General Information
Symbol
Dmel\RpS3
Species
D. melanogaster
Name
Ribosomal protein S3
Annotation Symbol
CG6779
Feature Type
FlyBase ID
FBgn0002622
Gene Model Status
Stock Availability
Enzyme Name (EC)
DNA-formamidopyrimidine glycosylase (3.2.2.23)
DNA-(apurinic or apyrimidinic site) lyase (4.2.99.18)
Gene Snapshot
Ribosomal protein S3 (RpS3) is a component of the small subunit of cytoplasmic ribosomes, which translate mRNAs encoded by the nuclear genome. The gene is haploinsufficient - heterozygous mutants display the 'Minute' phenotype, characterized by a slower developmental rate and small adult bristles. RpS3 also contains a DNA lyase activity and functions in DNA repair. [Date last reviewed: 2016-06-23]
Also Known As
M(3)95A, M(3)w, S3, M(3R)w, Mw
Genomic Location
Cytogenetic map
Sequence location
3R:23,358,812..23,360,207 [+]
Recombination map
3-78
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
GO Summary Ribbons
Families, Domains and Molecular Function
Protein Family (UniProt, Sequence Similarities)
Belongs to the universal ribosomal protein uS3 family. (Q06559)
Catalytic Activity (EC)
Experimental Evidence
Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine (3.2.2.23)
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate (4.2.99.18)
Predictions / Assertions
Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine (3.2.2.23)
Summaries
Gene Group Membership
CYTOPLASMIC SMALL RIBOSOMAL PROTEINS -
Cytoplasmic ribosomes are found on the endoplasmic reticulum and in the cytoplasm. They translate all mRNAs produced from nuclear genes and perform the majority of cellular protein synthesis. Ribosomes are formed by two ribonucleoprotein subunits, large and small. The principle function of the small subunit is to bind mRNA. (Adapted from FBrf0205398)
DNA-(APURINIC OR APYRIMIDINIC SITE) LYASES -
DNA-(apurinic or apyrimidinic site) lyases catalyze the cleavage of the C-O-P bond 3' from the apurinic or apyrimidinic site in DNA created when DNA glycosylase removes a damaged base. These enzymes are involved in the DNA base excision repair pathway (BER). (Adapted from FBrf0076708).
UniProt Contributed Function Data
Has DNA repair activity directed towards the mutagenic lesions 8-oxoguanine and abasic sites in DNA. It can cleave DNA containing 8-oxoguanine residues efficiently. Also acts as an ap lyase, cleaving phosphodiester bonds via a beta,delta elimination reaction.
(UniProt, Q06559)
Phenotypic Description from the Red Book (Lindsley and Zimm 1992)
M(3)95A
Strong Minute; eclosion delayed 40 hours (Ferrus, 1975, Genetics 79: 589-99).
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\RpS3 or the JBrowse view of Dmel\RpS3 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
Low-frequency RNA-Seq exon junction(s) not annotated.
Gene model reviewed during 5.46
Gene model reviewed during 5.56
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0084410
854
246
FBtr0346349
1133
246
Additional Transcript Data and Comments
Reported size (kB)
0.94, 0.9 (northern blot)
0.856 (longest cDNA)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0083802
27.5
246
9.90
FBpp0312066
27.5
246
9.90
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

246 aa isoforms: RpS3-PA, RpS3-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
246 (aa); 27.5 (kD predicted)
246 (aa); 27 (kD)
Comments
External Data
Subunit Structure (UniProtKB)
Interacts with LTV1; the interaction is RNA-independent.
(UniProt, Q06559)
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\RpS3 using the Feature Mapper tool.

External Data
Crossreferences
Linkouts
Gene Ontology (18 terms)
Molecular Function (7 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (6 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000205059
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000205059
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000205059
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000205059
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR004044, InterPro:IPR009019
(assigned by InterPro )
traceable author statement
inferred from biological aspect of ancestor with PANTHER:PTN000205057
(assigned by GO_Central )
Biological Process (7 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from genetic interaction with EchoBASE:EB0325
inferred from genetic interaction with EchoBASE:EB0645 , EchoBASE:EB1066
inferred from high throughput mutant phenotype
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
inferred by curator from GO:0022626
traceable author statement
inferred from biological aspect of ancestor with PANTHER:PTN000205059
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000924666
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000205059
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR001351, InterPro:IPR005703
(assigned by InterPro )
Cellular Component (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from high throughput direct assay
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
traceable author statement
inferred from biological aspect of ancestor with PANTHER:PTN000205057
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000205059
(assigned by GO_Central )
Expression Data
Transcript Expression
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from high throughput direct assay
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\RpS3 in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
Alleles, Insertions, Transgenic Constructs and Phenotypes
Classical and Insertion Alleles ( 10 )
For All Classical and Insertion Alleles Show
 
Allele of RpS3
Class
Mutagen
Associated Insertion
Stocks
Known lesion
    0
    --
    Other relevant insertions
    Transgenic Constructs ( 6 )
    Deletions and Duplications ( 14 )
    Summary of Phenotypes
    For more details about a specific phenotype click on the relevant allele symbol.
    Lethality
    Allele
    Sterility
    Allele
    Other Phenotypes
    Allele
    Phenotype manifest in
    Allele
    Orthologs
    Human Orthologs (via DIOPT v7.1)
    Homo sapiens (Human) (1)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Alignment
    Complementation?
    Transgene?
    13 of 15
    Yes
    Yes
    Model Organism Orthologs (via DIOPT v7.1)
    Mus musculus (laboratory mouse) (1)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Alignment
    Complementation?
    Transgene?
    14 of 15
    Yes
    Yes
    Rattus norvegicus (Norway rat) (1)
    13 of 13
    Yes
    Yes
    Xenopus tropicalis (Western clawed frog) (1)
    8 of 12
    Yes
    Yes
    Danio rerio (Zebrafish) (1)
    14 of 15
    Yes
    Yes
    Caenorhabditis elegans (Nematode, roundworm) (1)
    13 of 15
    Yes
    Yes
    Arabidopsis thaliana (thale-cress) (3)
    9 of 9
    Yes
    Yes
    9 of 9
    Yes
    Yes
    9 of 9
    Yes
    Yes
    Saccharomyces cerevisiae (Brewer's yeast) (1)
    15 of 15
    Yes
    Yes
    Schizosaccharomyces pombe (Fission yeast) (1)
    12 of 12
    Yes
    Yes
    Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190E43 )
    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 pseudoobscura pseudoobscura
    Drosophila persimilis
    Drosophila willistoni
    Drosophila virilis
    Drosophila mojavensis
    Drosophila grimshawi
    Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091509TE )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Musca domestica
    House fly
    Glossina morsitans
    Tsetse fly
    Lucilia cuprina
    Australian sheep blowfly
    Mayetiola destructor
    Hessian fly
    Aedes aegypti
    Yellow fever mosquito
    Anopheles darlingi
    American malaria mosquito
    Anopheles gambiae
    Malaria mosquito
    Culex quinquefasciatus
    Southern house mosquito
    Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0BE8 )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Bombyx mori
    Silkmoth
    Danaus plexippus
    Monarch butterfly
    Heliconius melpomene
    Postman butterfly
    Apis florea
    Little honeybee
    Apis mellifera
    Western honey bee
    Bombus impatiens
    Common eastern bumble bee
    Bombus impatiens
    Common eastern bumble bee
    Bombus terrestris
    Buff-tailed bumblebee
    Bombus terrestris
    Buff-tailed bumblebee
    Linepithema humile
    Argentine ant
    Megachile rotundata
    Alfalfa leafcutting bee
    Nasonia vitripennis
    Parasitic wasp
    Tribolium castaneum
    Red flour beetle
    Pediculus humanus
    Human body louse
    Rhodnius prolixus
    Kissing bug
    Cimex lectularius
    Bed 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) ( EOG090X0BBS )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Strigamia maritima
    European centipede
    Stegodyphus mimosarum
    African social velvet spider
    Tetranychus urticae
    Two-spotted spider mite
    Daphnia pulex
    Water flea
    Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0I8D )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Strongylocentrotus purpuratus
    Purple sea urchin
    Ciona intestinalis
    Vase tunicate
    Gallus gallus
    Domestic chicken
    Human Disease Model Data
    FlyBase Human Disease Model Reports
      Alleles Reported to Model Human Disease (Disease Ontology)
      Download
      Models ( 0 )
      Allele
      Disease
      Evidence
      References
      Interactions ( 0 )
      Allele
      Disease
      Interaction
      References
      Comments ( 0 )
       
      Human Orthologs (via DIOPT v7.1)
      Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
      Homo sapiens (Human)
      Gene name
      Score
      OMIM
      OMIM Phenotype
      Complementation?
      Transgene?
      Functional Complementation Data
      Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
      Interactions
      Summary of Physical Interactions
      esyN Network Diagram
      Show neighbor-neighbor interactions:
      Select Layout:
      Legend:
      Protein
      RNA
      Selected Interactor(s)
      Interactions Browser

      Please look at the Interaction Group reports for full details of the physical interactions
      protein-protein
      Interacting group
      Assay
      References
      RNA-protein
      Interacting group
      Assay
      References
      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
      suppressible
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      enhanceable
      External Data
      Subunit Structure (UniProtKB)
      Interacts with LTV1; the interaction is RNA-independent.
      (UniProt, Q06559 )
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
      Pathways
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      3R
      Recombination map
      3-78
      Cytogenetic map
      Sequence location
      3R:23,358,812..23,360,207 [+]
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      94E13-94E13
      Limits computationally determined from genome sequence between P{PZ}cnc03921 and P{PZ}l(3)0690606906
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      94F-95A
      (determined by in situ hybridisation)
      95A-95A
      (determined by in situ hybridisation)
      Experimentally Determined Recombination Data
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (15)
      Genomic Clones (14)
       

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

      cDNA Clones (1233)
       

      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
      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)
        Other clones
        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
        Other Comments
        Haploinsufficient locus.
        Minute gene.
        Deletions removing RpS3 but no other cytoplasmic ribosomal protein-encoding genes show Minute phenotypes.
        Molecularly-defined mutations in RpS3 result in Minute phenotypes.
        RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R+ cells.
        Identified with: GH06471 (BDGP-DGC) <up>FlyBase curator comment: EST subsequently found to be chimeric</up>.
        Analysis of complete and partial revertants of RpS3Plac92 reveals that different degrees of RpS3 insufficiency produces distinct phenotypes, in which the penultimate effect prior to lethality constitutes arrest of gametogenesis and many morphological defects.
        Calf thymus DNA exposed to γ-irradiation under N2O can be used as a means of testing for N-glycosylase activity. 8-oxoGua and FapyGua are efficiently released from the irradiated DNA substrate. The ability of RpS3 to act on base mismatches opposite 8-oxoGua and the formation of an amino intermediate are studied to characterise the N-glycosylase activity of the protein.
        RpS3 is demonstrated to have dRpase activities and this suggests the ribosomal protein may be active in several steps of the DNA base excision repair pathway.
        DNA repair activities are associated with RpS3 in vitro. The repair activities directed towards the mutagenic lesions 8-oxoguanine and abasic sites in DNA are able to act in vivo to protect yeast cells from H2O22 and MMS toxicity. Results suggest the possibility that RpS3 may participate in both base excision repair and protein translation.
        RpS3 encodes a ribosomal protein.
        P-element mutagenesis confirms S3 as a Minute gene, mobilisation of the P-element reverts the flies to wild type.
        Biochemical properties of the recombinant protein demonstrate RpS3 is capable of acting on DNA containing apurinic/apyrimidinic (AP) sites. The protein is tightly associated with the nuclear matrix suggesting the protein may have a function in DNA repair.
        Cloned by hybridization to rat S3 cDNA probe. The RpS3 gene product has AP endonuclease activity.
        Strong Minute; eclosion delayed 40 hours (Ferrus, 1975).
        Mutant alleles have the developmental delay and bristle phenotype that makes them useful as markers in clonal analysis.
        One of a class of genes (see MIN record) that when present in one, rather than two, copies, produce a characteristic phenotype consisting of short slender bristles and delayed development.
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 52 )
        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
        UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center cDNA clones
        DPiM - Drosophila Protein interaction map
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        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
        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 (31)
        Reported As
        Symbol Synonym
        M(3)124
        M(3)B
        M(3)B2
        M(3)Fla
        chr3R:19185518..19185701
        Secondary FlyBase IDs
        • FBgn0010267
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (174)