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General Information
Symbol
Dmel\ref(2)P
Species
D. melanogaster
Name
refractory to sigma P
Annotation Symbol
CG10360
Feature Type
FlyBase ID
FBgn0003231
Gene Model Status
Stock Availability
Gene Snapshot
In progress.Contributions welcome.
Also Known As
p62, Ref2P, SQSTM1, ref
Key Links
Genomic Location
Cytogenetic map
Sequence location
2L:19,542,468..19,545,548 [+]
Recombination map
2-54
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
-
Summaries
Protein Function (UniProtKB)
Required for selective autophagy activation by ubiquitinated proteins (PubMed:22622177). Implicated in sigma rhabdovirus multiplication and necessary for male fertility. Involved in activating transcription of Drs (PubMed:12446795, PubMed:2510997).
(UniProt, P14199)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
ref(2)P
ref(2)Pp is the first refractaire mutant found and the most thoroughly studied. Allele frequency about 0.2 in Paris population and approaches the same incidence in caged populations with or without the presence of sigma virus (Fleuriet, 1980, Genetics 95: 459-65; 1981, Genetics 97: 415-25). Refractaire phenotype expressed in cultured cells (Richard-Molard, 1975, Arch. Virol. 47: 139-46) and in imaginal disks transplanted into stably infected hosts (Bernard, 1968, Exp. Cell Res. 50: 117-26). Inhibition of viral multiplication increases with increased doses of ref(2)Pp, with added doses of ref(2)Po having an antagonistic effect (Nakamura, 1978, Mol. Gen. Genet. 159: 285-92). Strains of sigma virus capable of multiplication in restrictive strains can be selected; P+ virus strains multiply in ref(2)Pp hosts, whereas P-strains do not; no such distinction in ref(2)Po hosts. Also 5-FU-induced host-adapted strains of virus (haP) capable of replication in ref(2)Pp; many are temperature sensitive, suggesting that ref(2)Pp interacts with a viral protein (Coulon and Contamine, 1982, Virology 123: 381-92). Males homozygous for null alleles sterile; elongating spermatids display degeneration of axonemes (Dezelee, Bras, Contamine, Lopez-Ferber, Segretain, and Teninges, 1989, EMBO J. 8: 3437-46).
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\ref(2)P or the JBrowse view of Dmel\ref(2)P 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
Comments on Gene Model
Low-frequency RNA-Seq exon junction(s) not annotated.
Gene model reviewed during 5.52
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0081253
2305
599
FBtr0100289
2395
599
Additional Transcript Data and Comments
Reported size (kB)
2.4, 2.3 (unknown)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0080794
65.3
599
4.63
FBpp0099683
65.3
599
4.63
Polypeptides with Identical Sequences

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

599 aa isoforms: ref(2)P-PA, ref(2)P-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
115-125 (kD observed); 76 (kD predicted)
Comments
External Data
Subunit Structure (UniProtKB)
Interacts with aPKC and Traf6.
(UniProt, P14199)
Crossreferences
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\ref(2)P using the Feature Mapper tool.

External Data
Crossreferences
Linkouts
Gene Ontology (13 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000387090
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000387090
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR000433
(assigned by InterPro )
Biological Process (6 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
(assigned by UniProt )
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000387090
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000387090
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000387090
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000387090
(assigned by GO_Central )
Cellular Component (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000387090
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000387090
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000387090
(assigned by GO_Central )
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\ref(2)P in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 33 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 26 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of ref(2)P
Transgenic constructs containing regulatory region of ref(2)P
Deletions and Duplications ( 3 )
Phenotypes
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
6 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
4 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
3 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (2)
1 of 12
Yes
No
1 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
4 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (8)
5 of 15
Yes
Yes
5 of 15
Yes
Yes
4 of 15
No
Yes
4 of 15
No
Yes
3 of 15
No
Yes
2 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (1)
1 of 12
Yes
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091907WT )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091508NT )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Glossina morsitans
Tsetse fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Mayetiola destructor
Hessian fly
Mayetiola destructor
Hessian fly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W030Z )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Pediculus humanus
Human body louse
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X02XW )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G08ES )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (2)
1 of 10
1 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 2 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 1 )
    Allele
    Disease
    Interaction
    References
    Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
     
    Disease Associations of Human Orthologs (via DIOPT v7.1 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    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:
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Interactions Browser

    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    RNA-protein
    Physical Interaction
    Assay
    References
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    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
    External Data
    Subunit Structure (UniProtKB)
    Interacts with aPKC and Traf6.
    (UniProt, P14199 )
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Gene Group - Pathway Membership (FlyBase)
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2L
    Recombination map
    2-54
    Cytogenetic map
    Sequence location
    2L:19,542,468..19,545,548 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    37F1-37F1
    Limits computationally determined from genome sequence between P{EP}dntEP2158 and P{EP}EP623&P{PZ}spi01068
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    37E-37F
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    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 (240)
     

    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 GBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequences
    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)
      RNAi and Array Information
      Linkouts
      DRSC - Results frm RNAi screens
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      Antibody Information
      Laboratory Generated Antibodies
      Commercially Available Antibodies
       
      Other Information
      Relationship to Other Genes
      Source for database identify of
      Source for database merge of
      Additional comments
      permissive and restrictive alleles are codominant.
      Other Comments
      ref(2)P is required for the normal clearance of the paternal mitochondrial derivatives in developing embryos.
      Maternal transmission of the sigma virus is strongly affected by ref(2)P, whereas paternal transmission is affected by variation in both ref(2)P and other genes on the second chromosome.
      The N-terminal domain of the ref(2)P protein is required for its activity in vivo. Conformation-dependent epitopes common to those of the Sigma map to a site distinct from the site involved in virus restriction. Two distinct domains of the ref(2)P protein are involved in the control of Sigma multiplication.
      Comparisons with the D.erecta ref(2)P gene provide evidence for selective constraint on the protein.
      The ref(2)P locus shows unusual variability at the molecular level.
      Two types of sigma viruses are found in populations differing in sensitivity to the ref(2)P allele: Type I is very sensitive and is not transmitted by males in the presence of ref(2)P, Type I is more resistant and is transmitted in the presence of ref(2)P.
      Invasion hypothesis that Type II virus (resistant to ref(2)Pp genotype) is spreading by vertical transmission from central France through European populations is confirmed by data from Tubingen where Type II clones increased from 0.27 to 0.93 between 1985 and 1991. However over the same period no increase in the frequency of infected flies was observed.
      Development of the P-M system of transposable elements shows interesting correlations with the distribution of sigma rhabdovirus in D.melanogaster populations.
      ref(2)P thought to act at level of sigma virus replication.
      Males homozygous for null alleles sterile; elongating spermatids display degeneration of axonemes.
      Strains of sigma virus capable of multiplication in restrictive strains can be selected; P+ virus strains multiply in ref(2)Pp hosts, whereas P- strains do not; no such distinction in ref(2)Po hosts. Also 5-FU-induced host-adapted strains of virus (haP) capable of replication in ref(2)Pp; many are temperature-sensitive, suggesting that ref(2)Pp interacts with a viral protein.
      ref(2)Pp is the first refractaire mutant found and the most thoroughly studied. Allele frequency about 0.2 in Paris population and approaches the same incidence in caged populations with or without the presence of sigma virus.
      Mutant that interferes with the normal multiplication of some strains of sigma virus, as indicated by delayed acquisition of CO2 sensitivity following viral injection.
      Inhibition of viral multiplication increases with increased doses of ref(2)Pp, with added doses of ref(2)Po having an antagonistic effect.
      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 65 )
      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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
      Other crossreferences
      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
      Flygut - An atlas of the Drosophila adult midgut
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      KEGG Genes - Molecular building blocks of life in the genomic space.
      modMine - A data warehouse for the modENCODE project
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      FLIGHT - Cell culture data for RNAi and other high-throughput technologies
      FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
      FlyMine - An integrated database for Drosophila genomics
      InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Synonyms and Secondary IDs (25)
      Reported As
      Symbol Synonym
      Name Synonyms
      Secondary FlyBase IDs
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (248)