General Information
Symbol
Dmel\ry
Species
D. melanogaster
Name
rosy
Annotation Symbol
CG7642
Feature Type
FlyBase ID
FBgn0003308
Gene Model Status
Stock Availability
Enzyme Name (EC)
Xanthine dehydrogenase (1.17.1.4)
Xanthine oxidase (1.17.3.2)
Gene Snapshot
In progress.Contributions welcome.
Also Known As
Xdh, XOR
Genomic Location
Cytogenetic map
Sequence location
3R:13,032,528..13,038,020 [+]
Recombination map
3-53
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)
Belongs to the xanthine dehydrogenase family. (P10351)
Catalytic Activity (EC)
Experimental Evidence
Xanthine + NAD(+) + H(2)O = urate + NADH (1.17.1.4)
Predictions / Assertions
Xanthine + NAD(+) + H(2)O = urate + NADH (1.17.1.4)
Xanthine + H(2)O + O(2) = urate + H(2)O(2) (1.17.3.2)
Summaries
Gene Group Membership
CH OR CH2 GROUP OXIDOREDUCTASES -
CH or CH2 group oxidoreductases, include dehydrogenases that oxidize CH or CH2 group with the reduction of hydrogen or electron acceptor.
UniProt Contributed Function Data
Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid (By similarity).
(UniProt, P10351)
Phenotypic Description from the Red Book (Lindsley and Zimm 1992)
ry: rosy (A. Chovick and colleagues)
The structural gene for xanthine dehydrogenase [XDH (EC.1.2.1.37)]; it is a homodimer with subunit molecular weight estimated from its DNA sequence as 146,898 daltons (Keith, Riley, Kreitman, Lewontin, Curtis, and Chambers, 1987, Genetics 116: 67-73). Enzyme level responds to dose of ry+ alleles (Grell, 1962, Z. Indukt. Abstamm. Vererbungsl. 93: 371-77). XDH is a molybdenum hydroxylase and requires the activity of cin+, lxd+, mal+ for normal activity, though not for normal levels of CRM (Glassman, Shinoda, Duke, and Collins, 1968, Ann. N. Y. Acad. Sci. 151: 263-73). CRM (cross reacting material) contains bound molybdenum in the presence of mal; however, enzyme activity inhibited (Andres 1976, Eur. J. Biochem. 62: 591-600). Homozygotes for null alleles lack XDH activity (Forrest, Glassman, and Mitchell, 1956, Science 124: 725-26; Glassman and Mitchell, 1959, Genetics 44: 153-62; Hubby and Forrest, 1960, Genetics 45: 211-24) and have reddish brown eyes; accumulate enzyme's substrates, xanthine and 2-amino-4-hydroxypteridine as larvae plus hypoxanthine in the adult; precursors collect as solid granules in Malpighian tubules (Bonse, 1967, Z. Naturforsch. 22B: 1027-29); lack enzyme products uric acid and isoxanthopterin (Mitchell, Glassman, and Hadorn, 1959, Science 129: 268-69). Mutant homozygotes are also sensitive to administration of purine to the medium (Glassman, 1965, Fed. Proc. 24: 1243-51); survival on purine supplemented medium can be used to select for rare ry+ recombinants (Chovnick, Ballantyne, Baillie, and Holm, 1970, Genetics 66: 315-29) and unequal crossovers producing tandem duplications (Gelbart and Chovnick, 1979, Genetics 92: 849-59). Hypomorphic alleles that have normal eye color are also sensitive to appropriate levels of purine supplementation; furthermore, both wild types and hypomorphs can be made to display mutant eye color by administration of appropriate levels of the XDH inhibitor, HPP (allopurinol) [4-hydroxypyrazolo-(3,4-d) pyrimidine] (Glassman, 1965, Fed. Proc. 24: 1243-51; Boni, DeLerma, and Parisi, 1967, Experientia 23: 186-87; McCarron and Chovnick, 1981, Genetics 97: s70-71); in vitro and in vivo complementation between mal and ry products was demonstrated by Glassman (1952, Proc. Nat. Acad. Sci. USA 48: 1491-97; Glassman and McLean, 1962, Proc. Nat. Acad. Sci. USA 48: 1712-18). Pigmentation is nonautonomous in ry eye disks transplanted into wild-type hosts (Hadorn and Schwink, 1956, Nature 177: 940-41). Enzyme levels climb from low levels in the zygote to a peak at puparium formation; the level then falls but increases again to a maximum a few days after eclosion (Chovnick, McCarron, Hilliker, O'Donnell, Gelbart, and Clark, 1978, Cold Spring Harbor Symp. Quant. Biol. 42: 1011-21). Enzyme derived from the paternal genome appears during gastrulation; activity at time zero is low in ry+ zygotes produced by ry/+ females but undetectable in those produced by ry females (Sayles, Browder, and Williamson, 1973, Dev. Biol. 33: 213-17). Enzyme activity present in larval and adult fat bodies, larval and adult Malpighian tubules, and, in smaller amounts, in various regions of the larval and adult gut [Ursprung and Hadorn, 1961, Experientia 17: 230-31; Munz, 1964, Z. Indukt. Abstamm. Vererbungsl. 95: 195-210; Reaume, Clark, and Chovnick, 1989, Genetics 123: 503-09; Reaume (unpublished observations)]. XDH is not synthesized in the adult eye, but is transported there [Reaume et al., 1989].
ry409
Designation applied to the site at -1145 in ry+4 that is responsible for the higher than normal XDH CRM of that allele (i.e., ry409H vs. ry409N, the normal alternative; Curtis, Clark, Chovnick, and Bender, 1989, Genetics 122: 653-61). Enzyme activity two to three times that of other ry+ alleles (Chovnick, Gelbart, McCarron, Osmond, Candido, and Baillie, 1976, Genetics 84: 223-55); large tissue-specific increase in specific activity observed in late third-instar larval fat body, but not Malpighian tubules; mRNA levels 3.2 times higher than normal (Covington, Fleenor, and Devlin, 1976, Genetics 84: 211-32; see also Clark, Daniels, Rushlow, Hilliker, and Chovnick, 1984, Genetics 108: 953-68). Maps genetically to the right of ry1005 (Clark et al., 1984).
ry1005
Designation applied to the site at -1701 in ry+10 that is responsible for the lower than normal XDH CRM of that allele (i.e., ry1005L vs. ry1005N, the normal alternative) (Curtis, Clark, Chovnick, and Bender, 1989, Genetics 122: 653-61). Enzyme levels 50% those of other normal alleles (McCarron, O'Donnell, Chovnick, Bhullar, Hewitt, and Candido, 1979, Genetics 91: 275-93); mRNA levels 52% normal (Covington, Fleenor, and Devlin, 1976, Genetics 84: 211-32). Maps genetically to the left of ry409 (Clark, Daniels, Rushlow, Hilliker, and Chovnick, 1984, Genetics 108: 953-68).
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\ry or the JBrowse view of Dmel\ry 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 5.47
Low-frequency RNA-Seq exon junction(s) not annotated.
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0082704
4337
1335
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
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\ry 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 (19 terms)
Molecular Function (8 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (8 terms)
CV Term
Evidence
References
inferred from sequence or structural similarity with UniProtKB:P22985
(assigned by UniProt )
inferred from sequence or structural similarity with UniProtKB:P47989
(assigned by UniProt )
inferred from electronic annotation with InterPro:IPR001041
(assigned by InterPro )
inferred from electronic annotation with InterPro:IPR016166
(assigned by InterPro )
inferred from biological aspect of ancestor with PANTHER:PTN000225632
(assigned by GO_Central )
inferred from sequence or structural similarity with UniProtKB:P22985
(assigned by UniProt )
inferred from sequence or structural similarity with UniProtKB:P47989
(assigned by UniProt )
inferred from electronic annotation with InterPro:IPR016208
(assigned by InterPro )
inferred from sequence or structural similarity with UniProtKB:P22985
(assigned by UniProt )
inferred from sequence or structural similarity with UniProtKB:P47989
(assigned by UniProt )
inferred from sequence or structural similarity with UniProtKB:P22985
(assigned by UniProt )
inferred from biological aspect of ancestor with PANTHER:PTN000225632
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR014307
(assigned by InterPro )
Biological Process (10 terms)
Terms Based on Experimental Evidence (7 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000225632
(assigned by GO_Central )
inferred from sequence or structural similarity with UniProtKB:P22985
(assigned by UniProt )
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000225632
(assigned by GO_Central )
Expression Data
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
radioisotope in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism | ventral

Comment: ventral surface and anterior pole

organism | anterior

Comment: ventral surface and anterior pole

organism | anterior | posterior | ventral

Comment: ventral surface, anterior and posterior poles

Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Xanthine dehydrogenase, the ry product, is found in the granules of type II pigment cells.
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\ry 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) 4-6
  • Stages(s) 7-8
  • Stages(s) 11-12
  • Stages(s) 13-16
Alleles, Insertions, Transgenic Constructs and Phenotypes
Classical and Insertion Alleles ( 343 )
For All Classical and Insertion Alleles Show
 
Allele of ry
Class
Mutagen
Associated Insertion
Stocks
Known lesion
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                                                                                                          Other relevant insertions
                                                                                                          miscellaneous insertions
                                                                                                          Transgenic Constructs ( 20 )
                                                                                                          For All Alleles Carried on Transgenic Constructs Show
                                                                                                          Transgenic constructs containing/affecting coding region of ry
                                                                                                          Allele of ry
                                                                                                          Mutagen
                                                                                                          Associated Transgenic Construct
                                                                                                          Stocks
                                                                                                          Transgenic constructs containing regulatory region of ry
                                                                                                          characterization construct
                                                                                                          Name
                                                                                                          Expression Data
                                                                                                          Deletions and Duplications ( 83 )
                                                                                                          Not duplicated in
                                                                                                          Disrupted in
                                                                                                          Not disrupted in
                                                                                                          Summary of Phenotypes
                                                                                                          Orthologs
                                                                                                          Human Orthologs (via DIOPT v7.1)
                                                                                                          Homo sapiens (Human) (2)
                                                                                                          Species\Gene Symbol
                                                                                                          Score
                                                                                                          Best Score
                                                                                                          Best Reverse Score
                                                                                                          Alignment
                                                                                                          Complementation?
                                                                                                          Transgene?
                                                                                                          14 of 15
                                                                                                          Yes
                                                                                                          Yes
                                                                                                          7 of 15
                                                                                                          No
                                                                                                          Yes
                                                                                                          Model Organism Orthologs (via DIOPT v7.1)
                                                                                                          Mus musculus (laboratory mouse) (5)
                                                                                                          Species\Gene Symbol
                                                                                                          Score
                                                                                                          Best Score
                                                                                                          Best Reverse Score
                                                                                                          Alignment
                                                                                                          Complementation?
                                                                                                          Transgene?
                                                                                                          13 of 15
                                                                                                          Yes
                                                                                                          Yes
                                                                                                          7 of 15
                                                                                                          No
                                                                                                          Yes
                                                                                                          7 of 15
                                                                                                          No
                                                                                                          Yes
                                                                                                          7 of 15
                                                                                                          No
                                                                                                          Yes
                                                                                                          6 of 15
                                                                                                          No
                                                                                                          Yes
                                                                                                          Rattus norvegicus (Norway rat) (5)
                                                                                                          11 of 13
                                                                                                          Yes
                                                                                                          Yes
                                                                                                          5 of 13
                                                                                                          No
                                                                                                          Yes
                                                                                                          5 of 13
                                                                                                          No
                                                                                                          Yes
                                                                                                          4 of 13
                                                                                                          No
                                                                                                          Yes
                                                                                                          2 of 13
                                                                                                          No
                                                                                                          Yes
                                                                                                          Xenopus tropicalis (Western clawed frog) (3)
                                                                                                          6 of 12
                                                                                                          Yes
                                                                                                          Yes
                                                                                                          1 of 12
                                                                                                          No
                                                                                                          Yes
                                                                                                          1 of 12
                                                                                                          No
                                                                                                          Yes
                                                                                                          Danio rerio (Zebrafish) (3)
                                                                                                          14 of 15
                                                                                                          Yes
                                                                                                          Yes
                                                                                                          7 of 15
                                                                                                          No
                                                                                                          Yes
                                                                                                          6 of 15
                                                                                                          No
                                                                                                          Yes
                                                                                                          Caenorhabditis elegans (Nematode, roundworm) (4)
                                                                                                          15 of 15
                                                                                                          Yes
                                                                                                          Yes
                                                                                                          7 of 15
                                                                                                          No
                                                                                                          Yes
                                                                                                          6 of 15
                                                                                                          No
                                                                                                          Yes
                                                                                                          1 of 15
                                                                                                          No
                                                                                                          Yes
                                                                                                          Arabidopsis thaliana (thale-cress) (8)
                                                                                                          9 of 9
                                                                                                          Yes
                                                                                                          Yes
                                                                                                          7 of 9
                                                                                                          No
                                                                                                          Yes
                                                                                                          3 of 9
                                                                                                          No
                                                                                                          No
                                                                                                          3 of 9
                                                                                                          No
                                                                                                          No
                                                                                                          3 of 9
                                                                                                          No
                                                                                                          No
                                                                                                          3 of 9
                                                                                                          No
                                                                                                          No
                                                                                                          1 of 9
                                                                                                          No
                                                                                                          Yes
                                                                                                          1 of 9
                                                                                                          No
                                                                                                          Yes
                                                                                                          Saccharomyces cerevisiae (Brewer's yeast) (0)
                                                                                                          No orthologs reported.
                                                                                                          Schizosaccharomyces pombe (Fission yeast) (0)
                                                                                                          No orthologs reported.
                                                                                                          Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091900N2 )
                                                                                                          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 yakuba
                                                                                                          Drosophila ananassae
                                                                                                          Drosophila pseudoobscura pseudoobscura
                                                                                                          Drosophila persimilis
                                                                                                          Drosophila willistoni
                                                                                                          Drosophila virilis
                                                                                                          Drosophila mojavensis
                                                                                                          Drosophila grimshawi
                                                                                                          Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG0915004K )
                                                                                                          Organism
                                                                                                          Common Name
                                                                                                          Gene
                                                                                                          Multiple Dmel Genes in this Orthologous Group
                                                                                                          Musca domestica
                                                                                                          House fly
                                                                                                          Musca domestica
                                                                                                          House fly
                                                                                                          Musca domestica
                                                                                                          House fly
                                                                                                          Glossina morsitans
                                                                                                          Tsetse fly
                                                                                                          Lucilia cuprina
                                                                                                          Australian sheep blowfly
                                                                                                          Mayetiola destructor
                                                                                                          Hessian fly
                                                                                                          Aedes aegypti
                                                                                                          Yellow fever mosquito
                                                                                                          Aedes aegypti
                                                                                                          Yellow fever mosquito
                                                                                                          Aedes aegypti
                                                                                                          Yellow fever mosquito
                                                                                                          Anopheles darlingi
                                                                                                          American malaria mosquito
                                                                                                          Anopheles gambiae
                                                                                                          Malaria mosquito
                                                                                                          Anopheles gambiae
                                                                                                          Malaria mosquito
                                                                                                          Culex quinquefasciatus
                                                                                                          Southern house mosquito
                                                                                                          Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W00BW )
                                                                                                          Organism
                                                                                                          Common Name
                                                                                                          Gene
                                                                                                          Multiple Dmel Genes in this Orthologous Group
                                                                                                          Bombyx mori
                                                                                                          Silkmoth
                                                                                                          Danaus plexippus
                                                                                                          Monarch butterfly
                                                                                                          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
                                                                                                          Linepithema humile
                                                                                                          Argentine ant
                                                                                                          Megachile rotundata
                                                                                                          Alfalfa leafcutting bee
                                                                                                          Nasonia vitripennis
                                                                                                          Parasitic wasp
                                                                                                          Nasonia vitripennis
                                                                                                          Parasitic wasp
                                                                                                          Nasonia vitripennis
                                                                                                          Parasitic wasp
                                                                                                          Tribolium castaneum
                                                                                                          Red flour beetle
                                                                                                          Tribolium castaneum
                                                                                                          Red flour 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
                                                                                                          Zootermopsis nevadensis
                                                                                                          Nevada dampwood termite
                                                                                                          Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X00EY )
                                                                                                          Organism
                                                                                                          Common Name
                                                                                                          Gene
                                                                                                          Multiple Dmel Genes in this Orthologous Group
                                                                                                          Strigamia maritima
                                                                                                          European centipede
                                                                                                          Ixodes scapularis
                                                                                                          Black-legged tick
                                                                                                          Daphnia pulex
                                                                                                          Water flea
                                                                                                          Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G01AW )
                                                                                                          Organism
                                                                                                          Common Name
                                                                                                          Gene
                                                                                                          Multiple Dmel Genes in this Orthologous Group
                                                                                                          Strongylocentrotus purpuratus
                                                                                                          Purple sea urchin
                                                                                                          Strongylocentrotus purpuratus
                                                                                                          Purple sea urchin
                                                                                                          Strongylocentrotus purpuratus
                                                                                                          Purple sea urchin
                                                                                                          Strongylocentrotus purpuratus
                                                                                                          Purple sea urchin
                                                                                                          Strongylocentrotus purpuratus
                                                                                                          Purple sea urchin
                                                                                                          Strongylocentrotus purpuratus
                                                                                                          Purple sea urchin
                                                                                                          Ciona intestinalis
                                                                                                          Vase tunicate
                                                                                                          Ciona intestinalis
                                                                                                          Vase tunicate
                                                                                                          Ciona intestinalis
                                                                                                          Vase tunicate
                                                                                                          Gallus gallus
                                                                                                          Domestic chicken
                                                                                                          Gallus gallus
                                                                                                          Domestic chicken
                                                                                                          Gallus gallus
                                                                                                          Domestic chicken
                                                                                                          Human Disease Model Data
                                                                                                          FlyBase Human Disease Model Reports
                                                                                                          Alleles Reported to Model Human Disease (Disease Ontology)
                                                                                                          Download
                                                                                                          Models ( 3 )
                                                                                                          Allele
                                                                                                          Disease
                                                                                                          Evidence
                                                                                                          References
                                                                                                          model of  xanthinuria
                                                                                                          inferred from mutant phenotype
                                                                                                          model of  xanthinuria
                                                                                                          inferred from mutant phenotype
                                                                                                          model of  xanthinuria
                                                                                                          inferred from mutant phenotype
                                                                                                          Interactions ( 1 )
                                                                                                          Allele
                                                                                                          Disease
                                                                                                          Interaction
                                                                                                          References
                                                                                                          model of  xanthinuria
                                                                                                          is ameliorated by ZnT35CKK112697
                                                                                                          is ameliorated by Zip71BGD2461
                                                                                                          is NOT ameliorated by ZnT63CKK102261
                                                                                                          is NOT ameliorated by ZnT41FKK111282
                                                                                                          Comments ( 2 )
                                                                                                           
                                                                                                          The fly stones in the ryGD8894 model are physically and visually similar to human kidney stones, though smaller in size.
                                                                                                          The fly stones in the ryKK101010 model are physically and visually similar to human kidney stones, though smaller in size.
                                                                                                          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
                                                                                                          esyN Network Diagram
                                                                                                          Interactions Browser
                                                                                                          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
                                                                                                          Subunit Structure (UniProtKB)
                                                                                                          Homodimer.
                                                                                                          (UniProt, P10351 )
                                                                                                          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
                                                                                                          Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                                                                                                          Genomic Location and Detailed Mapping Data
                                                                                                          Chromosome (arm)
                                                                                                          3R
                                                                                                          Recombination map
                                                                                                          3-53
                                                                                                          Cytogenetic map
                                                                                                          Sequence location
                                                                                                          3R:13,032,528..13,038,020 [+]
                                                                                                          FlyBase Computed Cytological Location
                                                                                                          Cytogenetic map
                                                                                                          Evidence for location
                                                                                                          87D9-87D9
                                                                                                          Limits computationally determined from genome sequence between P{PZ}CtBP03463 and P{lacW}B52s2249&P{lacW}flflL4179
                                                                                                          Experimentally Determined Cytological Location
                                                                                                          Cytogenetic map
                                                                                                          Notes
                                                                                                          References
                                                                                                          87D11-87D12
                                                                                                          (determined by in situ hybridisation)
                                                                                                          87D-87D
                                                                                                          (determined by in situ hybridisation)
                                                                                                          87D7-87D12
                                                                                                          (determined by in situ hybridisation)
                                                                                                          87D5-87E5
                                                                                                          (determined by in situ hybridisation)
                                                                                                          Experimentally Determined Recombination Data
                                                                                                          Left of (cM)
                                                                                                          Right of (cM)
                                                                                                          Notes
                                                                                                          Stocks and Reagents
                                                                                                          Stocks (3,178)
                                                                                                          Genomic Clones (15)
                                                                                                           

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

                                                                                                          cDNA Clones (11)
                                                                                                           

                                                                                                          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 database merge of
                                                                                                            Additional comments
                                                                                                            ry alleles have been detected by several criteria, including electrophoretic mobility of XDH, purine sensitivity and rosy eye color, either in the absence or presence of allopurinol. Chovnick and his colleagues (Chovnick, Gelbart, and McCarron, 1980) identify at least seven different electromorphs in laboratory stocks; using a highly discriminating series of gel conditions, Buchanan and Johnson (1983) identified, among 62 wild-type chromosomes isolated from nature, fourteen electromorphs, two of which corresponded to those contained among the earlier seven. Both induced mutations and natural variable sites are designated by the number of the + progenitor followed by specific derivative numbers, e.g. ry102 is the second mutant derivative of ry+1d. Not all mutants with allelic designations with values less than 100 are known to be derivatives of ry+0; however, those numbered from 3a to 54 (excepting 17, 20 and 21) are known to be so derived. However, those mutations discovered by Girton, Green, Daniels, Lewis, Spradling and Rubin do not use this system of nomenclature. Finally, Chovnick's laboratory maintains several hundred mutants not reported here, including a group generated on a ry+11 background. ry+ allele designation refers to the entire rosy DNA sequence. Electrophoretic markers and control variants characteristic of a given allele represent only a few of the bp polymorphisms distinguishing one ry+ allele from another. ry+ alleles originated as iso-3 stocks from wild populations, with the exception of those marked (derivative) which are conversions to wild type of an unique rosy mutant allele. These may carry bp polymorphisms within the conversion segment not common to the original rosy mutant. 'tentative constitution': Polymorphic sites segregating in wild type alleles; the digits to the left of the slash bar represent the phenotype with respect to the 5' cis-acting control elements, 1005 and 409, with '0' indicating the CRM levels of ry+0, '+' representing higher CRM, and '-' indicating lower CRM. The remaining digits designate the electrophoretic charge relative to that of XDH produced by ry+0 attributable to the amino-acid residues inferred to correspond to the three sites inferred from mapping and sequencing results; the sites are indicated in order and are located at +736, +1551 and +3557 in the gene sequence (Curtis, unpublished): '0' indicates the relative charge at the three sites of ry+0; '-' indicates a more negative charge, i.e. less anodically migrating; and '+' a more positive charge. Nucleotide positions are defined with respect to +1 of the nucleotide sequence defined as the second base pair in an EcoRI site in the second exon; transcription from left to right. The molecular biology was referenced from one or more of the following: Curtis and Bender (unpublished results); Curtis, Clark, Chovnick and Bender, 1989; Gray and Bender (unpublished results); Lee, Curtis, McCarron, Love, Gray, Bender, and Chovnick, 1987.
                                                                                                            Other Comments
                                                                                                            In a sample of 79 genes with multiple introns, 33 showed significant heterogeneity in G+C content among introns of the same gene and significant positive correspondence between the intron and the third codon position G+C content within genes. These results are consistent with selection adding against preferred codons at the start of genes.
                                                                                                            Phylogenetic distribution of introns in the gene coding for ry in 37 species, including 31 dipterans, is analysed. Three narrowly distributed novel introns are identified across the species. The phylogenetic distribution of these introns favours the 'introns-late' theory of the origin of genes. Analysis of the nucleotide sequences indicates that all three introns have arisen by duplication of a preexisting intron, which is pervasive in Drosophila and other dipterans.
                                                                                                            A mutation in the flavin domain of ry is engineered and successfully expressed.
                                                                                                            The effects on the properties of the enzyme of specific mutations in different regions of the ry protein sequence are studied.
                                                                                                            Chromosome homologies of Muller's element D (J chromosome in the Paleartic species and XR chromosome arm in Nearctic species) and of element E (O chromosome in the Paleartic species and 2 chromosome in Nearctic species) have been confirmed by single copy probes in the species of the obscura group and in D.melanogaster.
                                                                                                            mRNA levels increase at adult day 5 in strain showing extended longevity phenotype (ELP).
                                                                                                            The parameters of meiotic gene conversion tract length distribution have been determined using extensive co-conversion data for selected and unselected sites of known molecular location in the ry locus. The mean conversion tract length of 352 base pairs indicates that gene conversion tract lengths are sufficiently small to allow for extensive shuffling of DNA sequence polymorphisms within a gene. For selected site conversions there is a bias towards recovery of longer tracts, the mean conversion tract length being 706 base pairs. Meiotic gene conversion and P element induced gap repair are distinct processes defined by different parameters and, possibly, mechanisms.
                                                                                                            In vivo crosslinking studies demonstrate that endogenous eve and ftz protein significantly interacts with the promoter region, although this is not an expected target gene.
                                                                                                            DNA elements 5' to the coding region that are important in proper regulation of expression have little evolutionary conservation in the vicinity of gene homologs.
                                                                                                            ry mutants have been characterised from amino acid sequence comparisons and from enzyme activity measurements.
                                                                                                            Wild type ry enzyme and a mutant ry enzyme, a point mutation within the iron-sulphur domain, are isolated and characterised.
                                                                                                            No difference in allele fixed in lines selected over 700 generations for high (negative) and low (positive) geotaxis.
                                                                                                            The distribution of ry protein in the tissues of the adult fly is altered in mutants of a number of genes, including bw, ltd, st, w, mal and ca. ry protein is absent from the eye in these mutants, but is present at normal levels in the fat body surrounding the eye as well as in other tissues where it is synthesised. The distribution of ry protein in the tissues of the adult fly is also altered in v and cn mutants; ry protein is absent from the eye in these mutants, but is present at normal levels in the fat body surrounding the eye. The localisation of ry protein within the eye is abnormal in cho and pn mutants.
                                                                                                            P element mediated transformation of the ry::Cvic\Xdh chimeric ry gene demonstrates it to be physiologically active. Activity levels are lower than wild type suggesting that the Cvic\Xdh sequences are inefficient for mRNA production or the mRNA is unstable.
                                                                                                            The sequence and organisation of the D.melanogaster ry gene has been compared with Cvic\Xdh.
                                                                                                            ry protein is not synthesised in the eye, but is transported and sequestered there.
                                                                                                            Dpse\ry has been cloned and sequenced, and compared with D.melanogaster ry.
                                                                                                            l(3)87Df maps immediately proximal to the 5' end of the ry gene.
                                                                                                            The locus has been extensively mapped by reciprocal recombination and conversion studies (see appended maps). Seven different classes of complementing or partially complementing alleles described; complementation map circular (Gelbart et al., 1976). ry+ commonly used as a marker in P-element transformation experiments (Spradling and Rubin, 1982; Rubin and Spradling, 1982).
                                                                                                            The structural gene for xanthine dehydrogenase (XDH); it is a homodimer with subunit molecular weight estimated from its DNA sequence as 146,898 daltons (Keith, Riley, Kreitman, Lewontin, Curtis and Chambers, 1987). Enzyme level responds to dose of ry+ alleles (Grell, 1962). XDH is a molybdenum hydroxylase and requires the activity of cin+, lxd+, mal+ for normal activity, though not for normal levels of CRM (Glassman, Shinoda, Duke and Collins, 1968). CRM (cross-reacting material) contains bound molybdenum in the presence of mal; however, enzyme activity inhibited (Andres, 1976). Homozygotes for null alleles lack XDH activity (Forrest, Glassman and Mitchell, 1956; Glassman and Mitchell, 1959; Hubby and Forrest, 1960) and have reddish brown eyes; accumulate enzyme's substrates, xanthine and 2-amino-4-hydroxypteridine as larvae plus hypoxanthine in the adult; precursors collect as solid granules in Malpighian tubules (Bonse, 1967); lack enzyme products uric acid and isoxanthopterin (Mitchell, Glassman and Hadorn, 1959). Mutant homozygotes are also sensitive to administration of purine to the medium (Glassman, 1965); survival on purine supplemented medium can be used to select for rare ry+ recombinants (Chovnick, Ballantyne, Baillie and Holm, 1970) and unequal crossovers producing tandem duplications (Gelbart and Chovnick, 1979). Hypomorphic alleles that have normal eye color are also sensitive to appropriate levels of purine supplementation; furthermore, both wild types and hypomorphs can be made to display mutant eye color by administration of appropriate levels of the XDH inhibitor, HPP (allopurinol) <up>4-hydroxypyrazolo-(3,4-d) pyrimidine</up> (Glassman, 1965; Boni, DeLerma and Parisi, 1967; McCarron and Chovnick, 1981); in vitro and in vivo complementation between mal and ry products was demonstrated by Glassman (1952) (Glassman and McLean, 1962). Pigmentation is nonautonomous in ry eye discs trans- planted into wild-type hosts (Hadorn and Schwink, 1956). Enzyme levels climb from low levels in the zygote to a peak at puparium formation; the level then falls but increases again to a maximum a few days after eclosion (Chovnick, McCarron, Hilliker, O'Donnell, Gelbart and Clark, 1978). Enzyme derived from the paternal genome appears during gastrulation; activity at time zero is low in ry+ zygotes produced by ry/+ females but undetectable in those produced by ry females (Sayles, Browder and Williamson, 1973). Enzyme activity present in larval and adult fat bodies, larval and adult Malpighian tubules, and, in smaller amounts, in various regions of the larval and adult gut (Ursprung and Hadorn, 1961; Munz, 1964; Reaume, Clark, and Chovnick, 1989; Reaume (unpublished observations)</up>. XDH is not synthesized in the adult eye, but is transported there (Reaume, Clark and Chovnick, 1989).
                                                                                                            Origin and Etymology
                                                                                                            Discoverer
                                                                                                            Etymology
                                                                                                            Identification
                                                                                                            External Crossreferences and Linkouts ( 51 )
                                                                                                            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
                                                                                                            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 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
                                                                                                            InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
                                                                                                            KEGG Genes - Molecular building blocks of life in the genomic space.
                                                                                                            modMine - A data warehouse for the modENCODE project
                                                                                                            Synonyms and Secondary IDs (13)
                                                                                                            Reported As
                                                                                                            Symbol Synonym
                                                                                                            Secondary FlyBase IDs
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                                                                                                              References (801)