FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\squ
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General Information
Symbol
Dmel\squ
Species
D. melanogaster
Name
squash
Annotation Symbol
CG4711
Feature Type
protein_coding_gene
FlyBase ID
FBgn0267347
Gene Model Status
Current
Stock Availability
10 publicly available
Gene Summary
squash (squ) encodes a protein acting in the piRNA pathway that responds to transposase activity in the germline. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
All Summaries
Also Known As

mat(2)cellHK35

Key Links
Genomic Location
Cytogenetic map
36A10-36A10
Sequence location
Recombination map
2-52
RefSeq locus
NT_033779 REGION:16680054..16681653
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 (4 terms)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (3 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
involved_in dorsal appendage formation
inferred from high throughput mutant phenotype
(Schupbach and Wieschaus, 1991)
involved_in oogenesis
inferred from high throughput mutant phenotype
(Schupbach and Wieschaus, 1991)
involved_in regulatory ncRNA-mediated gene silencing
inferred from mutant phenotype
(Pane et al., 2007)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in oogenesis
traceable author statement
(van Eeden and St. Johnston, 1999)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in P granule
inferred from direct assay
(Pane et al., 2007)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
    -
    Summaries
    Gene Snapshot
    squash (squ) encodes a protein acting in the piRNA pathway that responds to transposase activity in the germline. [Date last reviewed: 2019-03-14]
    Gene Model and Products
    Number of Transcripts
    3
    Number of Unique Polypeptides
    1

    Please see the JBrowse view of Dmel\squ 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 Q7KT57)

    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
    Comments on Gene Model

    Gene model reviewed during 5.47

    Shares 5' UTR with downstream gene.

    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    Assoc. CDS (aa)
    squ-RA
    FBtr0080887
    NM_206000
    1372
    241
    squ-RB
    FBtr0305565
    NM_001259115
    1029
    241
    squ-RC
    FBtr0335140
    NM_001273578
    1171
    241
    Additional Transcript Data and Comments
    Reported size (kB)
    Comments
    External Data
    Crossreferences
    Polypeptide Data
    Annotated Polypeptides
    Name
    FlyBase ID
    Predicted MW (kDa)
    Length (aa)
    Theoretical pI
    UniProt
    RefSeq ID
    GenBank
    squ-PA
    FBpp0099829
    27.6
    241
    5.45
    Q7KT57
    NP_995722
    AAS64715
    squ-PB
    FBpp0294016
    27.6
    241
    5.45
    Q7KT57
    NP_001246044
    AFH03718
    squ-PC
    FBpp0307139
    27.6
    241
    5.45
    Q7KT57
    NP_001260507
    AGB93042
    Polypeptides with Identical Sequences

    The group(s) of polypeptides indicated below share identical sequence to each other.

    241 aa isoforms: squ-PA, squ-PB, squ-PC
    Additional Polypeptide Data and Comments
    Reported size (kDa)
    Comments
    External Data
    Crossreferences
    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\squ 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).

    0.93

    Transcript Expression
    Additional Descriptive Data
    Marker for
     
    Subcellular Localization
    CV Term
    Polypeptide Expression
    Additional Descriptive Data
    Marker for
     
    Subcellular Localization
    CV Term
    Evidence
    References
    located_in P granule
    inferred from direct assay
    (Pane et al., 2007)
    Expression Deduced from Reporters
    High-Throughput Expression Data
    Associated Tools

    JBrowse - Visual display of RNA-Seq signals

    View Dmel\squ 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
    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
    Images
    FlyBase Wiki
    Image Based Resources
    Alleles, Insertions, Transgenic Constructs, and Aberrations
    Classical and Insertion Alleles ( 8 )
    For All Classical and Insertion Alleles Show
     
    Other relevant insertions
    Transgenic Constructs ( 6 )
    For All Alleles Carried on Transgenic Constructs Show
    Transgenic constructs containing/affecting coding region of squ
    Transgenic constructs containing regulatory region of squ
    Aberrations (Deficiencies and Duplications) ( 4 )
    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) (0)
    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) (0)
    Mus musculus (laboratory mouse) (0)
    Xenopus tropicalis (Western clawed frog) (0)
    Danio rerio (Zebrafish) (0)
    Caenorhabditis elegans (Nematode, roundworm) (0)
    Anopheles gambiae (African malaria mosquito) (0)
    Arabidopsis thaliana (thale-cress) (0)
    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:squ. Refer to their site for version information.
    Paralogs
    Downloads
    Download All DIOPT Paralogs
    Paralogs (via DIOPT v9.1)
    Gene Symbol
    Score
    Source
    Compara
    Domainoid
    eggNOG
    Homologene
    Inparanoid
    OMA
    OrthoDB
    OrthoFinder
    OrthoInspector
    orthoMCL
    Panther
    Phylome
    SonicParanoid
    Alignment
    Drosophila melanogaster (Fruit fly) (1)
    CG15484
    3 of 13
    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?
      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
      squ
      suppressible
      lok
      (Pane et al., 2007)
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      RanGAP
      enhanceable
      squ
      (Gell and Reenan, 2013)
      RanGAP
      suppressible
      squ
      (Gell and Reenan, 2013)
      External Data
      Linkouts
      DroID - A comprehensive database of gene and protein interactions.
      MIST (genetic) - An integrated Molecular Interaction Database
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      FlyBase
      External Links
      External Data
      Linkouts
      Class of Gene
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      2L
      Recombination map
      2-52
      Cytogenetic map
      36A10-36A10
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      36A10-36A10
      Left limit from molecular mapping relative to grp (FBrf0094733) Right limit from molecular mapping relative to her (FBrf0094733)
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location

      2-52

      (FlyBase, 2016)

      2-50.7

      (Comeron et al., 2012)

      2-54

      (Schupbach and Wieschaus, 1989)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (10)
      Genomic Clones (19)
       

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

      cDNA Clones (61)
       

      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
        Antibody Information
        Laboratory Generated Antibodies
         

        monoclonal

        (Kibanov et al., 2011)

        polyclonal

        (Haase et al., 2010)
        Commercially Available Antibodies
         
        Developmental Studies Hybridoma Bank - Monoclonal antibodies for use in research
        Cell Line Information
        Publicly Available Cell Lines
         
          Other Stable Cell Lines
           
          Other Comments

          squ is required for rasiRNA production in the female germline.

          (Pane et al., 2007)

          Mutants affect normal oogenesis.

          (Digilio et al., 1996)

          Mutations at the squ locus cause defects in midoogenesis.

          (Schupbach and Wieschaus, 1991)

          Mutant embryos exhibit variable cellularization defects: embryos form cuticles with holes, variable head defects and segment fusions.

          (Schupbach and Wieschaus, 1989)
          Relationship to Other Genes
          Source for database merge of

          Source for merge of: squ CG4711

          (Wehr and Schupbach, 2005)

          Source for merge of: squ atg

          (FlyBase, 1996-)
          Additional comments

          Annotation CG4711 has been restored as a distinct annotation from CG17161 in release 3.2 of the genome annotation. In addition, release 3.2 annotations CG17161 (which corresponds to grp) and CG4711 encode alternative transcripts which share untranslated sequences, but encode non-overlapping open reading frames.

          (FlyBase Genome Annotators, 2004)

          Release 1 annotation CG4711 (which was eliminated in release 2 of the genome annotation) has been merged with CG17161 in release 3 of the genome annotation.

          (FlyBase Genome Annotators, 2002-2003)

          Comparison of molecular map shown in Fig 6A of FBrf0094733 with current GBrowse (R5.56) indicates that 'atg' is identical to 'squ'.

          (FlyBase, 1996-)
          Nomenclature History
          Source for database identify of
          Nomenclature comments
          Etymology
          Synonyms and Secondary IDs (9)
          Reported As
          Symbol Synonym
          CG4711
          (National Institute of Genetics Fly Stocks, 2022-, Chen et al., 2012, Ni et al., 2011.7.19, Zhang et al., 2011, Zhang et al., 2010, Keleman et al., 2009.8.5, Pane et al., 2007, Wehr and Schupbach, 2005)
          SQU
          (Kumar and Chen, 2012, Kolaczkowski et al., 2011, Janic et al., 2010)
          atg
          mat(2)cell-A
          mat(2)cellHK35
          (Schupbach and Wieschaus, 1989)
          squ
          (Ilık et al., 2024, Ellison et al., 2020, Saint-Leandre et al., 2020, Hall et al., 2019, Joos et al., 2018, Nagy et al., 2018, Transgenic RNAi Project members, 2017-, Andress et al., 2016, Hsu et al., 2015, Patil et al., 2014, Czech et al., 2013, Gell and Reenan, 2013, Becalska et al., 2011, Haase et al., 2010, Kong et al., 2010, Nagao et al., 2010, Rouget et al., 2010, Todeschini et al., 2010, Buchon et al., 2009, Malone et al., 2009, Chambeyron et al., 2008, Georlette et al., 2007, Pane et al., 2007, Pane et al., 2007, Pane et al., 2007)
          Name Synonyms
          Squash
          (Sankaranarayanan and Weil, 2020, Felix et al., 2012, Becalska et al., 2011, Janic et al., 2010, Rouget et al., 2010, Wehr and Schupbach, 2001)
          adjacent-to-grapes
          (Fogarty et al., 1997)
          squash
          (Specchia et al., 2017, Blumenstiel et al., 2016, Han et al., 2015, Heimiller et al., 2014, Gell and Reenan, 2013, Handler et al., 2013, Hombría and Sotillos, 2013, Bozzetti et al., 2012, Castillo et al., 2011, Haase et al., 2010, Olivieri et al., 2010, Todeschini et al., 2010, Malone et al., 2009, Robine et al., 2009, Pane et al., 2007, Pane et al., 2007, Pane et al., 2007)
          Secondary FlyBase IDs
          • FBgn0002652
          • FBgn0032594
          • FBgn0069054
          • FBgn0020558
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 28 )
          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.
          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
          KEGG Genes - Molecular building blocks of life in the genomic space.
          MARRVEL_MODEL - MARRVEL (model organism gene)
          Linkouts
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          DroID - A comprehensive database of gene and protein interactions.
          Developmental Studies Hybridoma Bank - Monoclonal antibodies for use in research
          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
          MIST (genetic) - An integrated Molecular Interaction Database
          MIST (protein-protein) - An integrated Molecular Interaction Database
          References (82)