSa rappsm.Scer\UAS follicle cell & nucleus | somatic clone, with Scer\GAL4Act5C.PP rapScer\UAS.cSa imaginal disc & mitotic cell cycle, with Scer\GAL4en-e16E rapScer\UAS.cSa embryonic epidermis rapdsRNA.cJa rapie28 cycle 16 embryo raphs.PS eye disc & mitotic cell cycle rapx-3 eye rapx-3 ommatidium rapx-3 pigment cell rapx-3 interommatidial bristle rapx-3 morphogenetic furrow rapx-3 photoreceptor cell R7 rapx-3 photoreceptor cell R2 rapx-3 photoreceptor cell R5 rapx-3 photoreceptor cell R8 rapx-3 photoreceptor cell R1 rapx-3 photoreceptor cell R6 rapx-3
Classical Alleles ( 15 )
For All Classical Alleles Show
Allele of rap Class Mutagen Stocks Known lesion rap1 hypomorph P-element activity 0 -- rap2 P-element activity 0 -- rap3 amorph P-element activity 0 -- rap4 hypomorph P-element activity 0 -- rapG0326 P-element activity 1 Yes rapG0418 P-element activity 1 Yes rapP2241 P-element activity 0 Yes rape04550 piggyBac transposase 1 -- rape04581 piggyBac transposase 1 -- rape2 ethyl methanesulfonate 0 -- rape4 ethyl methanesulfonate 0 -- rape6 ethyl methanesulfonate 0 -- rapie28 amorph Δ2-3 0 Yes rapx-2 loss of function X ray 0 -- rapx-3 loss of function X ray 0 --
Alleles Carried on Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Allele of rap Class Mutagen Stocks Known lesion rapGD9960 in vitro construct | RNAi in vitro construct | regulatory fusion 2 Yes rapScer\UAS.cSa in vitro construct | regulatory fusion 0 Yes rapUbi-p63E.T:Avic\GFP-m6 in vitro construct | regulatory fusion in vitro construct | coding region fusion 0 Yes rapdsRNA.cJa in vitro construct | RNAi 0 Yes raphs.PS in vitro construct | regulatory fusion 0 Yes rappsm.Scer\UAS in vitro construct | regulatory fusion in vitro construct | site directed mutagenesis in vitro construct | amino acid replacement 0 Yes
Aneuploid Aberrations
Useful deficiency	Df(1)bi-D3
Disrupted in	Df(1)GA56 (Sigrist and Lehner, 1997) Df(1)bi-D3 (Jacobs et al., 2002, Sigrist and Lehner, 1997) Df(1)ovo41 (Sigrist and Lehner, 1997) Df(1)ovo6 (Sigrist and Lehner, 1997) Df(1)ovo7 (Sigrist and Lehner, 1997)
Not disrupted in	Df(1)JC70 (Sigrist and Lehner, 1997) Df(1)rb1 (Sigrist and Lehner, 1997) Df(1)rb27 (Sigrist and Lehner, 1997) Df(1)rb42 (Sigrist and Lehner, 1997)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD9960} NA P{UAS-fzr.psm} NA P{UAS-fzr2.J} NA characterization construct P{Ubi-p63E-rap.GFP} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions PBac{RB}rape04550 NA PBac{RB}rape04581 NA P{}rap1 NA P{}rap2 NA P{}rap3 NA P{}rap4 NA P{}rapP2241 NA insertion of enhancer trap P{lacW}rapG0326 No P{lacW}rapG0418 No
Related Comments
	Please look at the allele reports for the complete phenotype data Eyes grossly abnormal: rough surface texture and deep pseudopupil (DPP) has anomalous appearance; finer level observations show ommatidia to be aberra