General Information
Symbol
Dmel\r-l
Species
D. melanogaster
Name
rudimentary-like
Annotation Symbol
CG3593
Feature Type
FlyBase ID
FBgn0003257
Gene Model Status
Stock Availability
Enzyme Name (EC)
Orotate phosphoribosyltransferase (2.4.2.10)
Orotidine-5'-phosphate decarboxylase (4.1.1.23)
Gene Snapshot
In progress.Contributions welcome.
Genomic Location
Cytogenetic map
Sequence location
3R:21,070,557..21,073,319 [-]
Recombination map
3-70
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
GO Summary Ribbons
Families, Domains and Molecular Function
Gene Group Membership (FlyBase)
Protein Family (UniProt, Sequence Similarities)
-
Molecular Function (see GO section for details)
Catalytic Activity (EC)
Experimental Evidence
Orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate (2.4.2.10)
Orotidine 5'-phosphate = UMP + CO(2) (4.1.1.23)
Predictions / Assertions
-
Summaries
Gene Group Membership
CARBOXY-LYASES -
Carboxy-lyases are involved in the the addition of a carboxyl group to a compound (carboxylases) or the removal of a carboxyl group from a compound (decarboxylases). (Adapted from FBrf0238856).
Phenotypic Description from the Red Book (Lindsley and Zimm 1992)
r-l: rudimentary-like
Encodes a polypeptide with the enzyme activities that catalyze the fifth and sixth steps of de novo pyrimidine synthesis: orotate phosphoribosyl transferase [OPRT (EC. 2.4.2.10)] and orotidylate decarboxylase [ODC (EC. 4.1.1.23)] respectively. Thought to exist as a homodimer (Rawls, 1979, Comp. Biochem. Physiol. 62B: 207-16). The first three enzyme activities encoded by r and the fourth by Dhod. OPRT and ODC activities drastically reduced except that OPRT moderately reduced in r-lK7 and ODC above normal in r-lK6. All mutants accumulate orotic acid, the substrate of ODC. Flies hemizygous or homozygous for mutants at this locus resemble r in that they have obliquely truncated wings with deranged marginal hairs and virtual female sterility; they differ from r in having faintly mottled eyes and severely impaired viability (viability of hypomorphs moderately reduced). r is epistatic to r-l in that r; r-l flies display the r rather than the r-l phenotype, suggesting that mottled eyes and reduced viability are the consequence of orotic-acid accumulation rather than pyrimidine deficiency.
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\r-l or the JBrowse view of Dmel\r-l for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Comments on Gene Model
Gene model reviewed during 5.46
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0084038
2039
493
Additional Transcript Data and Comments
Reported size (kB)
1.75 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0083440
53.4
493
7.29
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\r-l using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (5 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (0 terms)
Biological Process (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR014732
(assigned by InterPro )
inferred from electronic annotation with InterPro:IPR000836
(assigned by InterPro )
Cellular Component (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
r-l transcripts are observed in embryos. Other stages were not tested.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\r-l in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 12 )
Transgenic Constructs ( 8 )
Deletions and Duplications ( 6 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
Allele
Phenotype manifest in
Allele
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
14 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
14 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
13 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
7 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
14 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
12 of 15
Yes
Yes
8 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (1)
8 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (3)
11 of 15
Yes
Yes
5 of 15
No
Yes
5 of 15
No
Yes
Schizosaccharomyces pombe (Fission yeast) (2)
9 of 12
Yes
Yes
4 of 12
No
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG0919079M )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091504LI )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W04DV )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Bombus terrestris
Buff-tailed bumblebee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X04AM )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G06JT )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Human Disease Model Data
FlyBase Human Disease Model Reports
    Alleles Reported to Model Human Disease (Disease Ontology)
    Download
    Models ( 0 )
    Allele
    Disease
    Evidence
    References
    Interactions ( 0 )
    Allele
    Disease
    Interaction
    References
    Comments ( 0 )
     
    Human Orthologs (via DIOPT v7.1)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    Complementation?
    Transgene?
    Functional Complementation Data
    Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
    Interactions
    Summary of Physical Interactions
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    Please look at the allele data for full details of the genetic interactions
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Linkouts
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    Pathways
    Gene Group - Pathway Membership (FlyBase)
    External Data
    Linkouts
    FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-70
    Cytogenetic map
    Sequence location
    3R:21,070,557..21,073,319 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    93B10-93B10
    Limits computationally determined from genome sequence between P{PZ}Atpα01164 and P{PZ}mod(mdg4)07038&P{lacW}mod(mdg4)L3101
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    93B6-93B7
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Location
    3-70.4
    Left of (cM)
    Right of (cM)
    Notes
    Mapping based on 240 gl-e recombinants.
    Stocks and Reagents
    Stocks (14)
    Genomic Clones (11)
     

    Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

    cDNA Clones (46)
     

    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 sequences
    BDGP DGC clones
    Other clones
    Drosophila Genomics Resource Center cDNA clones

    For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

    cDNA Clones, End Sequenced (ESTs)
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    Antibody Information
    Laboratory Generated Antibodies
     
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of
    Source for identity of: r-l CG3593
    Source for database merge of
    Additional comments
    Other Comments
    Full sequence and embryonic transcript of r-l have been determined and the deduced UMP synthase structure compared with other protein sequences; major structural features among these proteins are revealed.
    Molecular cloning of r-l has been performed to permit analysis of its regulation relative to other pyrimidine pathway genes.
    Encodes a polypeptide with the enzyme activities that catalyze the fifth and sixth steps of de novo pyrimidine synthesis: orotate phosphoribosyl transferase (OPRT) and orotidylate decarboxylase (ODC) respectively. Thought to exist as a homodimer (FBrf0032871). The first three enzyme activities encoded by r and the fourth by Dhod.
    OPRT and ODC activities drastically reduced except that OPRT moderately reduced in r-lK7 and ODC above normal in r-lK6. All mutants accumulate orotic acid, the substrate of ODC. Flies hemizygous or homozygous for mutants at this locus resemble r in that they have obliquely truncated wings with deranged marginal hairs and virtual female sterility; they differ from r in having faintly mottled eyes and severely impaired viability (viability of hypomorphs moderately reduced). r is epistatic to r-l in that r; r-l flies display the r rather than the r-l phenotype, suggesting that mottled eyes and reduced viability are the consequence of orotic-acid accumulation rather than pyrimidine deficiency.
    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 48 )
    Sequence Crossreferences
    NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
    GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
    GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
    RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
    UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
    Linkouts
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center cDNA clones
    DPiM - Drosophila Protein interaction map
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
    FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    Flygut - An atlas of the Drosophila adult midgut
    FlyMine - An integrated database for Drosophila genomics
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    KEGG Genes - Molecular building blocks of life in the genomic space.
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    modMine - A data warehouse for the modENCODE project
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Synonyms and Secondary IDs (10)
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    References (62)