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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 Summary
prune (pn) encodes a phosphoesterase that localizes to the mitochondrial matrix. It hydrolyzes cAMP and negatively regulates mitochondrial cAMP signaling. It is involved in mtDNA maintenance and eye pigment biosynthesis. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
Also Known As

EG:152A3.5

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
1-0.8
RefSeq locus
NC_004354 REGION:2181211..2182916
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (8 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:PTN000485779
(assigned by GO_Central )
Biological Process (4 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (0 terms)
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
is_active_in cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN001087311
(assigned by GO_Central )
Protein Family (UniProt)
-
Catalytic Activity (EC)
Experimental Evidence
-
Predictions / Assertions
(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate (3.6.1.11)
Summaries
Gene Snapshot
prune (pn) encodes a phosphoesterase that localizes to the mitochondrial matrix. It hydrolyzes cAMP and negatively regulates mitochondrial cAMP signaling. It is involved in mtDNA maintenance and eye pigment biosynthesis. [Date last reviewed: 2019-03-14]
Gene Group (FlyBase)
CYCLIC-NUCLEOTIDE PHOSPHODIESTERASES -
Cyclic-nucleotide phosphodiesterases are hydrolases that catalyze the hydrolysis of a nucleoside cyclic phosphate into a nucleoside phosphate.
OTHER ACID ANHYDRIDE HYDROLASES -
The OTHER PYROPHOSPHATASES group contains pyrophosphatases that do not fit into any of the other major classes of pyrophosphatases.
Phenotypic Description (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 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
Structure New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry O18399)

If you don't see the viewer to the right, 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.

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
UniProt
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
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:
 low
high 
Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.
Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:
 low
high 
as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. 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
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
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 103 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of pn
Transgenic constructs containing regulatory region of pn
Aberrations (Deficiencies and Duplications) ( 75 )
Inferred from experimentation ( 75 )
Inferred from location ( 0 )
Alleles Representing Disease-Implicated Variants
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 v8.0)
Homo sapiens (Human) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
15 of 15
Yes
Yes
3 of 15
No
No
1  
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
14 of 15
Yes
Yes
3 of 15
No
No
Rattus norvegicus (Norway rat) (2)
13 of 13
Yes
Yes
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (1)
9 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
14 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (0)
No records found.
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (1)
14 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
11 of 12
Yes
Yes
Other Organism Orthologs (via OrthoDB)
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (1)
1 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 1 )
    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 v8.0 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
    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.
    MIST (genetic) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    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
    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 (63)
    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 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)
      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 ( 50 )
      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.
      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      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
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      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
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
      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)
      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
      FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
      FlyMine - An integrated database for Drosophila genomics
      KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
      MIST (genetic) - An integrated Molecular Interaction Database
      Synonyms and Secondary IDs (9)
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      Study result (0)
      Result
      Result Type
      Title
      References (162)