General Information
Symbol
Dmel\pn
Species
D. melanogaster
Name
prune
Annotation Symbol
CG3461
Feature Type
FlyBase ID
FBgn0003116
Gene Model Status
Stock Availability
Enzyme Name (EC)
Exopolyphosphatase (3.6.1.11)
Gene Snapshot
Prune (Pn) is a phosphoesterase that localizes to the mitochondrial matrix. It hydrolyzes cAMP and negatively regulates mitochondrial cAMP signaling. Pn is involved in mtDNA maintenance and eye pigment biosynthesis. [Date last reviewed: 2016-09-15]
Also Known As
EG:152A3 .5
Genomic Location
Cytogenetic map
Sequence location
X:2,181,211..2,182,916 [+]
Recombination map
1-0.8
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
GO Summary Ribbons
Families, Domains and Molecular Function
Gene Group Membership (FlyBase)
Protein Family (UniProt, Sequence Similarities)
-
Molecular Function (see GO section for details)
Catalytic Activity (EC)
Experimental Evidence
-
Predictions / Assertions
(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate (3.6.1.11)
Summaries
Phenotypic Description from the Red Book (Lindsley and Zimm 1992)
pn: prune
Eye color of newly emerged flies transparent brownish red, becoming brownish purple with age. The eyes of pn males have about 25% as much drosopterin (red pigment) as the eyes of wild-type males (Gearhart and MacIntyre, 1970, Anal. Biochem. 37: 21-25); the concentrations of xanthopterin and sepiapterin (brown pigments) are increased to about 110% of wild-type (Nolte, 1959). Control of drosopterin synthesis seems to be related to the activity of the enzyme GTP cyclohydrolase (Evans and Howell, 1979, Biochem. Genet. 16: 13-26). The pn eye color is autonomous in larval optic disks transplanted into wild-type hosts (Beadle and Ephrussi, 1936). Larval Malpighian tube color is normal (Brehme and Demerec, 1942, Growth 6: 351-56). Standard pn mutants are homo- and hemizygous viable in a wild-type background, but show a lethal interaction with the third chromosome dominant awkK (Lifschytz and Falk, 1969; Orevi, 1973, DIS 50: 77). Some temperature-sensitive pn mutants (pnts-e), however, are insensitive to the killing action of awkK; one temperature-sensitive mutant (pnts-ek) is insensitive to awkK at permissive temperatures (18, 22), but sensitive to awkK at restrictive temperatures (25, 29) (Orevi, 1973, DIS 50: 80; Orevi and Falk, 1975). The TSP for the eye color phenotype occurs during the late pupal stage, while the TSP for the pn component of the pn-awkK interaction begins at the late pupal stage and lasts until eclosion (Orevi and Falk, 1975). Homo- and hemizygous pn deficiencies and other chromosomal rearrangements have been induced by Ilyina et al. (1980), as indicated in the allele table.
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\pn or the JBrowse view of Dmel\pn 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
Gene model reviewed during 5.39
Gene model reviewed during 5.51
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0070389
1638
405
Additional Transcript Data and Comments
Reported size (kB)
1.8 (northern blot)
1.4 (longest cDNA)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0070373
45.2
405
6.32
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)
405 (aa); 50 (kD)
404 (aa); 44 (kD predicted)
Comments
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\pn using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (10 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN001087311
(assigned by GO_Central )
Biological Process (6 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN001087311
(assigned by GO_Central )
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN001087311
(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

Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
A developmental western blot representing embryonic, larval, pupal and adult stages reveals that pn protein is present in all stages, with highest levels in pupae and adults, and lowest levels in mid-third instar larvae.
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\pn 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
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 102 )
For All Classical and Insertion Alleles Show
 
Allele of pn
Class
Mutagen
Associated Insertion
Stocks
Known lesion
    0
    --
      0
      --
      Other relevant insertions
      Transgenic Constructs ( 7 )
      Deletions and Duplications ( 75 )
      Phenotypes
      For more details about a specific phenotype click on the relevant allele symbol.
      Lethality
      Allele
      Other Phenotypes
      Allele
      Phenotype manifest in
      Allele
      Orthologs
      Human Orthologs (via DIOPT v7.1)
      Homo sapiens (Human) (5)
      Species\Gene Symbol
      Score
      Best Score
      Best Reverse Score
      Alignment
      Complementation?
      Transgene?
      15 of 15
      Yes
      Yes
      3 of 15
      No
      No
       
      1 of 15
      No
      No
      1 of 15
      No
      No
      1 of 15
      No
      No
      Model Organism Orthologs (via DIOPT v7.1)
      Mus musculus (laboratory mouse) (4)
      Species\Gene Symbol
      Score
      Best Score
      Best Reverse Score
      Alignment
      Complementation?
      Transgene?
      15 of 15
      Yes
      Yes
      3 of 15
      No
      No
      1 of 15
      No
      No
      1 of 15
      No
      No
      Rattus norvegicus (Norway rat) (5)
      13 of 13
      Yes
      Yes
      2 of 13
      No
      No
      1 of 13
      No
      No
      1 of 13
      No
      No
      1 of 13
      No
      No
      Xenopus tropicalis (Western clawed frog) (1)
      8 of 12
      Yes
      Yes
      Danio rerio (Zebrafish) (6)
      14 of 15
      Yes
      Yes
      1 of 15
      No
      No
      1 of 15
      No
      No
      1 of 15
      No
      No
      1 of 15
      No
      No
      1 of 15
      No
      No
      Caenorhabditis elegans (Nematode, roundworm) (0)
      No orthologs reported.
      Arabidopsis thaliana (thale-cress) (0)
      No orthologs reported.
      Saccharomyces cerevisiae (Brewer's yeast) (1)
      15 of 15
      Yes
      Yes
      Schizosaccharomyces pombe (Fission yeast) (1)
      12 of 12
      Yes
      Yes
      Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190BWF )
      Organism
      Common Name
      Gene
      AAA Syntenic Ortholog
      Multiple Dmel Genes in this Orthologous Group
      Drosophila melanogaster
      fruit fly
      Drosophila simulans
      Drosophila sechellia
      Drosophila erecta
      Drosophila yakuba
      Drosophila ananassae
      Drosophila pseudoobscura pseudoobscura
      Drosophila persimilis
      Drosophila willistoni
      Drosophila virilis
      Drosophila mojavensis
      Drosophila grimshawi
      Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091508I8 )
      Organism
      Common Name
      Gene
      Multiple Dmel Genes in this Orthologous Group
      Musca domestica
      House fly
      Glossina morsitans
      Tsetse fly
      Lucilia cuprina
      Australian sheep blowfly
      Mayetiola destructor
      Hessian fly
      Aedes aegypti
      Yellow fever mosquito
      Anopheles darlingi
      American malaria mosquito
      Anopheles gambiae
      Malaria mosquito
      Culex quinquefasciatus
      Southern house mosquito
      Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W096U )
      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
      Dendroctonus ponderosae
      Mountain pine beetle
      Tribolium castaneum
      Red flour beetle
      Pediculus humanus
      Human body louse
      Zootermopsis nevadensis
      Nevada dampwood termite
      Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0934 )
      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
      Tetranychus urticae
      Two-spotted spider mite
      Daphnia pulex
      Water flea
      Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0E88 )
      Organism
      Common Name
      Gene
      Multiple Dmel Genes in this Orthologous Group
      Strongylocentrotus purpuratus
      Purple sea urchin
      Strongylocentrotus purpuratus
      Purple sea urchin
      Ciona intestinalis
      Vase tunicate
      Ciona intestinalis
      Vase tunicate
      Ciona intestinalis
      Vase tunicate
      Gallus gallus
      Domestic chicken
      Gallus gallus
      Domestic chicken
      Gallus gallus
      Domestic chicken
      Gallus gallus
      Domestic chicken
      Human Disease Model Data
      FlyBase Human Disease Model Reports
        Alleles Reported to Model Human Disease (Disease Ontology)
        Download
        Models ( 1 )
        Allele
        Disease
        Evidence
        References
        in combination with awdK
        Interactions ( 0 )
        Allele
        Disease
        Interaction
        References
        Comments ( 0 )
         
        Human Orthologs (via DIOPT v7.1)
        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
        Interactions Browser
        Summary of Genetic Interactions
        esyN Network Diagram
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        External Data
        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.
        Pathways
        Gene Group - Pathway Membership (FlyBase)
        External Data
        Linkouts
        KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        X
        Recombination map
        1-0.8
        Cytogenetic map
        Sequence location
        X:2,181,211..2,182,916 [+]
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        2E1-2E1
        Limits computationally determined from genome sequence between P{EP}ActnEP1193&P{EP}CG4322EP1631 and P{EP}EP1460&P{EP}CG2924EP1596
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        2E1-2E2
        (determined by in situ hybridisation)
        Experimentally Determined Recombination Data
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (68)
        Genomic Clones (7)
         

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

        cDNA Clones (18)
         

        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 identity of: pn CG3461
          Source for database merge of
          Additional comments
          Other Comments
          dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology.
          Shows particularly robust cycling of transcription in adult heads, as assessed by expression analysis using high density oligonucleotide arrays with probe generated during three 12-point time course experiments over the course of 6 days.
          Novel family of predicted phosphoesterases is identified, including the pn gene product.
          In a sample of 79 genes with multiple introns, 33 showed significant heterogeneity in G+C content among introns of the same gene and significant positive correspondence between the intron and the third codon position G+C content within genes. These results are consistent with selection adding against preferred codons at the start of genes.
          In(1LR)pn2a causes pn-coloured eyes in pn heterozygous females.
          To understand the function of pn the nucleotide sequence of a pn cDNA and pn genomic DNA have been determined. Verification that the cDNA encodes a functional pn product is demonstrated by rescue of both the pn eye phenotype and the pn/awdK interaction.
          Full length pn cDNA has been cloned and sequenced.
          Genetic interactions suggest that pn product in same haematopoetic pathway as awd and hop gene products.
          pn shows a lethal interaction with awdK: a small number of larvae reach second instar. A maternal effect can shift the phenocritical period for one larval stage. This effect is temperature sensitive: low temperature, more larvae reach third instar. The perineurium, glia and lymph gland are the main cellular targets of the pn/awdK interaction.
          Eye color of newly emerged flies transparent brownish red, becoming brownish purple with age. The eyes of pn1 males have about 25% as much drosopterin (red pigment) as the eyes of wild-type males (FBrf0021089); the concentrations of xanthopterin and sepiapterin (brown pigments) are increased to about 110% of wild-type (FBrf0012680). Control of drosopterin synthesis seems to be related to the activity of the enzyme GTP cyclohydrolase (FBrf0031059). The pn1 eye color is autonomous in larval optic discs transplanted into wild-type hosts (FBrf0003530). Larval Malpighian tube color is normal (FBrf0005752). Standard pn mutants are homo- and hemizygous viable in a wild-type background, but show a lethal interaction with the third chromosome dominant awdK (FBrf0020565; FBrf0024856). Some temperature-sensitive pn mutants ('pnts-e' series), however, are insensitive to the killing action of awdK; one temperature-sensitive mutant (pnts-ek) is insensitive to awdK at permissive temperatures (18oC, 22oC), but sensitive to awdK at restrictive temperatures (25oC, 29oC) (FBrf0024860; FBrf0027926). The TSP for the eye color phenotype occurs during the late pupal stage, while the TSP for the pn component of the pn-awdK interaction begins at the late pupal stage and lasts until eclosion (FBrf0027926). Homo- and hemizygous pn deficiencies and other chromosomal rearrangements have been induced by Ilyina (FBrf0034407).
          pn has been cloned and sequence homology comparisons show a cDNA of pn has similarity to the catalytic domain of bovine GTPase activating protein.
          Molecular analysis of pn.
          Analysis of the pn locus suggests that it may encode a cloned 1.4kb cDNA, which encodes a protein with similarity to the catalytic domain of mammalian GTPase-activating proteins.
          One copy of awdK carried in a P element is sufficient to evoke a lethal interaction with pn.
          Identification: A saturation analysis of the 2D3--2F5 region detected the pn complementation group.
          Origin and Etymology
          Discoverer
          Etymology
          Identification
          External Crossreferences and Linkouts ( 47 )
          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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
          Other crossreferences
          BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
          InterPro - A database of protein families, domains and functional sites
          Linkouts
          BioGRID - A database of protein and genetic interactions.
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center 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.
          FLIGHT - Cell culture data for RNAi and other high-throughput technologies
          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
          FlyMine - An integrated database for Drosophila genomics
          GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
          KEGG Genes - Molecular building blocks of life in the genomic space.
          KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
          MIST (genetic) - An integrated Molecular Interaction Database
          modMine - A data warehouse for the modENCODE project
          Synonyms and Secondary IDs (9)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          References (157)