A Database of Drosophila Genes & Genomes

 

Gene Dmel\pcm

General Information
SymbolDmel\pcmSpeciesD. melanogaster
NamepacmanAnnotation symbolCG3291
Feature typeprotein_coding_geneFlyBase IDFBgn0020261
Created / Updated2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)XRecombination map
Cytogenetic map 18C7-18C7 Sequence locationX:19,379,780..19,385,984 [-]
Map ( GBrowse ) detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
The gene pacman is referred to in FlyBase by the symbol pcm (CG3291, FBgn0020261). It has the cytological map location 18C7. Its sequence location is X:19379780..19385984. Its molecular function is described by 5'-3' exoribonuclease activity; nucleic acid binding. It is involved in the biological processes: RNA catabolic process; gastrulation; mRNA catabolic process, nonsense-mediated decay; RNA interference. One allele is reported. No phenotypic data is available. It has one annotated transcript and one annotated polypeptide.
hide Detailed Mapping Data
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
18C1-18C4
 
(Newbury et al., 1998)
18C1-18C4
 
(Newbury and Till, 1997)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology)
References
Gene Order (overall orientation not stated)
References
hide Gene Model & Products
Please see the GBrowse view of Dmel\pcm for information on other features
detailed view FBtr0074711 FBtr0074784 FBtr0074712 FBtr0074783 FBpp0074480 FBpp0074553 FBpp0074481 FBpp0074552 FBti0011933 FBti0035762 FBti0035765
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
pcm-RA
FBtr0074784
 NM_078684
  5333
  1612
Additional Transcript Data & Comments
Reported size (kB)
5.2 (northern blot)
(Till et al., 1998)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kD)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
pcm-PA  
FBpp0074553  
184.5  
1612  
7.03  
  NP_523408
  AAF48958
Additional Polypeptide Data & Comments
Reported size (kD)
1613 (aa)
(Till et al., 1998)
Comments
External Data
Linkouts
PANTHER - Protein classification by function, families, and pathways
•
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
Putative 5-3 exonuclease (IPR004859)
Exonuclease, Xnr (IPR016494)
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
AA695377
 
AA817398
 
AA820637
 
AA820728
 
AA942280
 
AA949784
 
AE003512
AAF48958
 
AI061920
 
AI134050
 
AI512305
 
AI516353
 
AI531870
 
AI945245
 
AJ242529
CAB43711
 
AW942649
 
AY051675
AAK93099
 
BF486421
 
BF488539
 
BF493587
 
BF501867
 
BF503215
 
BG638473
 
BG639602
 
CK660988
 
CO293802
 
CO325716
 
CO328077
 
EC062057
 
EC212680
 
EC235441
 
EC252880
 
EC255547
 
LD26388
 
 
UniProtKB/Swiss-Prot
    UniProtKB/TrEMBL
    Maps to
    Does NOT map to
    Identified with
    (Oliver, 2001.8.16)
    (BDGP Project Members, 2000-)
    hide Mapped Features & Mutations
    Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here
    Type
    Symbol & Location
    Additional Notes
    References
    hide External Data
    Linkouts
    DEDB - Drosophila exon database: splicing graphs
    •
    Crossreferences
    hide Expression Data
    FlyBase-Curated Data
    Transcript and
    Protein data     		Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
    hide Summary of Transcript Expression
    Stage
    Tissue/Position
    Reference
     oogenesis stage,adult stage
     nurse cell
    (Till et al., 1998)
     adult stage | male
     
    (Till et al., 1998)
     adult stage | female
     
    (Till et al., 1998)
     embryonic stage | 0-8hr
     
    (Till et al., 1998)
     oogenesis stage,adult stage
     oocyte
    (Till et al., 1998)
     embryonic stage | stage 1-7
     
    (Till et al., 1998)
    Marker for
      Subcellular Localization
      CV Term
      hide Summary of Polypeptide Expression
      Stage
      Tissue/Position
      Reference
      Marker for
        Subcellular Localization
        CV Term
        hide Microarray Data
        Developmental timecourse, Costello et al., 2008 (Original data from Arbeitman et al., 2002)
        Untitled Document detailed view FBtr0074711 FBtr0074784 FBtr0074712 FBtr0074783
        AI061920
        AA942280
        AI531870
        AA820637
        hide External Data & Images
        Linkouts
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        •
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        •
        GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies
        •
        hide Alleles & Phenotypes
        hide Summary of Allele Phenotypes
        Phenotype manifest in
        Allele
        hide Classical Alleles ( 0 )
        For All Classical Alleles Show

        Allele of pcmClassMutagenStocksKnown lesion
        hide Alleles Carried on Transgenic Constructs ( 1 )
        For All Alleles Carried on Transgenic Constructs Show

        Allele of pcmClassMutagenStocksKnown lesion
        pcmGD109261 Yes
        hide Aneuploid Aberrations
        Useful deficiency
         
        Useful duplication
         
        Disrupted in
        (Ryder, 2004.4.26)
        hide Transgenic Constructs & Insertions
        Transgenic Constructs
        Type of construct
        Name
        Expression data
        UAS construct
        P{GD10926}
        NA
        Insertions
        Type of insertions
        Name
        Expression data
        insertion of mobile activating element
        P{EP}EP1526
        NA
        hide Related Comments
        Please look at the allele reports for the complete phenotype data
        hide Gene Ontology: Function, Process & Cellular Component ( 8 )
        hide Molecular Function
        CV term
        Evidence
        References
        5'-3' exoribonuclease activity
        inferred from sequence or structural similarity
        (Newbury, 1997)
        inferred from direct assay
        (Newbury et al., 2000)
        nucleic acid binding
        inferred from electronic annotation with InterPro:IPR004859
        (FlyBase Curators et al., 2004-)
        hide Biological Process
        CV term
        Evidence
        References
        RNA catabolic process
        non-traceable author statement
        (Morgan, 2002)
        RNA interference
        inferred from mutant phenotype
        (Rehwinkel et al., 2005)
        gastrulation
        non-traceable author statement
        (Morgan, 2002)
        mRNA catabolic process, nonsense-mediated decay
        inferred from mutant phenotype
        (Rehwinkel et al., 2005)
        hide Cellular Component
        CV term
        Evidence
        References
        cytoplasm
        non-traceable author statement
        (Morgan, 2002)
        intracellular
        inferred from electronic annotation with InterPro:IPR004859
        (FlyBase Curators et al., 2004-)
        hide Sequence Ontology: Class of Gene
        protein_coding_gene
         
        nuclear_gene
         
        hide Interactions & Pathways
        hide Summary of Genetic Interactions
        Interacts with
        Please look at the allele data for full details of the genetic interactions
        pcm allele
        Gene
        References
        hide External Data
        Linkouts
        BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions
        •
        hide Orthologs
        Genome-wide drosophilid orthologs
        Curated drosophilid orthologs
         
        Linkouts
        InParanoid orthologs - Eukaryotic orthologs
        •
        hide Functional Complementation between Species
        Functionally complements
        Scer\KEM1
        (Newbury, 1998)
        Scer\KEM1
        (Till et al., 1998)
        hide Inter-Species Misexpression Data
        Produces phenotype in
        Produces NO phenotype in
        hide Stocks & Reagents
        hide Stocks Listed in FlyBase ( 3 )
        Szeged
        -
        P{EP}EP1526
        Bloomington
        11456
        w1118 P{EP}EP1526
        VDRC
        v21677
        w1118; P{GD10926}v21677
        hide Genomic Clones ( 2 )
        hide cDNA Clones ( 20 )
        cDNA Clones, Fully Sequenced
        BDGP DGC clones
        Other clones
        cDNA Clones, End Sequenced (ESTs)
        BDGP DGC clones
        Other clones
        hide RNAi & Array Information
        Affy Oligo
        Linkouts
        DRSC - RNAi screening (Harvard): high-throughput cell culture data and design
        •
        GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data
        •
        hide Antibody Information
        hide Other Information
        hide Discoverer
        hide Etymology
        hide Identification
        hide Position Effect Variegation Data
        hide Relationship to Other Genes
        Source for database identity of
        Source for identity of: pcm CG3291
        (Benos, 1999.11)
        Source for database merge of
        Additional comments
        hide Comments About Role
        The pcm product is required for the degradation of 3' decay intermediates.
        (Rehwinkel et al., 2005)
        hide Comments About Molecular Function
        hide 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.
        (Hollien and Weissman, 2006)
        dsRNA has been made from templates generated with primers directed against this gene.
        (Rehwinkel et al., 2005)
        hide External Crossreferences & Linkouts
        Sequence Crossreferences
        RefSeq (Transcripts)
        •
        RefSeq (Proteins)
        •
        DDBJ / EMBL / GenBank
        •
        UniProtKB/TrEMBL
        •
        Other Crossreferences
        InterPro domains - A database of protein families, domains, and functional sites
        •
        Putative 5-3 exonuclease (IPR004859)
        Exonuclease, Xnr (IPR016494)
        Linkouts
        BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions
        •
        DEDB - Drosophila exon database: splicing graphs
        •
        DRSC - RNAi screening (Harvard): high-throughput cell culture data and design
        •
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        •
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        •
        FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans
        •
        GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies
        •
        GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data
        •
        InParanoid orthologs - Eukaryotic orthologs
        •
        PANTHER - Protein classification by function, families, and pathways
        •
        University of Chicago Dev. Expression
        •
        hide Synonyms & Secondary IDs ( 7 )
        Reported As
        Symbol Synonym
        CG3291
        (Labourier et al., 2002, Hollien and Weissman, 2006)
        pcm
         
        XRN1
        (Valencia-Sanchez and Maquat, 2004, Rehwinkel et al., 2005)
        XRN1/pcm
        (Hollien and Weissman, 2006)
        Xrn1p
        (Valencia-Sanchez et al., 2006)
        Name Synonym
        Pacman
        (Morgan, 2002, Rehwinkel et al., 2005, Zaessinger et al., 2006)
        pacman
        (Newbury, 1999.5.25, Newbury and Till, 1997)
        Secondary FlyBase IDs
          hide References ( 28 )
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          hide Recent research papers ( 1 )
          Zaessinger et al., 2006, Development 133(22): 4573--4583
          Oskar allows nanos mRNA translation in Drosophila embryos by preventing its deadenylation by Smaug/CCR4. [FBrf0193114]
          Show all research papers ...
          hide Recent reviews ( 1 )
          Valencia-Sanchez et al., 2006, Genes Dev. 20(5): 515--524
          Control of translation and mRNA degradation by miRNAs and siRNAs. [FBrf0199315]
          Show all reviews ...