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General Information
Symbol
Dmel\lncRNA:flam
Species
D. melanogaster
Name
flamenco
Annotation Symbol
CR46037
Feature Type
FlyBase ID
FBgn0267704
Gene Model Status
Stock Availability
Gene Summary
Contribute a Gene Snapshot for this gene.
Also Known As

flam, XLOC_024457, COM, lincRNA.1041

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
1-66
RefSeq locus
NC_004354 REGION:21631891..21790731
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (3 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
inferred from mutant phenotype
involved_in oogenesis
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
    -
    Summaries
    Gene Model and Products
    Number of Transcripts
    16
    Number of Unique Polypeptides
    0

    Please see the JBrowse view of Dmel\lncRNA:flam 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

    Transcripts flam-RA through flam-RJ characterized by 5' RACE, but 3' ends have not been determined (FBrf0224576).

    Gene model reviewed during 6.02

    Gene is a putative piRNA precursor.

    Evidence exists for additional alternatively spliced transcripts (FBrf0224576); additional unannotated transcripts may have noncanonical splices.

    Gene model supported by FBrf0224576.

    Gene model reviewed during 6.03

    Corresponds to XLOC_024457 (FBrf0240702).

    Gene model reviewed during 6.32

    Sequence Ontology: Class of Gene
    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    FBtr0479732
    13313
    Additional Transcript Data and Comments
    Reported size (kB)
    Comments
    External Data
    Crossreferences
    Sequences Consistent with the Gene Model
    Nucleotide / Polypeptide Records
    Mapped Features

    Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\lncRNA:flam using the Feature Mapper tool.

    External Data
    Crossreferences
    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
    Additional Descriptive Data
    Marker for
     
    Subcellular Localization
    CV Term
    Polypeptide Expression
    Additional Descriptive Data
    Marker for
     
    Subcellular Localization
    CV Term
    Evidence
    References
    Expression Deduced from Reporters
    High-Throughput Expression Data
    Associated Tools

    GBrowse - Visual display of RNA-Seq signals

    View Dmel\lncRNA:flam in GBrowse 2
    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
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    Images
    Alleles, Insertions, Transgenic Constructs, and Aberrations
    Classical and Insertion Alleles ( 26 )
    For All Classical and Insertion Alleles Show
     
    Other relevant insertions
    Transgenic Constructs ( 1 )
    For All Alleles Carried on Transgenic Constructs Show
    Transgenic constructs containing/affecting coding region of lncRNA:flam
    Transgenic constructs containing regulatory region of lncRNA:flam
    Aberrations (Deficiencies and Duplications) ( 41 )
    Inferred from experimentation ( 41 )
    Inferred from location ( 0 )
    Alleles Representing Disease-Implicated Variants
    Phenotypes
    For more details about a specific phenotype click on the relevant allele symbol.
    Sterility
    Allele
    Other Phenotypes
    Allele
    Phenotype manifest in
    Allele
    Orthologs
    Human Orthologs (via DIOPT v8.0)
    Homo sapiens (Human) (0)
    No records found.
    Model Organism Orthologs (via DIOPT v8.0)
    Mus musculus (laboratory mouse) (0)
    No records found.
    Rattus norvegicus (Norway rat) (0)
    No records found.
    Xenopus tropicalis (Western clawed frog) (0)
    No records found.
    Danio rerio (Zebrafish) (0)
    No records found.
    Caenorhabditis elegans (Nematode, roundworm) (0)
    No records found.
    Arabidopsis thaliana (thale-cress) (0)
    No records found.
    Saccharomyces cerevisiae (Brewer's yeast) (0)
    No records found.
    Schizosaccharomyces pombe (Fission yeast) (0)
    No records found.
    Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( None identified )
    No orthologies identified
    Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( None identified )
    No non-Drosophilid orthologies identified
    Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( None identified )
    No non-Dipteran orthologies identified
    Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( None identified )
    No non-Insect Arthropod orthologies identified
    Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
    No non-Arthropod Metazoa orthologies identified
    Paralogs
    Paralogs (via DIOPT v8.0)
    Drosophila melanogaster (Fruit fly) (0)
    No records found.
    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 ( 2 )
      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
      esyN Network Diagram
      Show neighbor-neighbor interactions:
      Select Layout:
      Legend:
      Protein
      RNA
      Selected Interactor(s)
      Interactions Browser

      Please see the Physical Interaction reports below for full details
      RNA-protein
      Physical Interaction
      Assay
      References
      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
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      External Data
      Linkouts
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      X
      Recombination map
      1-66
      Cytogenetic map
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      20A1-20A2
      Left limit from inclusion within Df(1)R20 (FBrf0080334) Right limit from inclusion within Df(1)LB6 (FBrf0080334)
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      20A1-20A3
      (determined by in situ hybridisation)
      Experimentally Determined Recombination Data
      Notes
      Stocks and Reagents
      Stocks (7)
      Genomic Clones (30)
      cDNA Clones (200)
       

      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
        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: lncRNA:flam flam

        Source for database merge of

        Source for merge of: flam CR46037

        Additional comments

        "DIP1" does not correspond to the "flam" locus.

        "flam" appears to map outside the region controlling ZAM and Idefix mobilisation ("COM").

        Other Comments

        New annotation (CR46037) in release 6.02 of the genome annotation.

        The flam locus corresponds to a cluster of piRNA's derived from nested transposable elements which span at least 130kb proximal to DIP1.

        The proportion of normally copulating males is reduced in flam mutants compared to wild type. This reduction is due to changes in male behaviour. The proportion of males that perform consecutive courtship stages is significantly lower than in wild type. The sequence and duration of some courtship stages (in particular, orientation and wing vibration) is altered in mutant flies.

        Cell lines carrying the permissive flam1 allele accumulate many nuclear virus-like particles, cytoplasmic dense particles and cisternae filled with fibrous material. Two of three such cell lines have an increased copy number of the gypsy element.

        In some stocks active gypsy elements are found restricted to the Y chromosome. The presence of flam alleles tends to be associated with the confinement of active gypsy elements to the Y chromosome. This might be a result of the female-specific effect of flam on gypsy activity.

        gypsy virus-like particles (VLPs) accumulate inside flam1 follicle cells close to envelope-containing membranes.

        The length of time the existence of endogenous genomic gypsy was accompanied by host-virus co-evolution is studied. Host-virus co-evolution probably led to the acquisition by flam gene of the ability to control gypsy multiplication.

        The expression of gypsy encoded proteins is analysed to explore how gypsy is transmitted between generations. Assembly of gypsy particles is visualised in the follicle cells of flam females by electron microscopy, these observations provide the basis for a novel model to explain how gypsy is transmitted from generation to generation. gypsy virions appear to move through the perivitelline space during a brief developmental window and infect the oocyte, providing a mechanism to explain gypsy insertion in the next generation.

        Multiplication of gypsy in the germline is under the control of flam.

        gypsy can be transmitted from flam strains in which it transposes to strains devoid of functional elements by egg plasm transfer or growing "empty" larvae in the presence of homogenized pupae of the flam stock. Transposition of gypsy occurs only in the progeny of females homozygous for permissive alleles of flam, where gypsy transcripts are restricted to the somatic follicle cells in the ovaries. Infectious particles which then infect the oocyte are apparently produced in these cells.

        Mature gypsy particles are produced in the context of the flam mutation, which derepresses gypsy env production.

        Deletion of flam does not lead to lethality or other abnormality of the flies. The only effect is on deregulation of gypsy mobilization.

        The chromosomal flam locus controls the infective properties of gypsy.

        Production of the gypsy\env message and corresponding protein is strongly repressed by one copy of the non-permissive allele of flam, flamN. A less dramatic reduction in the accumulation of other transcripts and retrotranscripts is also observed. These effects correlate with the inhibition of gypsy transposition in the progeny of these females and is likely to be responsible for this phenomenon. The effects of flam on gypsy\env expression are restricted to the somatic follicle cells that surround the maternal germline.

        Females homozygous for mutant flam allele show a very high rate of gypsy mobilisation, for example 10-15% reversion of ovoD1. gypsy transcript altered on a mutant flam background.

        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 43 )
        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.
        RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
        Other crossreferences
        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
        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
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        KEGG Genes - Molecular building blocks of life in the genomic space.
        MARRVEL_MODEL - MARRVEL (model organism gene)
        Synonyms and Secondary IDs (13)
        Reported As
        Symbol Synonym
        Secondary FlyBase IDs
        • FBgn0005628
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (163)