FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\Pym
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General Information
Symbol
Dmel\Pym
Species
D. melanogaster
Name
Partner of Y14 and Mago
Annotation Symbol
CG30176
Feature Type
protein_coding_gene
FlyBase ID
FBgn0034918
Gene Model Status
Current
Stock Availability
7 publicly available
Gene Summary
Regulator of the exon junction complex (EJC), a multiprotein complex that associates immediately upstream of the exon-exon junction on mRNAs and serves as a positional landmark for the intron exon structure of genes and directs post-transcriptional processes in the cytoplasm such as mRNA export, nonsense-mediated mRNA decay (NMD) or translation. Acts as an EJC disassembly factor by disrupting mature EJC from spliced mRNAs. Required for normal localization of osk mRNA to the posterior pole of the developing oocyte. Does not interact with the small ribosomal unit or components of the translation initiation complex. May not function in cap-dependent translation regulation. (UniProt, P82804)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

wibg

Key Links
Genomic Location
Cytogenetic map
60A4-60A4
Sequence location
Recombination map
2-105
RefSeq locus
NT_033778 REGION:23855954..23856936
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (11 terms)
Molecular Function (6 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
enables exon-exon junction complex binding
inferred from physical interaction with FLYBASE:mago; FB:FBgn0002736
(Ghosh et al., 2014)
inferred from physical interaction with FLYBASE:tsu; FB:FBgn0033378
(Ghosh et al., 2014)
enables protein binding
inferred from physical interaction with UniProtKB:P49028
(Bono et al., 2004, Forler et al., 2003)
inferred from physical interaction with UniProtKB:Q9V535
(Bono et al., 2004, Forler et al., 2003)
enables RNA binding
inferred from direct assay
(Bono et al., 2004)
NOT enables eukaryotic initiation factor 4E binding
inferred from physical interaction with FLYBASE:eIF4E1; FB:FBgn0015218
(Ghosh et al., 2014)
NOT enables eukaryotic initiation factor 4G binding
inferred from physical interaction with FLYBASE:eIF4G1; FB:FBgn0023213
(Ghosh et al., 2014)
NOT enables ribosomal small subunit binding
inferred from direct assay
(Ghosh et al., 2014)
inferred from physical interaction with FLYBASE:RpL32; FB:FBgn0002626
(Ghosh et al., 2014)
inferred from physical interaction with FLYBASE:RpS6; FB:FBgn0261592
(Ghosh et al., 2014)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables RNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000539124
(GO Reference Genome Project, 2011-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in exon-exon junction complex disassembly
inferred from mutant phenotype
(Ghosh et al., 2014)
NOT involved_in cap-dependent translational initiation
inferred from physical interaction with FLYBASE:Cbp20; FB:FBgn0022943
(Ghosh et al., 2014)
inferred from physical interaction with FLYBASE:pAbp; FB:FBgn0265297
(Ghosh et al., 2014)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in exon-exon junction complex disassembly
inferred from electronic annotation with InterPro:IPR039333
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN000539124
(GO Reference Genome Project, 2011-)
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
inferred from sequence or structural similarity with UniProtKB:Q9BRP8
(Gene Ontology Curators, 2002-)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Bono et al., 2004)
part_of exon-exon junction complex
inferred from direct assay
(Bono et al., 2004)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
is_active_in cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN000539124
(GO Reference Genome Project, 2011-)
part_of exon-exon junction complex
inferred from biological aspect of ancestor with PANTHER:PTN000539124
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the pym family. (P82804)
Protein Signatures (InterPro)
Summaries
Protein Function (UniProtKB)
Regulator of the exon junction complex (EJC), a multiprotein complex that associates immediately upstream of the exon-exon junction on mRNAs and serves as a positional landmark for the intron exon structure of genes and directs post-transcriptional processes in the cytoplasm such as mRNA export, nonsense-mediated mRNA decay (NMD) or translation. Acts as an EJC disassembly factor by disrupting mature EJC from spliced mRNAs. Required for normal localization of osk mRNA to the posterior pole of the developing oocyte. Does not interact with the small ribosomal unit or components of the translation initiation complex. May not function in cap-dependent translation regulation.
(UniProt, P82804)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Pym 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
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry P82804)

If you don't see a structure in the viewer, 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.

Experimentally Determined Structures
Crossreferences
PDB - An information portal to biological macromolecular structures
Comments on Gene Model

Gene model reviewed during 5.52

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Pym-RA
FBtr0072233
NM_166627
983
207
Additional Transcript Data and Comments
Reported size (kB)

1.0 (northern blot)

(Ohlstein et al., 2000)

1 (northern blot)

(Lukacsovich et al., 1999)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
Pym-PA
FBpp0072142
23.4
207
10.56
P82804
NP_726372
AAM68273
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)

207 (aa)

(Lukacsovich et al., 1999)
Comments
External Data
Subunit Structure (UniProtKB)

Interacts (via N-terminus) with mago and tsu/RBM8A; the interaction is direct.

(UniProt, P82804)
Crossreferences
InterPro - A database of protein families, domains and functional sites
PDB - An information portal to biological macromolecular structures
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\Pym 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
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

0.88

Transcript Expression
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage | female
germarium
(Ghosh et al., 2014)
oocyte

Comment: uniformly distributed

(Ghosh et al., 2014)
nurse cell
(Ghosh et al., 2014)
follicle cell
(Ghosh et al., 2014)
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 4
(Ghosh et al., 2014)
adult stage | female
(Ghosh et al., 2014)
adult stage | male
(Ghosh et al., 2014)
Additional Descriptive Data

Immunostaining of ovaries reveals that Pym protein is present in the germarium, nurse cell and follicle cell cytoplasm, and within the oocyte is uniformly distributed in the

(Ghosh et al., 2014)

cytoplasm.

(Ghosh et al., 2014)
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Bono et al., 2004)
part_of exon-exon junction complex
inferred from direct assay
(Bono et al., 2004)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Pym in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
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
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 1 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 16 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Pym
Transgenic constructs containing regulatory region of Pym
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
Inferred from location ( 7 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (1)
Hsap\PYM1
12 of 14
Yes
Yes
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (1)
Rnor\Pym1
12 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Pym1
12 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\pym1
10 of 13
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\pym1
11 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\T20G5.9
10 of 14
Yes
Yes
Cele\eif-2A
1 of 14
No
No
Anopheles gambiae (African malaria mosquito) (1)
Agam\WIBG_ANOGA
11 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
Atha\PYM
9 of 13
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (0)
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Pym. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Human Disease Associations
FlyBase Human Disease Model Reports
    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 v9.1 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?
    PYM1; PYM1 exon junction complex associated factor
    12 of 14
    619753
        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
        Interaction Browsers
        View in FlyBase Interactions Browser   View in MIST tool (external link)
        Please look at the allele data for full details of the genetic interactions
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Pym
        suppressible
        bgcn
        (Ghosh et al., 2014)
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        External Data
        Subunit Structure (UniProtKB)
        Interacts (via N-terminus) with mago and tsu/RBM8A; the interaction is direct.
        (UniProt, P82804 )
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        FlyBase
        External Links
        External Data
        Linkouts
        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        Class of Gene
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        2R
        Recombination map
        2-105
        Cytogenetic map
        60A4-60A4
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        60A4-60A4
        Limits computationally determined from genome sequence between P{lacW}eIF6k13214 and P{lacW}kenk11035&P{EP}CG17658EP730
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        2-105

        (FlyBase, 2016)

        2-109.6

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (7)
        Genomic Clones (18)
         

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

        cDNA Clones (46)
         

        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 JBrowse 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)
        BDGP DGC clones
        Other clones
        RNAi and Array Information
        Linkouts
        DRSC - Results frm RNAi screens
        Antibody Information
        Laboratory Generated Antibodies
         

        polyclonal

        (Bono et al., 2004)
        Commercially Available Antibodies
         
        Cell Line Information
        Publicly Available Cell Lines
         
          Other Stable Cell Lines
           
            Other Comments
            Relationship to Other Genes
            Source for database merge of

            Source for merge of: wibg BEST:HL05757

            (Ohlstein et al., 2000)
            Additional comments

            Annotation CG10330 split into CG30176 (wibg) and part of CG30170 (bgcn) in release 3 of the genome annotation. In addition, release 3 annotation CG30170 (bgcn) contains sequences corresponding to release 2 annotation CG10331.

            (FlyBase Genome Annotators, 2002-2003)
            Nomenclature History
            Source for database identify of

            Source for identity of: Pym wibg

            (FlyBase, 2009-)
            Nomenclature comments

            This gene was originally named 'wibg' / 'within bgcn' in FBrf0130002 based on it's genomic location in an intron of the 'bgcn' gene. However, subsequent papers that focus on and characterize the gene (product) refer to the gene with the more informative nomenclature 'Pym' / 'Partner of Y14 and Mago' (see FBrf0155992, FBrf0167892, FBrf0174607, FBrf0209868, FBrf0225497). Therefore, 'wibg' is renamed to 'Pym' as of FB2014_05.

            (FlyBase, 2009-)
            Etymology
            Synonyms and Secondary IDs (12)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            Study result (0)
            Result
            Result Type
            Title
            External Crossreferences and Linkouts ( 41 )
            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/Swiss-Prot - Manually annotated and reviewed 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
            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
            FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
            FlyMine - An integrated database for Drosophila genomics
            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)
            PDB - An information portal to biological macromolecular structures
            Linkouts
            Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) 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.
            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
            iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
            KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
            MIST (protein-protein) - An integrated Molecular Interaction Database
            References (35)