FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\RPA3
Open Close
General Information
Symbol
Dmel\RPA3
Species
D. melanogaster
Name
Replication protein A3
Annotation Symbol
CG15220
Feature Type
protein_coding_gene
FlyBase ID
FBgn0288833
Gene Model Status
Current
Stock Availability
8 publicly available
Gene Summary
Replication protein A3 (RPA3) encodes a protein involved in the maintenance of the neuronal stem cell population. [Date last reviewed: 2019-09-19] (FlyBase Gene Snapshot)
All Summaries
Also Known As

dRP-A, l(1)G0241, RPA, RP-A

Key Links
Genomic Location
Cytogenetic map
10D1-10D1
Sequence location
Recombination map
1-35
RefSeq locus
NC_004354 REGION:11615097..11615840
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 (14 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
enables damaged DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN001031498
(GO Reference Genome Project, 2011-)
enables DNA binding
inferred from electronic annotation with InterPro:IPR013970
(InterPro Project Members, 2004-)
enables single-stranded DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN001031498
(GO Reference Genome Project, 2011-)
Biological Process (8 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in neuronal stem cell population maintenance
inferred from mutant phenotype
(Zhou and Luo, 2013)
Terms Based on Predictions or Assertions (7 terms)
CV Term
Evidence
References
involved_in base-excision repair
inferred from biological aspect of ancestor with PANTHER:PTN001031498
(GO Reference Genome Project, 2011-)
involved_in DNA recombination
inferred from electronic annotation with InterPro:IPR013970
(InterPro Project Members, 2004-)
involved_in DNA repair
inferred from electronic annotation with InterPro:IPR013970
(InterPro Project Members, 2004-)
involved_in DNA replication
inferred from biological aspect of ancestor with PANTHER:PTN001031498
(GO Reference Genome Project, 2011-)
inferred from electronic annotation with InterPro:IPR013970
(InterPro Project Members, 2004-)
involved_in double-strand break repair via homologous recombination
inferred from biological aspect of ancestor with PANTHER:PTN001031498
(GO Reference Genome Project, 2011-)
involved_in mismatch repair
inferred from biological aspect of ancestor with PANTHER:PTN001031498
(GO Reference Genome Project, 2011-)
involved_in nucleotide-excision repair
inferred from biological aspect of ancestor with PANTHER:PTN001031498
(GO Reference Genome Project, 2011-)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
(Zhou and Luo, 2013)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
part_of DNA replication factor A complex
inferred from biological aspect of ancestor with PANTHER:PTN001031498
(GO Reference Genome Project, 2011-)
located_in nucleus
inferred from electronic annotation with InterPro:IPR013970
(InterPro Project Members, 2004-)
is_active_in site of double-strand break
inferred from biological aspect of ancestor with PANTHER:PTN001031498
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Replication protein A3 (RPA3) encodes a protein involved in the maintenance of the neuronal stem cell population. [Date last reviewed: 2019-09-19]
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\RPA3 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 Q9VYW3)

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 5.52

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
RPA3-RA
FBtr0073535
NM_132509
541
112
RPA3-RB
FBtr0343586
NM_001298202
673
112
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
RPA3-PA
FBpp0073380
12.0
112
5.09
Q9VYW3
NP_572737
AAF48070
RPA3-PB
FBpp0310183
12.0
112
5.09
Q9VYW3
NP_001285131
AHN59601
Polypeptides with Identical Sequences

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

112 aa isoforms: RPA3-PA, RPA3-PB
Additional Polypeptide Data and Comments
Reported size (kDa)

8 (kD)

(Mitsis et al., 1993)
Comments

RPA3 protein, the 8kD subunit of single-stranded DNA-binding protein or SSB (a heterotrimer), was purified from 0-18hr embryos. SSB was characterized biochemically and was shown to stimulate the extent and processivity of DNA synthesis of its cognate DNA polymerase α. It is the Drosophila cognate of yeast and human SSB/RP-A proteins.

(Mitsis et al., 1993)
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\RPA3 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).

0.94

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
third instar larval stage
optic lobe neuroepithelial cell
(Wang et al., 2013)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
enzyme assay or biochemical detection
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage
(Mitsis et al., 1993)
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
late third instar larval stage
larval brain | restricted
• nucleus
(Zhou and Luo, 2013)
larval outer optic anlage
(Zhou and Luo, 2013)
medulla forming neuroblast
(Zhou and Luo, 2013)
ganglion mother cell of larval brain | faint
(Zhou and Luo, 2013)
neuroblast of larval ventral nerve cord
(Zhou and Luo, 2013)
neuroblast of larval brain
(Zhou and Luo, 2013)
Additional Descriptive Data

In late third instar larva, RPA3 protein is expressed in neuroepithelial cells in the outer optic anlage, lamina precursor cells, in developing lamina cortex neurons, medulla, central brain and ventral nerve cord neuroblasts and weakly in ganglion mother cells. RPA3 protein is not expressed in medulla and lamina neurons.

(Zhou and Luo, 2013)
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
(Zhou and Luo, 2013)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\RPA3 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
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
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 1 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 8 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of RPA3
Transgenic constructs containing regulatory region of RPA3
Aberrations (Deficiencies and Duplications) ( 2 )
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\RPA3
9 of 14
Yes
Yes
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) (2)
Rnor\Rpa3
6 of 14
Yes
Yes
Rnor\LOC100362927
4 of 14
No
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Rpa3
4 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\rpa3
2 of 13
Yes
Yes
Xtro\socs4
1 of 13
No
No
Danio rerio (Zebrafish) (1)
Drer\rpa3
5 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (0)
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP010177
10 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (2)
Atha\AT3G52630
7 of 13
Yes
Yes
Atha\AT4G18590
7 of 13
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\ssb3
4 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:RPA3. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
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 ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    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?
    RPA3; replication protein A3
    9 of 14
    179837
        Functional Complementation Data
        Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
        Interactions
        Summary of Physical Interactions
        Summary of Genetic Interactions
        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
        RPA3
        suppressible
        N
        (Zhou and Luo, 2013)
        RPA3
        suppressible
        numb
        (Zhou and Luo, 2013)
        RPA3
        suppressible
        yki
        (Zhou and Luo, 2013)
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        External Data
        Linkouts
        Pathways
        Class of Gene
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        X
        Recombination map
        1-35
        Cytogenetic map
        10D1-10D1
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        10D1-10D1
        Left limit from in situ hybridisation (FBrf0108529) Right limit from in situ hybridisation (FBrf0108529); Limits computationally determined from genome sequence between P{EP}CG32666EP1452 and P{EP}Ptp10DEP1172
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        10D1-10D3
        (determined by in situ hybridisation)
        (Schäfer et al., 1999.6.15)
        Experimentally Determined Recombination Data
        Location

        1-35

        (FlyBase, 2016)

        1-36.7

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (8)
        Genomic Clones (7)
         

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

        cDNA Clones (19)
         

        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
          Antibody Information
          Laboratory Generated Antibodies
           

          polyclonal

          (Zhou and Luo, 2013)
          Commercially Available Antibodies
           
          Cell Line Information
          Publicly Available Cell Lines
           
            Other Stable Cell Lines
             
              Other Comments

              RPA3 is required to prevent neuroepithelial cells from differentiating into medulla neuroblast in the developing optic lobe in larvae.

              (Zhou and Luo, 2013)

              The Replication Protein A complex from ovaries and early embryos has multiple phosphorylated forms. The relative abundance of these forms is tightly regulated during development. The localization of the Replication Protein A complex varies during the cell cycle in both ovaries and embryos.

              (Mitsis, 1995)

              RpA-30, RpA-70 and RpA-8 can substitute for human RP-A for the initiation of SV40 DNA replication.

              (Kamakaka et al., 1994)

              Replication protein A has been purified and characterised. The protein consists of three subunits (encoded by RpA-30, RpA-70 and RpA-8), and binds single-stranded DNA very tightly via the large subunit (encoded by RpA-70).

              (Marton et al., 1994)

              Drosophila single stranded binding protein is a trimer with subunits of 70kD, 30kD and 8kD representing the cognates of the human and yeast SSB/RP-A proteins.

              (Mitsis et al., 1993)
              Relationship to Other Genes
              Source for database merge of

              Source for merge of: RPA3 RpA-8

              (Yamamoto, 2022.4.27)

              Source for merge of: CG15220 BcDNA:RH55360

              (FlyBase, 1996-)

              Source for merge of: RPA3 l(1)G0241

              (Zhou and Luo, 2013)
              Additional comments

              "l(1)G0241" may affect "CG15220".

              (Peter et al., 2002)

              Source for merge of CG15220 BcDNA:RH55360 was a shared cDNA ( date:030728 ).

              (FlyBase, 1996-)
              Nomenclature History
              Source for database identify of

              Source for identity of: RPA3 CG15220

              (Zhou and Luo, 2013)
              Nomenclature comments
              Etymology
              Synonyms and Secondary IDs (18)
              Reported As
              Symbol Synonym
              BcDNA:RH55360
              CG15220
              (Kwon et al., 2016, Hosono et al., 2015, Kwon et al., 2013, Wang et al., 2013, Zhou and Luo, 2013, Japanese National Institute of Genetics, 2012.5.21, Keleman et al., 2009.8.5, Perkins et al., 2009, Somma et al., 2008, Stanyon et al., 2004)
              D-SSB
              (Mitsis et al., 1993)
              DRP-A
              (Mitsis, 1995)
              DmRPA
              (Takeuchi et al., 2004)
              RP-A
              (Oshige et al., 1999, Kamakaka et al., 1994)
              RPA
              (Plank et al., 2006, Murawsky et al., 2003)
              RPA3
              (Barrio et al., 2023, Murcia et al., 2019, Hu et al., 2017.6.13, Transgenic RNAi Project members, 2017-, Zhou and Luo, 2013)
              RpA-8
              Ssb-8
              dRP-A
              (Thommes et al., 1995, Marton et al., 1994)
              l(1)G0241
              (Cook et al., 2010)
              Name Synonyms
              Drosophila Replication Protein A
              (Mitsis, 1995)
              Replication Protein A 8
              Replication protein A3
              Single stranded-binding protein 8
              lethal (1) G0241
              replication protein A
              (Zhou and Luo, 2013)
              Secondary FlyBase IDs
              • FBgn0010175
              • FBgn0266421
              • FBgn0030322
              • FBgn0062930
              • FBgn0027257
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              Study result (0)
              Result
              Result Type
              Title
              External Crossreferences and Linkouts ( 49 )
              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.
              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
              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
              FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
              Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
              iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
              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.
              References (53)