FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\Rad60
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General Information
Symbol
Dmel\Rad60
Species
D. melanogaster
Name
Rad60
Annotation Symbol
CG4449
Feature Type
protein_coding_gene
FlyBase ID
FBgn0039065
Gene Model Status
Current
Stock Availability
9 publicly available
Gene Summary
Required for repair of DNA double strand breaks which occur during replication or are induced by ionizing radiation (IR) (PubMed:26502056). Functions with dgrn and downstream of the SMC5-SMC6 complex to regulate strand break repair (PubMed:26502056). Likely functions by stabilizing the association of heterochromatic double strand breaks (DSBs) with the nuclear periphery as part of the homologous recombination (HR) repair process (PubMed:26502056). (UniProt, Q9VCP1)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

dRad60, RENi

Key Links
Genomic Location
Cytogenetic map
94E8-94E9
Sequence location
Recombination map
3-78
RefSeq locus
NT_033777 REGION:23249443..23251477
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 (1 term)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in nuclear periphery
inferred from direct assay
(Ryu et al., 2015)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Protein Function (UniProtKB)
Required for repair of DNA double strand breaks which occur during replication or are induced by ionizing radiation (IR) (PubMed:26502056). Functions with dgrn and downstream of the SMC5-SMC6 complex to regulate strand break repair (PubMed:26502056). Likely functions by stabilizing the association of heterochromatic double strand breaks (DSBs) with the nuclear periphery as part of the homologous recombination (HR) repair process (PubMed:26502056).
(UniProt, Q9VCP1)
Gene Model and Products
Number of Transcripts
6
Number of Unique Polypeptides
4

Please see the JBrowse view of Dmel\Rad60 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 Q9VCP1)

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 5.47

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Rad60-RA
FBtr0084388
NM_142877
1677
424
Rad60-RB
FBtr0301088
NM_001170227
1671
422
Rad60-RC
FBtr0334499
NM_001275937
1494
422
Rad60-RD
FBtr0334500
NM_001275938
1500
424
Rad60-RE
FBtr0334501
NM_001275939
1497
423
Rad60-RF
FBtr0334502
NM_001275940
1491
421
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
Rad60-PA
FBpp0083780
47.7
424
6.53
Q9VCP1
NP_651134
AAF56116
Rad60-PB
FBpp0290310
47.6
422
6.53
E1JIU3
NP_001163698
ACZ94993
Rad60-PC
FBpp0306566
47.6
422
6.53
E1JIU3
NP_001262866
AGB96246
Rad60-PD
FBpp0306567
47.7
424
6.53
Q9VCP1
NP_001262867
AGB96247
Rad60-PE
FBpp0306568
47.6
423
6.53
A0A0B4KHY5
NP_001262868
AGB96248
Rad60-PF
FBpp0306569
47.5
421
6.53
A0A0B4KHP8
NP_001262869
AGB96249
Polypeptides with Identical Sequences

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

424 aa isoforms: Rad60-PA, Rad60-PD
422 aa isoforms: Rad60-PB, Rad60-PC
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Forms a complex with dgrn; likely required for localization to the nuclear periphery (PubMed:26502056). Interacts with the SMC5-SMC6 complex members SMC5 and SMC6/jnj following ionizing radiation (IR) to induce DNA damage (PubMed:26502056). Interaction between the SMC5-SMC6 complex and the dgrn-Rad60 complex, may stabilize the association of heterochromatic DSBs with the nuclear periphery (PubMed:26502056).

(UniProt, Q9VCP1)
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\Rad60 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).

1.63

Transcript Expression
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in nuclear periphery
inferred from direct assay
(Ryu et al., 2015)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Rad60 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
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
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
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 3 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Rad60
Transgenic constructs containing regulatory region of Rad60
Aberrations (Deficiencies and Duplications) ( 2 )
Inferred from experimentation ( 2 )
Gene disrupted in
Df(3R)Exel6274
(Ryder, 2004.4.26)
Df(3R)Exel6280
(Ryder, 2004.4.26)
Inferred from location ( 6 )
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
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
Other Phenotypes
Allele
abnormal DNA repair
Phenotype manifest in
Allele
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) (5)
Hsap\NFATC2IP
2 of 14
Yes
Yes
Hsap\SUMO1
1 of 14
No
No
2  
Hsap\SUMO2
1 of 14
No
No
Hsap\SUMO3
1 of 14
No
No
2  
Hsap\SUMO4
1 of 14
No
No
2  
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\Sumo1
1 of 14
Yes
No
Rnor\Sumo2
1 of 14
Yes
No
Rnor\Sumo3
1 of 14
Yes
No
Rnor\Sumo4
1 of 14
Yes
No
Mus musculus (laboratory mouse) (4)
Mmus\Nfatc2ip
1 of 14
Yes
No
Mmus\Sumo1
1 of 14
Yes
No
Mmus\Sumo2
1 of 14
Yes
No
Mmus\Sumo3
1 of 14
Yes
No
Xenopus tropicalis (Western clawed frog) (0)
Danio rerio (Zebrafish) (4)
Drer\nfatc2ip
1 of 14
Yes
No
Drer\sumo1
1 of 14
Yes
No
Drer\sumo3a
1 of 14
Yes
No
Drer\sumo3b
1 of 14
Yes
No
Caenorhabditis elegans (Nematode, roundworm) (3)
Cele\F28A10.1
1 of 14
Yes
Yes
Cele\smo-1
1 of 14
Yes
No
Cele\W09C3.3
1 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (3)
Agam\AgaP_AGAP005272
6 of 12
Yes
Yes
Agam\AgaP_AGAP000852
1 of 12
No
No
Agam\AgaP_AGAP001701
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (7)
Atha\AT5G48700
1 of 13
Yes
No
Atha\AT5G48710
1 of 13
Yes
No
Atha\AT5G55856
1 of 13
Yes
No
Atha\SUMO1
1 of 13
Yes
No
Atha\SUMO2
1 of 13
Yes
No
Atha\SUMO3
1 of 13
Yes
No
Atha\SUMO5
1 of 13
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\SMT3
1 of 13
Yes
No
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\pmt3
1 of 12
Yes
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Rad60. 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) (1)
Sumo
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 ( 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?
    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
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Subunit Structure (UniProtKB)
    Forms a complex with dgrn; likely required for localization to the nuclear periphery (PubMed:26502056). Interacts with the SMC5-SMC6 complex members SMC5 and SMC6/jnj following ionizing radiation (IR) to induce DNA damage (PubMed:26502056). Interaction between the SMC5-SMC6 complex and the dgrn-Rad60 complex, may stabilize the association of heterochromatic DSBs with the nuclear periphery (PubMed:26502056).
    (UniProt, Q9VCP1 )
    Linkouts
    DroID - A comprehensive database of gene and protein interactions.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    FlyBase
    External Links
    External Data
    Linkouts
    Class of Gene
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-78
    Cytogenetic map
    94E8-94E9
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    94E8-94E9
    Limits computationally determined from genome sequence between P{PZ}cnc03921 and P{PZ}l(3)0690606906
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    3-78

    (FlyBase, 2016)

    3-79.9

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (9)
    Genomic Clones (19)
     

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

    cDNA Clones (32)
     

    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
        Relationship to Other Genes
        Source for database merge of
        Additional comments
        Nomenclature History
        Source for database identify of

        Source for identity of: Rad60 CG4449

        (Ryu et al., 2015)
        Nomenclature comments
        Etymology

        Named 'Rad60' based on the S. pombe ortholog.

        (Ryu et al., 2015)
        Synonyms and Secondary IDs (5)
        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/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
        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.
        BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
        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
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        MIST (protein-protein) - An integrated Molecular Interaction Database
        References (28)