FB2025_01 , released February 20, 2025
Gene: Dmel\RPA2
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General Information
Symbol
Dmel\RPA2
Species
D. melanogaster
Name
Replication protein A2
Annotation Symbol
CG9273
Feature Type
protein_coding_gene
FlyBase ID
FBgn0288834
Gene Model Status
Current
Stock Availability
11 publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

RPA30, dRP-A, RP-A, RPA, RpA-30

Key Links
Genomic Location
Cytogenetic map
38F6-38F6
Sequence location
Recombination map
2-54
RefSeq locus
NT_033779 REGION:20924975..20926147
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 (12 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 DNA binding
inferred from electronic annotation with InterPro:IPR014646
(InterPro Project Members, 2004-)
enables single-stranded DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000360435
(GO Reference Genome Project, 2011-)
enables telomeric DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN008553235
(GO Reference Genome Project, 2011-)
Biological Process (5 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
involved_in DNA recombination
inferred from electronic annotation with InterPro:IPR014646
(InterPro Project Members, 2004-)
involved_in DNA repair
inferred from electronic annotation with InterPro:IPR014646
(InterPro Project Members, 2004-)
involved_in DNA replication
inferred from biological aspect of ancestor with PANTHER:PTN000360435
(GO Reference Genome Project, 2011-)
inferred from electronic annotation with InterPro:IPR014646
(InterPro Project Members, 2004-)
involved_in double-strand break repair via homologous recombination
inferred from biological aspect of ancestor with PANTHER:PTN000360435
(GO Reference Genome Project, 2011-)
involved_in nucleotide-excision repair
inferred from biological aspect of ancestor with PANTHER:PTN000360435
(GO Reference Genome Project, 2011-)
Cellular Component (4 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
is_active_in chromosome, telomeric region
inferred from biological aspect of ancestor with PANTHER:PTN000360435
(GO Reference Genome Project, 2011-)
part_of DNA replication factor A complex
inferred from biological aspect of ancestor with PANTHER:PTN000360435
(GO Reference Genome Project, 2011-)
located_in nucleus
inferred from electronic annotation with InterPro:IPR014646
(InterPro Project Members, 2004-)
is_active_in site of double-strand break
inferred from biological aspect of ancestor with PANTHER:PTN000360435
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\RPA2 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 Q9VIH1)

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

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

Gene model reviewed during 5.46

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
RPA2-RA
FBtr0081438
NM_136233
963
246
RPA2-RB
FBtr0333011
NM_001273723
905
246
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
RPA2-PA
FBpp0080967
26.4
246
4.72
Q9VIH1
NP_610077
AAF53948
RPA2-PB
FBpp0305226
26.4
246
4.72
Q9VIH1
NP_001260652
AGB93187
Polypeptides with Identical Sequences

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

246 aa isoforms: RPA2-PA, RPA2-PB
Additional Polypeptide Data and Comments
Reported size (kDa)

30 (kD)

(Mitsis et al., 1993)
Comments

RPA2 protein, the 30kD 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\RPA2 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).

0.74

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 4 -- 6
organism | faint | ubiquitous
(Fisher et al., 2012)
embryonic stage 7 -- 8
organism | ubiquitous
(Fisher et al., 2012)
ventral nerve cord primordium

Comment: reported as ventral nerve cord anlage

(Fisher et al., 2012)
embryonic stage 9 -- 10
antennal primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
central brain primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
visual primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
dorsal head epidermis primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
lateral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
ventral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
anterior endoderm
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
posterior endoderm
(Fisher et al., 2012)
ventral nerve cord primordium
(Fisher et al., 2012)
embryonic stage 11 -- 12
anterior midgut primordium
(Fisher et al., 2012)
central brain primordium
(Fisher et al., 2012)
organism | faint | ubiquitous
(Fisher et al., 2012)
posterior midgut primordium
(Fisher et al., 2012)
ventral nerve cord primordium
(Fisher et al., 2012)
embryonic stage 13 -- 16
embryonic brain
(Fisher et al., 2012)
embryonic hindgut
(Fisher et al., 2012)
embryonic/larval lymph gland
(Fisher et al., 2012)
embryonic/larval midgut
(Fisher et al., 2012)
larval nervous system
(Fisher et al., 2012)
lateral cord neuron
(Fisher et al., 2012)
larval ventral nerve cord
(Fisher et al., 2012)
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)
Additional Descriptive Data

Purified from embryos.

(Mitsis et al., 1993)
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\RPA2 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
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 6 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 9 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of RPA2
Transgenic constructs containing regulatory region of RPA2
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(2L)Exel7080
(Ryder, 2004.4.26)
Inferred from location ( 9 )
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) (3)
Hsap\RPA2
13 of 14
Yes
Yes
Hsap\RPA4
12 of 14
No
Yes
1  
Hsap\STN1
1 of 14
No
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\Rpa2
13 of 14
Yes
Yes
Rnor\Stn1
1 of 14
No
Yes
Mus musculus (laboratory mouse) (2)
Mmus\Rpa2
12 of 14
Yes
Yes
Mmus\Stn1
1 of 14
No
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\rpa2
11 of 13
Yes
Yes
Xtro\LOC101730710
9 of 13
No
Yes
Danio rerio (Zebrafish) (2)
Drer\rpa2
13 of 14
Yes
Yes
Drer\stn1
1 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\rpa-2
5 of 14
Yes
Yes
Cele\rpa-4
4 of 14
No
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP008332
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (3)
Atha\RPA2
10 of 13
Yes
Yes
Atha\RPA32B
10 of 13
Yes
Yes
Atha\STN1
1 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\RFA2
11 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\ssb2
10 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:RPA2. 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?
    RPA2; replication protein A2
    13 of 14
    179836
        RPA4; replication protein A4
        12 of 14
        300767
             
            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:
            Show/hide secondary interactors 
            (data from AllianceMine provided by esyN)
            Select Layout:
            Legend:
            Protein
            RNA
            Selected Interactor(s)
            Other Interaction Browsers
            View in FlyBase Interactions Browser   View in MIST tool (external link)
            Please see the Physical Interaction reports below for full details
            protein-protein
            Physical Interaction
            Assay
            References
            RPA2 - CG3165
            experimental knowledge based
            (Guruharsha et al., 2011)
            RPA2 - CG3548
            experimental knowledge based
            (Guruharsha et al., 2011)
            RPA2 - Dlc90F
            experimental knowledge based
            (Guruharsha et al., 2011)
            RPA2 - Gnf1
            experimental knowledge based
            (Guruharsha et al., 2011)
            RPA2 - Irbp
            experimental knowledge based
            (Guruharsha et al., 2011)
            RPA2 - JMJD7
            experimental knowledge based
            (Guruharsha et al., 2011)
            RPA2 - Ku80
            experimental knowledge based
            (Guruharsha et al., 2011)
            RPA2 - Lam
            experimental knowledge based
            (Guruharsha et al., 2011)
            RPA2 - Parp1
            experimental knowledge based
            (Guruharsha et al., 2011)
            RPA2 - RPA1
            experimental knowledge based, ion exchange chromatography, molecular weight estimation by staining, anti bait coimmunoprecipitation, western blot, molecular sieving
            (Guruharsha et al., 2011, Mitsis, 1995, Marton et al., 1994, Mitsis et al., 1993)
            RPA2 - RPA3
            anti bait coimmunoprecipitation, western blot, two hybrid, ion exchange chromatography, molecular sieving, molecular weight estimation by staining, experimental knowledge based
            (Hu et al., 2017.6.13, Guruharsha et al., 2011, Mitsis, 1995, Marton et al., 1994, Mitsis et al., 1993)
            RPA2 - RfC3
            experimental knowledge based
            (Guruharsha et al., 2011)
            RPA2 - RfC4
            experimental knowledge based
            (Guruharsha et al., 2011)
            RPA2 - TFAM
            experimental knowledge based
            (Guruharsha et al., 2011)
            RPA2 - bocks
            experimental knowledge based
            (Guruharsha et al., 2011)
            RPA2 - psq
            experimental knowledge based
            (Guruharsha et al., 2011)
            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
            CycB
            suppressible
            RPA2
            (Crest et al., 2007)
            External Data
            Linkouts
            Pathways
            Class of Gene
            Genomic Location and Detailed Mapping Data
            Chromosome (arm)
            2L
            Recombination map
            2-54
            Cytogenetic map
            38F6-38F6
            Sequence location
            FlyBase Computed Cytological Location
            Cytogenetic map
            Evidence for location
            38F6-38F6
            Limits computationally determined from genome sequence between P{PZ}l(2)38EFd04530 and P{PZ}l(2)0528705287
            Experimentally Determined Cytological Location
            Cytogenetic map
            Notes
            References
            Experimentally Determined Recombination Data
            Location

            2-54

            (FlyBase, 2016)

            2-54.4

            (Comeron et al., 2012)
            Left of (cM)
            Right of (cM)
            Notes
            Stocks and Reagents
            Stocks (11)
            Genomic Clones (17)
             

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

            cDNA Clones (46)
             

            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
                 
                Commercially Available Antibodies
                 
                Cell Line Information
                Publicly Available Cell Lines
                 
                  Other Stable Cell Lines
                   
                    Other Comments

                    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: RPA2 RpA-30

                    (Yamamoto, 2022.4.27)
                    Additional comments
                    Nomenclature History
                    Source for database identify of

                    Source for identity of: RPA2 CG9273

                    (Crest et al., 2007)
                    Nomenclature comments
                    Etymology
                    Synonyms and Secondary IDs (22)
                    Datasets (0)
                    Study focus (0)
                    Experimental Role
                    Project
                    Project Type
                    Title
                    Study result (0)
                    Result
                    Result Type
                    Title
                    External Crossreferences and Linkouts ( 58 )
                    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
                    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 (80)