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Gene Dvir\Rh4

General Information
Symbol	Dvir\Rh4	Species	D. virilis
Name	Rhodopsin 4	Annotation symbol	GJ11339
Feature type	protein_coding_gene	FlyBase ID	FBgn0013092
Gene Model Status	Current	Stock availability	None publicly available
Genomic Location
Chromosome (arm)	scaffold_13049	Recombination map
Cytogenetic map		Sequence location	scaffold_13049:22,737,179..22,738,330 [-]
Genomic Maps	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene Rhodopsin 4 is referred to in FlyBase by the symbol Dvir\Rh4 (GJ11339, FBgn0013092). It is a protein_coding_gene from Drosophila virilis. An electronic pipeline based on InterPro domains suggests that it has the molecular function: G-protein coupled receptor activity. An electronic pipeline based on InterPro domains suggests that it is involved in the biological process: G-protein coupled receptor signaling pathway; phototransduction; visual perception. No alleles are reported. It has one annotated transcript and one annotated polypeptide. Protein features are: G protein-coupled receptor, rhodopsin-like; GPCR, rhodopsin-like, 7TM; Opsin; Opsin RH3/RH4. Gene sequence location is scaffold_13049:22737179..22738330.
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.
FB2013_03
FB2013_02	Controlled Vocabulary Terms G-protein coupled receptor activity
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
Experimentally Determined Cytological Location
Cytogenetic map Notes References
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dvir\Rh4 for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Dvir\Rh4-RA FBtr0227264  XM_002048430   1152   383
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein Dvir\Rh4-PA   FBpp0225756   42.9   383   7.61     XP_002048466   EDW70808
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • G protein-coupled receptor, rhodopsin-like (IPR000276) Opsin RH3/RH4 (IPR000856) GPCR, rhodopsin-like, 7TM (IPR017452) Visual pigments (opsins) retinal binding site (IPR027430)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name CH940647 EDW70808   M77281 AAA28855   X51351 CAA35743
UniProtKB/Swiss-Prot	P17646
UniProtKB/TrEMBL	Q8I169
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
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
modENCODE Anatomy RNA-Seq
modENCODE Development RNA-Seq
modENCODE Cell Lines RNA-Seq
modENCODE Treatments RNA-Seq
Expression Clusters
External Data & Images
Linkouts
Alleles & Phenotypes
Summary of Allele Phenotypes
Phenotype manifest in Allele
Classical Alleles ( 0 )
For All Classical Alleles Show
Allele of Dvir\Rh4 Class Mutagen Stocks Known lesion
Alleles Carried on Transgenic Constructs ( 0 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Dvir\Rh4 Class Mutagen Stocks Known lesion
Aneuploid Aberrations
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data
Insertions
	Type of insertions Name Expression data
Gene Ontology: Function, Process & Cellular Component ( 5 unique terms )
Terms Based on Experimental Evidence ( 0 terms )
Terms Based on Predictions or Assertions ( 5 terms )
Molecular Function
CV term Evidence References
G-protein coupled receptor activity inferred from electronic annotation with InterPro:IPR000276 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
G-protein coupled receptor signaling pathway inferred from electronic annotation with InterPro:IPR000276, InterPro:IPR000856, InterPro:IPR001760 (FlyBase Curators et al., 2004-) phototransduction inferred from electronic annotation with InterPro:IPR000856 (FlyBase Curators et al., 2004-) visual perception inferred from electronic annotation with InterPro:IPR000856, InterPro:IPR001760 (FlyBase Curators et al., 2004-)
Cellular Component
CV term Evidence References
integral to membrane inferred from electronic annotation with InterPro:IPR000276, InterPro:IPR000856, InterPro:IPR001760 (FlyBase Curators et al., 2004-)
Sequence Ontology: Class of Gene
	gene   nuclear_gene (Drosophila 12 Genomes Consortium, 2008) protein_coding_gene (Drosophila 12 Genomes Consortium, 2008)
Interactions & Pathways
Summary of Physical Interactions
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions Dvir\Rh4 allele Gene References
External Data
Linkouts
Orthologs
OrthoDB Orthologs (1) - based on analysis using Dmel annotation version 5.41
OrthoDB Ortholog Groups
	OrthoDB orthology group searches (Waterhouse et al., 2011, Nucleic Acids Res. 39(Database issue): D283--D288) Drosophila inclusive ortholog search EOG62RDT9 Dipteran inclusive ortholog search EOG66WZJ2 Insect inclusive ortholog search EOG6J3VCK Arthropod inclusive ortholog search EOG61JWTR Metazoa inclusive ortholog search EOG6JHR8B
Ortholog(s) in Drosophila melanogaster (EOG62RDT9)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\Rh4 Y
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (1) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila melanogaster Dmel\Rh4
Stocks & Reagents
Stocks Listed in FlyBase ( 0 )
Genomic Clones ( 0 )
cDNA Clones ( 0 )
	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
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones
RNAi & Array Information
Linkouts
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments
Other Comments
	In contrast to D.melanogaster, where the sina gene is located within an intron of Rh4, Dvir\sina and Dvir\Rh4 are widely separated in D.virilis. This different structural arrangement may have been caused by the translocation of the Dvir\Rh4 gene to a different chromosomal location by a retrotransposition event in D.virilis. (Neufeld et al., 1991) Ecol\CAT reporter gene analysis has been used to identify the minimal R7 opsin regulatory regions of the Dvir\Rh4 promoter region. Dvir\Rh4 promoter can functionally interact with D.melanogaster transcriptional machinery to generate R7 specific patterns of gene expression. (Fortini and Rubin, 1990)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • XM_002048430 RefSeq (Proteins) • XP_002048466 DDBJ / EMBL / GenBank • AAA28855 CAA35743 EDW70808 M77281 X51351 Entrez Gene - A searchable database of RefSeq genes. • 6622763 UniProtKB/Swiss-Prot • P17646 UniProtKB/TrEMBL • Q8I169
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • G protein-coupled receptor, rhodopsin-like (IPR000276) Opsin RH3/RH4 (IPR000856) GPCR, rhodopsin-like, 7TM (IPR017452) Visual pigments (opsins) retinal binding site (IPR027430)
Linkouts
	FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0013092
Synonyms & Secondary IDs ( 5 )
Reported As
Symbol Synonym	dvir_GLEANR_11385 (Drosophila 12 Genomes Consortium, 2008) Dvir\Rh4 (Drosophila 12 Genomes Consortium, 2008) DVIRRH4 (Papatsenko et al., 2001) Rh4 (Drosophila 12 Genomes Consortium, 2008)
Name Synonym	Rhodopsin 4 (Zhang et al., 2004)
Secondary FlyBase IDs
References ( 14 )
Research paper	Drosophila 12 Genomes Consortium et al., 2007, Nature 450(7167): 203--218 Evolution of genes and genomes on the Drosophila phylogeny. [FBrf0200326] Zhang et al., 2004, Mol. Biol. Evol. 21(11): 2130--2139 Molecular evolution of sex-biased genes in Drosophila. [FBrf0180516] Tahayato et al., 2003, Dev. Cell 5(3): 391--402 Otd/Crx, a dual regulator for the specification of ommatidia subtypes in the Drosophila retina. [FBrf0162062] Wittkopp et al., 2003, Proc. Natl. Acad. Sci. U.S.A. 100(4): 1808--1813 Drosophila pigmentation evolution: Divergent genotypes underlying convergent phenotypes. [FBrf0157184] Papatsenko et al., 2001, Mech. Dev. 101(1-2): 143--153 A conserved regulatory element present in all Drosophila rhodopsin genes mediates Pax6 functions and participates in the fine-tuning of cell-specific expression. [FBrf0134746] McVean and Vieira, 1999, J. Mol. Evol. 49(1): 63--75 The evolution of codon preferences in Drosophila: a maximum-likelihood approach to parameter estimation and hypothesis testing. [FBrf0108927] Moriyama and Powell, 1997, J. Mol. Evol. 45(5): 514--523 Codon usage bias and tRNA abundance in Drosophila. [FBrf0098854] Akashi, 1994, Genetics 136(3): 927--935 Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. [FBrf0072469] Carulli et al., 1994, J. Mol. Evol. 38(3): 250--262 Phylogeny and physiology of Drosophila opsins. [FBrf0072778] Neufeld et al., 1991, Proc. Natl. Acad. Sci. U.S.A. 88: 10203--10207 Evolution of gene position: chromosomal arrangement and sequence comparison of the Drosophila melanogaster and Drosophila virilis sina and Rh4 genes. [FBrf0054938] Fortini and Rubin, 1990, Genes Dev. 4: 444--463 Analysis of cis-acting requirements of the Rh3 and Rh4 genes reveals a bipartite organization to rhodopsin promoters in Drosophila melanogaster. [FBrf0051852]
Personal communication to FlyBase	Drosophila 12 Genomes Consortium, 2008, personal communication to FlyBase Symbols and class of gene information for the GLEANR consensus sequences of the 11 sequenced non-melanogaster Drosophila species (Drosophila ananassae, erecta, grimshawi, mojavensis, persimilis, pseudoobscura, sechellia, simulans, willistoni, virilis and yakuba). [FBrf0202436] FlyBase Curators et al., 2004-, Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. [FBrf0174215]
FlyBase analysis	FlyBase, 2008, Newly sequenced Drosophila genomes: associations of GLEANR gene predictions (Releases 1.0) with previously known genes in FlyBase. Newly sequenced Drosophila genomes: associations of GLEANR gene predictions (Releases 1.0) with previously known genes in FlyBase. [FBrf0202439]