FlyBase Gene Report: Dmel\Xrcc2

General Information

Symbol

Dmel\Xrcc2

Species

D. melanogaster

Name

X-ray repair cross complementing 2

Annotation Symbol

CG6318

Feature Type

protein_coding_gene

FlyBase ID

FBgn0030931

Gene Model Status

Current

Stock Availability

5 publicly available

Gene Summary

X-ray repair cross complementing 2 (Xrcc2) encodes a protein involved in DNA repair. [Date last reviewed: 2019-09-26] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

Rad51D

Key Links

Genomic Location

Cytogenetic map

17B6-17B6

Sequence location

X:18,500,127..18,501,258 [+]

Recombination map

1-60

RefSeq locus

NC_004354 REGION:18500127..18501258

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (9 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables DNA strand exchange activity

inferred from sequence or structural similarity with HGNC:12829

(Sekelsky et al., 2000)

contributes_to four-way junction DNA binding

inferred from biological aspect of ancestor with PANTHER:PTN002505836

(GO Reference Genome Project, 2011-)

Biological Process (4 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

involved_in DNA recombination

inferred from sequence or structural similarity with HGNC:12829

(Sekelsky et al., 2000)

involved_in DNA repair

inferred from sequence or structural similarity with HGNC:12829

(Sekelsky et al., 2000)

involved_in DNA strand invasion

inferred from biological aspect of ancestor with PANTHER:PTN002505836

(GO Reference Genome Project, 2011-)

involved_in double-strand break repair via homologous recombination

inferred from electronic annotation with InterPro:IPR030547

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN002505836

(GO Reference Genome Project, 2011-)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

is_active_in centrosome

inferred from biological aspect of ancestor with PANTHER:PTN002505836

(GO Reference Genome Project, 2011-)

part_of Rad51B-Rad51C-Rad51D-XRCC2 complex

inferred from electronic annotation with InterPro:IPR030547

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN002505836

(GO Reference Genome Project, 2011-)

is_active_in replication fork

inferred from biological aspect of ancestor with PANTHER:PTN002505836

(GO Reference Genome Project, 2011-)

located_in replication fork

inferred from electronic annotation with InterPro:IPR030547

(InterPro Project Members, 2004-)

Gene Group (FlyBase)

RAD51-LIKE ATPASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

X-ray repair cross complementing 2 (Xrcc2) encodes a protein involved in DNA repair. [Date last reviewed: 2019-09-26]

Gene Group (FlyBase)

RAD51-LIKE ATPASES -: Rad51-like ATPases include RAD51 and its paralogs, which play an essential role in repair of double-strand DNA breaks through homologous recombination. They act to transduce the DNA damage signal to effector kinases and to promote break repair. (Adapted from PMID:21821141.)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Xrcc2 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 Q9VWT5)

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 5.51

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Xrcc2-RA

FBtr0074592

NM_133074

1132

250

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

Xrcc2-PA

FBpp0074364

28.0

250

6.86

Q9VWT5

NP_573302

AAF48852

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

Q9VWT5

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Xrcc2 using the Feature Mapper tool.

External Data

Crossreferences

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

Rad51D_1

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).

-0.26

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\Xrcc2 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\Xrcc2

View exonic expression by tissue for Dmel\Xrcc2

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

32837/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0030931

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0030931

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0030931

Flygut - An atlas of the Drosophila adult midgut

FBgn0030931

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 ( 5 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Xrcc2

Transgenic constructs containing regulatory region of Xrcc2

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 17 )

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

partially lethal - majority die | conditional

Xrcc2^CC

viable

Xrcc2^CC

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Xrcc2^GD4509

viable, with Scer\GAL4^Mef2.PR

Xrcc2^GD4509

viable, with Scer\GAL4^pnr-MD237

Xrcc2^GD4509

viable, with Scer\GAL4^tin.CΔ4

Xrcc2^GD4509

Sterility

Allele

fertile | female

Xrcc2^CC

Other Phenotypes

Allele

abnormal DNA repair | third instar larval stage

Xrcc2^CC

radiation sensitive

Xrcc2^CC

Phenotype manifest in

Allele

larval neuroblast | third instar larval stage

Xrcc2^CC

nuclear chromosome | third instar larval stage

Xrcc2^CC

wing disc | third instar larval stage

Xrcc2^CC

X chromosome | adult stage

Xrcc2^CC

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (7)

Hsap\XRCC2

8 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (6)

Rnor\Xrcc2

6 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (6)

Mmus\Xrcc2

5 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (4)

Xtro\xrcc2

2 of 13

Yes

Xtro\rad51c

1 of 13

Xtro\rad51d

1 of 13

Xtro\xrcc3

1 of 13

Danio rerio (Zebrafish) (7)

Drer\xrcc2

5 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\rad-51

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (5)

Agam\AgaP_AGAP006734

7 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (7)

Atha\XRCC2

6 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (3)

Scer\DMC1

1 of 13

Yes

Scer\RAD51

1 of 13

Yes

Scer\RAD57

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\dmc1

1 of 12

Yes

Spom\rhp51

1 of 12

Yes

Spom\rhp57

1 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Xrcc2. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (4)

1 of 13

1 of 13

1 of 13

1 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 ( 3 )

Human Ortholog

Disease

Evidence

References

XRCC2; X-ray repair cross complementing 2

model of primary ovarian insufficiency 17

IEA

(FlyBase, 2019-)

model of spermatogenic failure 50

IEA

(FlyBase, 2019-)

model of Fanconi anemia complementation group U

IEA

(FlyBase, 2019-)

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?

XRCC2; X-ray repair cross complementing 2

8 of 14

600375

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

spn-B

enhanceable

Xrcc2

(Bayer et al., 2020)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

59150

DroID - A comprehensive database of gene and protein interactions.

FBgn0030931

MIST (protein-protein) - An integrated Molecular Interaction Database

32837

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-60

Cytogenetic map

17B6-17B6

Sequence location

X:18,500,127..18,501,258 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

17B6-17B6

Limits computationally determined from genome sequence between P{EP}CG32549^EP1317 and P{EP}EP443^EP443&P{EP}Bx^EP1383

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-60

(FlyBase, 2016)

1-59.4

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (5)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

93860

w^* Xrcc2^CC

FlyORF

F002360

M{UAS-Xrcc2.ORF.3xHA.GW}ZH-86Fb

NIG-Fly

6318R-1

P{NIG.6318R}1/CyO, P{ActGFP}JMR1

VDRC

v104627

P{KK111396}VIE-260B

v10758

w¹¹¹⁸; P{GD4509}v10758

Genomic Clones (7)

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

cDNA Clones (6)

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.

FBgn0030931

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0030931

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Relationship to Other Genes

Source for database merge of

Additional comments

Source for identity of Rad51D CG6318 was sequence comparison ( date:000815 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Source for identity of: Rad51D CG6318

(FlyBase, 1996-)

Source for identity of: Xrcc2 Rad51D

(Sekelsky, 2016.5.27)

Nomenclature comments

FlyBase curator comment: For clarity and consistency with the vertebrate nomenclature, the gene previously called 'Rad51C' (CG2412/FBgn0033389) was renamed 'Rad51D', and the gene previously called 'Rad51D' (CG6318,FBgn0030931) was renamed 'Xrcc2'. (These changes occurred in the FB2016_04 release.)

(Sekelsky, 2016.5.27)

Etymology

Named 'Xrcc2' after the vertebrate ortholog.

(Sekelsky, 2016.5.27)

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CG6318

(Felix et al., 2012, Keleman et al., 2009.8.5, Sekelsky et al., 2000)

Dm CG6318

(Abdu et al., 2003)

Rad51D

(Godin et al., 2015, Ober et al., 2015, Japanese National Institute of Genetics, 2012.5.21, Guest et al., 2011)

XRCC2

(Mota et al., 2019)

Xrcc2

(Robinson et al., 2020, Sekelsky, 2017)

dmRad51D

(Godin et al., 2015)

Name Synonyms

Rad51D

X-ray repair cross complementing 2

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 25 )

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.

32837

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.

AAF48852

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.

Q9VWT5

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Q9VWT5

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.

Q9VWT5

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

32837/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0030931

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0030931

FlyMine - An integrated database for Drosophila genomics

FBgn0030931

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG6318

MARRVEL_MODEL - MARRVEL (model organism gene)

32837

Linkouts

BioGRID - A database of protein and genetic interactions.

59150

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0030931

DroID - A comprehensive database of gene and protein interactions.

FBgn0030931

DRSC - Results frm RNAi screens

FBgn0030931

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

Rad51D_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0030931

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0030931

Flygut - An atlas of the Drosophila adult midgut

FBgn0030931

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC006372

MIST (protein-protein) - An integrated Molecular Interaction Database

32837

References (32)

The following external sites may use different assemblies or annotations than FlyBase.

-0.26

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