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General Information
Symbol
Dmel\lncRNA:roX2
Species
D. melanogaster
Name
long non-coding RNA on the X 2
Annotation Symbol
CR32665
Feature Type
FlyBase ID
FBgn0019660
Gene Model Status
Stock Availability
Gene Summary
non-coding RNA - dosage compensation - activation of male specific lethal proteins - Upstream of N-Ras is a conserved RNA-binding protein that promotes the targeting of the activating male-specific-lethal complex to the X-chromosome by facilitating the interaction of two crucial subunits: the RNA helicase MLE and the long non-coding RNA roX2. (Interactive Fly, lncRNA:roX2 )
Contribute a Gene Snapshot for this gene.
Also Known As

roX2, roX, RNA on the X 2, RNA on the X2

Key Links
Genomic Location
Cytogenetic map
Sequence location
X:11,579,065..11,580,432 [+]
Recombination map
1-35
RefSeq locus
NC_004354 REGION:11579065..11580432
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (4 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from physical interaction with FLYBASE:mle; FB:FBgn0002774
Terms Based on Predictions or Assertions (0 terms)
Biological Process (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from direct assay
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
part_of MSL complex
inferred from direct assay
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
    -
    Summaries
    Gene Group (FlyBase)
    MALE SPECIFIC LETHAL COMPLEX -
    The Male Specific Lethal (MSL) complex is a chromatin modifying complex composed of five protein subunits and two non-coding RNAs. MSL is involved in X chromosome dosage compensation in males. (Adapted from FBrf0228243).
    Summary (Interactive Fly)

    non-coding RNA - dosage compensation - activation of male specific lethal proteins - Upstream of N-Ras is a conserved RNA-binding protein that promotes the targeting of the activating male-specific-lethal complex to the X-chromosome by facilitating the interaction of two crucial subunits: the RNA helicase MLE and the long non-coding RNA roX2.

    Gene Model and Products
    Number of Transcripts
    6
    Number of Unique Polypeptides
    0

    Please see the JBrowse view of Dmel\lncRNA:roX2 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 5.50

    Gene model reviewed during 5.40

    Low-frequency RNA-Seq exon junction(s) not annotated.

    Gene model reviewed during 5.53

    Sequence Ontology: Class of Gene
    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    Additional Transcript Data and Comments
    Reported size (kB)

    1.1 (northern blot)

    Comments
    External Data
    Crossreferences
    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\lncRNA:roX2 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
    in situ
    Stage
    Tissue/Position (including subcellular localization)
    Reference
    cell

    Comment: expression is male-specific

    cell

    Comment: expression is male-specific

    northern blot
    Stage
    Tissue/Position (including subcellular localization)
    Reference
    Additional Descriptive Data

    roX2 transcript is detected in the nuclei of all body parts, and is associated with the X chromosome. In embryos, roX2 transcript colocalizes exactly with msl-1 protein.

    In adult males, roX2 transcripts are expressed in the cell bodies of the central brain and mushroom bodies, the neurons of the optic lobe, and the interneurons of the antennal lobes. They are also expressed in peripheral neurons including the photoreceptor cells and the olfactory neurons of the third antennal segment. Strong expression is observed in the thoracic ganglia and weak expression is seen in the gut. Expression appears to be confined to the nucleus. No expression is observed in females.

    Marker for
     
    Subcellular Localization
    CV Term
    Polypeptide Expression
    Additional Descriptive Data
    Marker for
     
    Subcellular Localization
    CV Term
    Evidence
    References
    part_of MSL complex
    inferred from direct assay
    Expression Deduced from Reporters
    High-Throughput Expression Data
    Associated Tools

    GBrowse - Visual display of RNA-Seq signals

    View Dmel\lncRNA:roX2 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
    EMBL-EBI Single Cell Expression Atlas
    Images
    Alleles, Insertions, Transgenic Constructs, and Aberrations
    Classical and Insertion Alleles ( 5 )
    For All Classical and Insertion Alleles Show
     
    Other relevant insertions
    Transgenic Constructs ( 33 )
    For All Alleles Carried on Transgenic Constructs Show
    Transgenic constructs containing/affecting coding region of lncRNA:roX2
    Transgenic constructs containing regulatory region of lncRNA:roX2
    Aberrations (Deficiencies and Duplications) ( 7 )
    Alleles Representing Disease-Implicated Variants
    Phenotypes
    For more details about a specific phenotype click on the relevant allele symbol.
    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 ( 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
      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
      DroID - A comprehensive database of gene and protein interactions.
      MIST (genetic) - An integrated Molecular Interaction Database
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      External Data
      Linkouts
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      X
      Recombination map
      1-35
      Cytogenetic map
      Sequence location
      X:11,579,065..11,580,432 [+]
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      10C7-10C7
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      10B17-10B17
      10B-10B
      (determined by in situ hybridisation)
      Experimentally Determined Recombination Data
      Location
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (3)
      Genomic Clones (6)
       

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

      cDNA Clones (27)
       

      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)
        BDGP DGC clones
        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: lncRNA:roX2 roX2

        Source for database merge of
        Additional comments
        Other Comments

        The DNaseI hypersensitive site (DHS) within the roX2 transcription unit is not required for initiation of cis spreading of the MSL complex.

        New annotation (CR32665) in release 3 of the genome annotation.

        roX1 and roX2 produce redundant transcripts required for the targeting of the MSL complex.

        The roX2 gene is a nucleation site for MSL complex spreading into flanking chromatin in cis.

        roX1 and roX2 RNAs are required for the association of male-specific lethal (MSL) proteins with the male X chromosome.

        roX1 and roX2 RNAs are redundant and may have a direct function in dosage compensation.

        Complete and partial MSL complexes bind to a construct containing promoterless roX2 cDNA, indicating that the MSL proteins probably recognize exonic DNA.

        The roX2 gene contains sequences that seem to provide an entry site for the MSL complex to recognize the X chromosome. This site is termed the "roX2 chromatin entry site" (roX2-CES).

        roX2 encodes an RNA with no apparent reading frame that shows male-specific expression in the adult fly, and is regulated by genes of the dosage compensation pathway. It is closely linked to nod, a female-specific gene expressed in the ovary.

        Origin and Etymology
        Discoverer
        Etymology
        Identification
        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.
        RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
        RNAcentral - A comprehensive ncRNA sequence collection representing all ncRNA types from a broad range of organisms
        Other crossreferences
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        EMBL-EBI Single Cell Expression Atlas
        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
        modMine - A data warehouse for the modENCODE project
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        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
        MIST (genetic) - An integrated Molecular Interaction Database
        Synonyms and Secondary IDs (13)
        Reported As
        Symbol Synonym
        lncRNA-roX2
        roX2
        (Higareda Alvear et al., 2021, Ota et al., 2021, Valsecchi et al., 2021, Ellison and Bachtrog, 2019, Li et al., 2019, Lv et al., 2019, Prayitno et al., 2019, Bell et al., 2018, Cheetham and Brand, 2018, Deshpande and Meller, 2018, Kang et al., 2018, Kim et al., 2018, Lucchesi, 2018, Valsecchi et al., 2018, Ilik et al., 2017, Joshi and Meller, 2017, Rogoyski et al., 2017, Urban et al., 2017, Urban et al., 2017, Kuroda et al., 2016, Kuzu et al., 2016, Quinn et al., 2016, Cugusi et al., 2015, Koya and Meller, 2015, Lakhotia, 2015, Lindehell et al., 2015, Lucchesi and Kuroda, 2015, Prabu et al., 2015, Ramírez et al., 2015, Vensko and Stone, 2015, Alekseyenko et al., 2014, Chen et al., 2014, Ferrari et al., 2014, Figueiredo et al., 2014, Lee et al., 2014, McElroy et al., 2014, Militti et al., 2014, Quinn et al., 2014, Ferrari et al., 2013, Ilik et al., 2013, Lim and Kelley, 2013, Lundberg et al., 2013, Philip and Stenberg, 2013, Soruco et al., 2013, Vicoso and Bachtrog, 2013, Wang et al., 2013, Conrad et al., 2012, Dunlap et al., 2012, Hallacli et al., 2012, Larschan et al., 2012, Lim and Kelley, 2012, Maenner et al., 2012, Prabhakaran and Kelley, 2012, Birchler et al., 2011, Georgiev et al., 2011, Larschan et al., 2011, Morra et al., 2011, Simon et al., 2011, Stenberg and Larsson, 2011, Straub and Becker, 2011, Gallach et al., 2010, Gladstein et al., 2010, modENCODE Consortium et al., 2010, Park et al., 2010, Prabhakaran and Kelley, 2010, Deng et al., 2009, Gelbart et al., 2009, Grimaud and Becker, 2009, Lebo et al., 2009, Menon and Meller, 2009, Patalano et al., 2009, Spirollari et al., 2009, Alekseyenko et al., 2008, Aratani et al., 2008, Bachtrog, 2008, Bell et al., 2008, Izzo et al., 2008, Kelley et al., 2008, Kind et al., 2008, Li et al., 2008, Morra et al., 2008, Park et al., 2008, Pierre et al., 2008, Spierer et al., 2008, Straub et al., 2008, Sural et al., 2008, Bai et al., 2007, Kind and Akhtar, 2007, Larschan et al., 2007, Larschan et al., 2007, Mendjan and Akhtar, 2007, Park et al., 2007, Prasanth and Spector, 2007, Stark et al., 2007, Straub and Becker, 2007, Worringer and Panning, 2007, Yokoyama et al., 2007, Buscaino et al., 2006, Dahlsveen et al., 2006, Deng and Meller, 2006, Deng and Meller, 2006, Mendjan et al., 2006, Pal Bhadra et al., 2006, Schubeler, 2006, Deng et al., 2005, Park et al., 2005, Ray and Fox, 2005, Straub et al., 2005, Zhimulev et al., 2003)
        Secondary FlyBase IDs
        • FBgn0052665
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (227)