FB2024_02 , released April 23, 2024
Gene: Dmel\RpS28a
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General Information
Symbol
Dmel\RpS28a
Species
D. melanogaster
Name
Ribosomal protein S28a
Annotation Symbol
CG15527
Feature Type
protein_coding_gene
FlyBase ID
FBgn0039739
Gene Model Status
Current
Stock Availability
3 publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Key Links
Genomic Location
Cytogenetic map
99D2-99D2
Sequence location
Recombination map
3-100
RefSeq locus
NT_033777 REGION:30022345..30022648
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 (8 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables structural constituent of ribosome
inferred from sequence or structural similarity with SGD:S000005693
(Gene Ontology Curators, 2002-)
traceable author statement
(Marygold et al., 2007)
inferred from biological aspect of ancestor with PANTHER:PTN000080571
(GO Reference Genome Project, 2011-)
inferred from electronic annotation with InterPro:IPR000289
(InterPro Project Members, 2004-)
Biological Process (5 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in wing disc development
inferred from mutant phenotype
(Chen et al., 2010)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
involved_in cytoplasmic translation
traceable author statement
(Marygold et al., 2007)
inferred by curator from GO:0022627
(Gene Ontology Curators, 2002-)
involved_in maturation of SSU-rRNA
inferred from biological aspect of ancestor with PANTHER:PTN000080571
(GO Reference Genome Project, 2011-)
involved_in ribosomal small subunit assembly
inferred from biological aspect of ancestor with PANTHER:PTN000080571
(GO Reference Genome Project, 2011-)
involved_in translation
inferred from electronic annotation with InterPro:IPR000289
(InterPro Project Members, 2004-)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
part_of cytosolic small ribosomal subunit
traceable author statement
(Marygold et al., 2007)
inferred from biological aspect of ancestor with PANTHER:PTN000080571
(GO Reference Genome Project, 2011-)
inferred from sequence or structural similarity with SGD:S000005693
(Gene Ontology Curators, 2002-)
located_in ribosome
inferred from electronic annotation with InterPro:IPR000289
(InterPro Project Members, 2004-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
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)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\RpS28a 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 Q9VAB9)

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 5.47

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
RpS28a-RA
FBtr0085601
NM_143507
304
64
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
RpS28a-PA
FBpp0084966
7.3
64
10.79
Q9VAB9
NP_651764
AAF56992
Polypeptides with Identical Sequences

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

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
UniProt
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\RpS28a using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
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).

5.19

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
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\RpS28a 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
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
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 2 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of RpS28a
Transgenic constructs containing regulatory region of RpS28a
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(3R)X3F
(Marygold et al., 2007, Cook, 2006.1.31)
Inferred from location ( 0 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
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) (1)
Hsap\RPS28
12 of 14
Yes
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) (4)
Rnor\LOC100359503
12 of 14
Yes
No
Rnor\Rps28
12 of 14
Yes
No
Rnor\LOC108353424
10 of 14
No
No
Rnor\LOC108352027
1 of 14
No
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Rps28
11 of 14
Yes
No
Xenopus tropicalis (Western clawed frog) (1)
Xtro\rps28p9
7 of 13
Yes
No
Danio rerio (Zebrafish) (1)
Drer\rps28
11 of 14
Yes
No
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\rps-28
13 of 14
Yes
No
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP003412
7 of 12
Yes
No
Arabidopsis thaliana (thale-cress) (3)
Atha\AT3G10090
12 of 13
Yes
No
Atha\AT5G03850
12 of 13
Yes
No
Atha\RPS28
12 of 13
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\RPS28A
12 of 13
Yes
No
Scer\RPS28B
12 of 13
Yes
No
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\rps2801
11 of 12
Yes
No
Spom\rps2802
11 of 12
Yes
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:RpS28a. 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) (2)
RpS28b
12 of 13
RpS28-like
3 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?
    RPS28; ribosomal protein S28
    12 of 14
    603685
    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
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Linkouts
    DroID - A comprehensive database of gene and protein interactions.
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-100
    Cytogenetic map
    99D2-99D2
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    99D2-99D2
    Limits computationally determined from genome sequence between P{PZ}ncd05884 and P{lacW}l(3)s2500s2500
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    3-100

    (FlyBase, 2016)

    3-97.4

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (3)
    Genomic Clones (13)
     

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

    cDNA Clones (1)
     

    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

              Not a Minute gene.

              (Marygold et al., 2007)

              The Minute phenotype of a deletion removing RpS28a and RpL32 is rescued by a RpL32 transgene, proving that RpS28a is not a Minute gene.

              (Marygold et al., 2007)

              Likely retrogene.

              (Marygold et al., 2007)

              RpS28a is not a haploinsufficnet locus.

              (Cook, 2006.1.31)
              Relationship to Other Genes
              Source for database merge of
              Additional comments

              The RpS28a gene may have been derived from the RpS28b gene, but as the region of similarity between the two genes does not span an exon-exon junction in the parental gene, retroposition cannot necessarily be inferred.

              (Zhang et al., 2011)

              The RpS28a gene may have been derived from the RpS28b gene by retroposition.

              (Pan and Zhang, 2009, Marygold et al., 2007, Dai et al., 2006)

              The RpS28b and RpS28a genes share at least 50% identity.

              (Langille and Clark, 2007)

              Does not correspond to any previously defined Minute locus.

              (Cook, 2006.1.31)
              Nomenclature History
              Source for database identify of
              Nomenclature comments
              Etymology
              Synonyms and Secondary IDs (3)
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              Study result (0)
              Result
              Result Type
              Title
              External Crossreferences and Linkouts ( 24 )
              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 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.
              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
              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
              Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
              FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
              FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
              Flygut - An atlas of the Drosophila adult midgut
              KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
              References (36)