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General Information
Symbol
Dmel\pcm
Species
D. melanogaster
Name
pacman
Annotation Symbol
CG3291
Feature Type
FlyBase ID
FBgn0020261
Gene Model Status
Stock Availability
Gene Summary
pacman (pcm) encodes an exoribonuclease that degrades decapped mRNA. It is involved in epithelial closure, male fertility, apoptosis and growth control. [Date last reviewed: 2019-09-26] (FlyBase Gene Snapshot)
Also Known As

XRN1, dXRN1

Key Links
Genomic Location
Cytogenetic map
Sequence location
X:19,485,759..19,492,011 [-]
Recombination map
1-62
RefSeq locus
NC_004354 REGION:19485759..19492011
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (24 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN002643517
(assigned by GO_Central )
enables RNA binding
inferred from biological aspect of ancestor with PANTHER:PTN002643517
(assigned by GO_Central )
Biological Process (16 terms)
Terms Based on Experimental Evidence (14 terms)
CV Term
Evidence
References
involved_in dorsal closure
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from direct assay
inferred from mutant phenotype
inferred from mutant phenotype
inferred from genetic interaction with FLYBASE:pix; FB:FBgn0086706
inferred from mutant phenotype
involved_in RNA interference
inferred from mutant phenotype
involved_in spermatogenesis
inferred from mutant phenotype
involved_in wound healing
inferred from mutant phenotype
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN002643517
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN004352441
(assigned by GO_Central )
Cellular Component (6 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
(assigned by UniProt )
located_in P-body
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
located_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN002643517
(assigned by GO_Central )
Gene Group (FlyBase)
Protein Family (UniProt)
-
Summaries
Gene Snapshot
pacman (pcm) encodes an exoribonuclease that degrades decapped mRNA. It is involved in epithelial closure, male fertility, apoptosis and growth control. [Date last reviewed: 2019-09-26]
Gene Group (FlyBase)
5'-3'-EXORIBONUCLEASES -
5'-3'-exoribonucleases catalyze the sequential degradation of mononucleotides from a free 5' terminus of an RNA molecule.
Summary (Interactive Fly)

exoribonuclease that degrades decapped mRNA - directly interacts with Decapping protein 1 to couple mRNA decapping to 5' exonucleolytic degradation - required for degradation of mRNAs targeted by NMD and RNAi - regulates polycomb silencing - regulates insulin-like peptide and the neuropeptide-like precursor Nplp2 mRNA levels - affects apoptosis and regulates expression of and - regulates expression of the heat shock protein Hsp67Bc and the microRNA miR-277-3p in wing imaginal discs

Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\pcm 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 5.45

Gene model reviewed during 5.56

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0074784
5260
1612
FBtr0302082
5384
1613
Additional Transcript Data and Comments
Reported size (kB)

5.2 (northern blot)

Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0074553
184.5
1612
7.03
FBpp0291292
184.6
1613
7.03
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
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\pcm 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 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
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference

Comment: reference states 0-8 hr AEL

Additional Descriptive Data

pcm transcripts are abundantly expressed in 0-4 and 4-8hr embryos and in adult males and females. pcm transcripts are first detected by in situ hybridization in stage 3 egg chambers in both nurse cells and the oocyte. By stage 10, expression is mainly in nurse cells with very little expression in the oocyte. In embryos, transcripts are ubiquitously distributed and are particularly abundant in the germ band and in head structures.

Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
nurse cell

Comment: in discrete foci

oocyte

Comment: concentrated at posterior end

Additional Descriptive Data

pcm protein is localized to the apical end of the testis, and to cytoplasmic foci in spermatogonia and primary spermatocytes. pcm is colocalized with DCP1 and me31B protein in the cytoplasmic foci.

Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
(assigned by UniProt )
located_in P-body
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\pcm 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
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, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 9 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of pcm
Transgenic constructs containing regulatory region of pcm
Aberrations (Deficiencies and Duplications) ( 4 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
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?
12 of 15
Yes
Yes
2  
3 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
12 of 15
Yes
Yes
2 of 15
No
No
Rattus norvegicus (Norway rat) (3)
11 of 13
Yes
Yes
3 of 13
No
No
2 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (2)
8 of 12
Yes
Yes
2 of 12
No
No
Danio rerio (Zebrafish) (2)
11 of 15
Yes
Yes
3 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (2)
12 of 15
Yes
Yes
3 of 15
No
No
Arabidopsis thaliana (thale-cress) (3)
4 of 9
Yes
No
4 of 9
Yes
No
3 of 9
No
No
Saccharomyces cerevisiae (Brewer's yeast) (2)
10 of 15
Yes
Yes
5 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (2)
10 of 12
Yes
Yes
2 of 12
No
No
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091900LL )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
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
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091500D4 )
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) ( EOG090W00TE )
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
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X00S5 )
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
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G00A4 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
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
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (1)
5 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 ( 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.
    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
    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
    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
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    X
    Recombination map
    1-62
    Cytogenetic map
    Sequence location
    X:19,485,759..19,492,011 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    18C7-18C7
    Limits computationally determined from genome sequence between P{EP}EP1526&P{EP}PfrxEP1150 and P{EP}Tao-1EP1455
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (5)
    Genomic Clones (13)
     

    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 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: pcm CG3291

      Source for database merge of
      Additional comments
      Other Comments

      Changes in expression profiles associated with the unfolded protein response have been analyzed in S2 cells following treatment with dsRNA made from templates generated with primers directed against this gene.

      dsRNA has been made from templates generated with primers directed against this gene.

      The pcm product is required for the degradation of 3' decay intermediates.

      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 46 )
      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
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      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
      FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
      FlyMine - An integrated database for Drosophila genomics
      Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
      InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
      KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Synonyms and Secondary IDs (12)
      Reported As
      Secondary FlyBase IDs
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (90)