FB2024_04 , released June 25, 2024
Gene: Dmel\su(r)
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General Information
Symbol
Dmel\su(r)
Species
D. melanogaster
Name
suppressor of rudimentary
Annotation Symbol
CG2194
Feature Type
protein_coding_gene
FlyBase ID
FBgn0086450
Gene Model Status
Current
Stock Availability
12 publicly available
Enzyme Name (EC)
dihydropyrimidine dehydrogenase (NADP(+)) (1.3.1.2)
Gene Summary
suppressor of rudimentary (su(r)) encodes a dihydropyrimidine dehydrogenase, the first step of pyrimidine catabolism. su(r) depletion does not produce visible phenotypes, but synergistic effects are exhibited by combining mutants with genes affecting pyrimidine biosynthesis and beta-alanine metabolism. [Date last reviewed: 2019-09-26] (FlyBase Gene Snapshot)
All Summaries
Also Known As

Reg-3, Dreg-3, Drosophila Rhythmically expressed gene 3

Key Links
Genomic Location
Cytogenetic map
8D1-8D1
Sequence location
Recombination map
1-27
RefSeq locus
NC_004354 REGION:9196808..9201820
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (10 terms)
Molecular Function (5 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
enables dihydropyrimidine dehydrogenase (NADP+) activity
inferred from biological aspect of ancestor with PANTHER:PTN000234105
(GO Reference Genome Project, 2011-)
inferred from sequence or structural similarity with UniProtKB:Q12882
(Gene Ontology Curators, 2002-)
enables iron-sulfur cluster binding
inferred from electronic annotation with InterPro:IPR009051
(InterPro Project Members, 2004-)
enables NADP binding
inferred from biological aspect of ancestor with PANTHER:PTN000234105
(GO Reference Genome Project, 2011-)
enables oxidoreductase activity, acting on the CH-CH group of donors
inferred from electronic annotation with InterPro:IPR001295, InterPro:IPR005720
(InterPro Project Members, 2004-)
enables uracil binding
inferred from biological aspect of ancestor with PANTHER:PTN000234105
(GO Reference Genome Project, 2011-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in 'de novo' pyrimidine nucleobase biosynthetic process
inferred from genetic interaction with FLYBASE:r; FB:FBgn0003189
(Rawls, 2006)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
involved_in 'de novo' pyrimidine nucleobase biosynthetic process
inferred from electronic annotation with InterPro:IPR001295
(InterPro Project Members, 2004-)
involved_in thymine catabolic process
inferred from biological aspect of ancestor with PANTHER:PTN000234105
(GO Reference Genome Project, 2011-)
involved_in uracil catabolic process
inferred from biological aspect of ancestor with PANTHER:PTN000234105
(GO Reference Genome Project, 2011-)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
located_in cytoplasm
inferred from electronic annotation with InterPro:IPR005720
(InterPro Project Members, 2004-)
is_active_in cytosol
inferred from biological aspect of ancestor with PANTHER:PTN000234106
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Catalytic Activity (EC/Rhea)
dihydropyrimidine dehydrogenase (NADP+) activity
5,6-dihydrouracil + NADP(+) = H(+) + NADPH + uracil (1.3.1.2)
RHEA 18093:
Summaries
Gene Snapshot
suppressor of rudimentary (su(r)) encodes a dihydropyrimidine dehydrogenase, the first step of pyrimidine catabolism. su(r) depletion does not produce visible phenotypes, but synergistic effects are exhibited by combining mutants with genes affecting pyrimidine biosynthesis and beta-alanine metabolism. [Date last reviewed: 2019-09-26]
Gene Group (FlyBase)
UNCLASSIFIED CH-CH OXIDOREDUCTASES, NAD OR NADP AS ACCEPTOR -
*D This group comprises CH-CH oxidoreductases using NAD or NADP as acceptor that do not classify under other groups in FlyBase.
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
su(r): suppressor of rudimentary
Suppresses both the phenotypic effects and the female sterility of all r alleles; also suppresses the r phenocopying and lethal effects of 6-azauracil administration. Little or no dihydrouracil dehydrogenase (EC 1.3.99.11) activity. Thought to interfere with pyrimidine catabolism. Unable to degrade uracil and extremely sensitive to exogenous pyrimidine. Enhances the expression of dp and net, and causes b flies to have very black bodies, darker than wild type, especially along the wing veins; forms synthetic lethals in combination with tt and whd.
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\su(r) 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
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9W374)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Gene model reviewed during 5.50

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.55

Sequence Ontology: Class of Gene
gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
su(r)-RC
FBtr0071338
NM_167182
3399
1031
Additional Transcript Data and Comments
Reported size (kB)

2.7 (northern blot)

(van Gelder et al., 1995)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
su(r)-PC
FBpp0071273
111.2
1031
6.78
Q9W374
NP_727320
AAN09247
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)

626 (aa)

(van Gelder et al., 1995)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
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\su(r) using the Feature Mapper tool.

External Data
Crossreferences
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.66

Transcript Expression
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 17
organism
(van Gelder et al., 1995)
adult stage
adult head
(van Gelder et al., 1995)
Additional Descriptive Data

su(r) transcripts are expressed with a circadian rhythm and show a single daily peak and trough of expression. The peak occurs at ZT 2 and the trough at ZT 14. The phase of expression could be altered by a change in the feeding time. Transcript levels continue to cycle in the absence of a light-dark cycle. Transcripts were detected in adult heads but not bodies and were also detected in late embryos.

(van Gelder et al., 1995)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\su(r) in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
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
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 16 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of su(r)
Transgenic constructs containing regulatory region of su(r)
Aberrations (Deficiencies and Duplications) ( 0 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
viable
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4pnr-MD237
Sterility
Allele
fertile
Other Phenotypes
Allele
chemical sensitive
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (3)
Hsap\DPYD
13 of 14
Yes
Yes
1  
Hsap\DHODH
1 of 14
No
No
Hsap\FDXR
1 of 14
No
No
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (3)
Rnor\Dpyd
12 of 14
Yes
Yes
Rnor\Dhodh
1 of 14
No
No
Rnor\Fdxr
1 of 14
No
No
Mus musculus (laboratory mouse) (3)
Mmus\Dpyd
12 of 14
Yes
Yes
Mmus\Dhodh
1 of 14
No
No
Mmus\Fdxr
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (3)
Xtro\dpyd
7 of 13
Yes
Yes
Xtro\dhodh
1 of 13
No
No
Xtro\znf554
1 of 13
No
Yes
Danio rerio (Zebrafish) (5)
Drer\dpydb
13 of 14
Yes
Yes
Drer\dpyda.1
4 of 14
No
Yes
Drer\aifm4
1 of 14
No
No
Drer\dhodh
1 of 14
No
No
Drer\fdxr
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (4)
Cele\dpyd-1
13 of 14
Yes
Yes
Cele\dhod-1
1 of 14
No
No
Cele\W07E11.1
1 of 14
No
No
Cele\Y62E10A.6
1 of 14
No
No
Anopheles gambiae (African malaria mosquito) (4)
Agam\AgaP_AGAP001021
11 of 12
Yes
Yes
Agam\AgaP_AGAP002037
1 of 12
No
No
Agam\AgaP_AGAP005419
1 of 12
No
No
Agam\AgaP_AGAP006360
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (5)
Atha\PYD1
7 of 13
Yes
Yes
Atha\AT4G32360
1 of 13
No
No
Atha\GLT1
1 of 13
No
No
Atha\NTRC
1 of 13
No
No
Atha\PYRD
1 of 13
No
No
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\URA1
3 of 13
Yes
No
Scer\GLT1
1 of 13
No
No
Schizosaccharomyces pombe (Fission yeast) (3)
Spom\arh1
1 of 12
Yes
No
Spom\glt1
1 of 12
Yes
No
Spom\ura3
1 of 12
Yes
No
Escherichia coli (enterobacterium) (8)
Ecol\preA
6 of 11
Yes
Yes
Ecol\preT
5 of 11
No
Yes
Ecol\aegA
4 of 11
No
Yes
Ecol\gltD
4 of 11
No
Yes
Ecol\ygfT
4 of 11
No
Yes
Ecol\ygfK
3 of 11
No
Yes
Ecol\fadH
1 of 11
No
Yes
Ecol\pyrD
1 of 11
No
No
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:su(r). Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (3)
CG9674
2 of 13
dare
2 of 13
Dhod
2 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 1 )
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
    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
    DO term
    Complementation?
    Transgene?
    DPYD; dihydropyrimidine dehydrogenase
    13 of 14
    612779
     
    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
    Other Interaction Browsers
    Summary of Genetic Interactions
    esyN Network Diagram
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    esyN Network Key:
    Suppression
    Enhancement
    Other Interaction Browsers
    View in FlyBase Interactions Browser   View in MIST tool (external link)
    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
    r
    suppressible
    su(r)
    (Rawls, 2006, Bahn, 1972)
    External Data
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    MIST (genetic) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    KEGG Metabolic Pathways - A collection of manually drawn metabolic pathway maps representing knowledge of molecular interaction, reaction and relation networks.
    Reactome Metabolic Pathways - An open-source, open access, manually curated and peer-reviewed metabolic pathway database.
    External Data
    Linkouts
    KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    X
    Recombination map
    1-27
    Cytogenetic map
    8D1-8D1
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    8D1-8D1
    Limits computationally determined from genome sequence between P{EP}EP1450&P{EP}EP1356 and P{EP}EP912EP912
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    1-27

    (FlyBase, 2016, Gojkovic, 2002.9.10)

    1-28.1

    (Comeron et al., 2012)

    1-27.7

    (Bahn, 1972)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (12)
    Genomic Clones (14)
     

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

    cDNA Clones (71)
     

    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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequenced
    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)
      BDGP DGC clones
      Other clones
      RNAi and Array Information
      Linkouts
      DRSC - Results frm RNAi screens
      Antibody Information
      Laboratory Generated Antibodies
       
      Commercially Available Antibodies
       
      Cell Line Information
      Publicly Available Cell Lines
       
        Other Stable Cell Lines
         
          Other Comments

          Isolated as a rhythmically expressed transcript in fly heads. Transcript shows a single daily peak and a single daily trough in expression, highest expression is in the 'morning'. Reg-3 expression oscillation is dependent on a light-dark cycle, on timed feeding and on the function of the per gene.

          (van Gelder et al., 1995)
          Relationship to Other Genes
          Source for database merge of

          Source for merge of: su(r) Reg-3

          (Rawls, 2006)
          Additional comments
          Nomenclature History
          Source for database identify of

          Source for identity of: Reg-3 CG2194

          (Nusskern, 1999.11)
          Nomenclature comments
          Etymology
          Synonyms and Secondary IDs (11)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 65 )
          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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
          UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
          Other crossreferences
          AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
          BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
          DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
          EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
          FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
          FlyMine - An integrated database for Drosophila genomics
          InterPro - A database of protein families, domains and functional sites
          KEGG Genes - Molecular building blocks of life in the genomic space.
          MARRVEL_MODEL - MARRVEL (model organism gene)
          Linkouts
          BioGRID - A database of protein and genetic interactions.
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          DroID - A comprehensive database of gene and protein interactions.
          DRSC - Results frm RNAi screens
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          FlyCyc Genes - 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
          FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          KEGG Metabolic Pathways - A collection of manually drawn metabolic pathway maps representing knowledge of molecular interaction, reaction and relation networks.
          KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
          MIST (genetic) - An integrated Molecular Interaction Database
          Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
          Reactome Metabolic Pathways - An open-source, open access, manually curated and peer-reviewed metabolic pathway database.
          References (66)