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General Information
Symbol
Dmel\lncRNA:roX1
Species
D. melanogaster
Name
long non-coding RNA on the X 1
Annotation Symbol
CR32777
Feature Type
FlyBase ID
FBgn0019661
Gene Model Status
Stock Availability
Gene Summary
X chomosome associated RNA - chromatin associated non-translated RNA involved in dosage compensation - ectopically expressed roX1 and roX2 RNAs target high-affinity sites on the X chromosome in trans and, via spatial proximity, induce spreading of the MSL complex in cis, leading to increased expression of neighboring autosomal genes - The MSL complex regulates nucleosome positioning at high-affinity sites, therefore acting locally rather than influencing the overall chromosomal architecture. (Interactive Fly, lncRNA:roX1 )
Contribute a Gene Snapshot for this gene.
Also Known As

roX1, roX, RNA on the X 1, yang, RNA on the X1

Key Links
Genomic Location
Cytogenetic map
Sequence location
X:3,857,230..3,862,697 [-]
Recombination map
1-5
RefSeq locus
NC_004354 REGION:3857230..3862697
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 (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
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)

    X chomosome associated RNA - chromatin associated non-translated RNA involved in dosage compensation - ectopically expressed roX1 and roX2 RNAs target high-affinity sites on the X chromosome in trans and, via spatial proximity, induce spreading of the MSL complex in cis, leading to increased expression of neighboring autosomal genes - The MSL complex regulates nucleosome positioning at high-affinity sites, therefore acting locally rather than influencing the overall chromosomal architecture.

    Gene Model and Products
    Number of Transcripts
    5
    Number of Unique Polypeptides
    0

    Please see the JBrowse view of Dmel\lncRNA:roX1 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 5.48

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

    Gene model reviewed during 5.56

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

    3.7 (northern blot)

    3.8, 3.6 (northern blot)

    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:roX1 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
    No Assay Recorded
    Stage
    Tissue/Position (including subcellular localization)
    Reference
    in situ
    Stage
    Tissue/Position (including subcellular localization)
    Reference
    cell

    Comment: expression is male-specific

    cell

    Comment: expression is male-specific

    organism

    Comment: maternally deposited

    antennal anlage

    Comment: reported as procephalic ectoderm anlage

    central brain anlage

    Comment: reported as procephalic ectoderm anlage

    dorsal head epidermis anlage

    Comment: reported as procephalic ectoderm anlage

    visual anlage

    Comment: reported as procephalic ectoderm anlage

    ventral nerve cord primordium

    Comment: reported as ventral nerve cord anlage

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

    roX1 transcript is detected in the nuclei of all body parts, and is associated with the X chromosome. In embryos, roX1 transcript colocalizes exactly with msl-1 protein.

    In adult males, roX1 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.

    In cryosections of adults, roX1 transcription is strongest in the central nervous system of the male brain. Most cells of the brain and thoracic ganglia stain strongly. Weaker expression is observed in the gut, parts of the reproductive tract (especially the ejaculatory bulb), and in fat cells. In embryos, roX1 transcripts are expressed in both sexes starting at about 2.5 hours after egg laying. Expression is strong in cells of the CNS until ~stage 13 at which point the expression in females subsides. The staining disappears first from the ventral nerve cord and then from the brain. In male larvae, strong staining is seen in many tissues, including the large polyploid cells of the gastric caecae, the ring gland and the nephrocytes, and the salivary glands. This staining is nuclear and localizes to the X chromosome. roX1 expression is controlled by the dosage compensation pathway and not by tra.

    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:roX1 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
    BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
    EMBL-EBI Single Cell Expression Atlas
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    Images
    • Stages(s) 4-6
    • Stages(s) 7-8
    • Stages(s) 11-12
    • Stages(s) 13-16
    Alleles, Insertions, Transgenic Constructs, and Aberrations
    Classical and Insertion Alleles ( 24 )
    For All Classical and Insertion Alleles Show
     
    Other relevant insertions
    Transgenic Constructs ( 45 )
    For All Alleles Carried on Transgenic Constructs Show
    Transgenic constructs containing/affecting coding region of lncRNA:roX1
    Transgenic constructs containing regulatory region of lncRNA:roX1
    Aberrations (Deficiencies and Duplications) ( 0 )
    Inferred from experimentation ( 0 )
    Inferred from location ( 0 )
    Alleles Representing Disease-Implicated Variants
    Phenotypes
    For more details about a specific phenotype click on the relevant allele symbol.
    Lethality
    Allele
    Sterility
    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 ( 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
      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
      BioGRID - A database of protein and genetic interactions.
      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
      1-5
      Cytogenetic map
      Sequence location
      X:3,857,230..3,862,697 [-]
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      3F3-3F3
      Limits computationally determined from genome sequence between P{EP}EP1200EP1200&P{EP}EP1343 and P{EP}CG2930EP1352
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      3F-3F
      (determined by in situ hybridisation)
      Experimentally Determined Recombination Data
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (7)
      Genomic Clones (17)
       

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

      cDNA Clones (274)
       

      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)
        Other 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:roX1 roX1

        Source for database merge of

        Source for merge of: roX1 BcDNA:GH10432

        Additional comments

        Source for merge of roX1 BcDNA:GH10432 was a shared cDNA ( date:030728 ).

        Other Comments

        Transcription of the roX1 gene is directly regulated by the DNaseI hypersensitive site (DHS) within the roX1 transcription unit. This regulation requires the msl-1, msl-2, msl-3 and mle proteins but not roX (roX1 and roX2) RNAs. The DHS is not required for initiation of cis spreading of the MSL complex.

        msl-2 protein controls male-specific transcription of roX1 and does not require any other MSL protein for this role.

        New annotation (CR32777) in release 3 of the genome annotation.

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

        The "roX1 chromatin entry site" (roX1-CES) is a region within the roX1 gene that is able to recruit the MSL complex. A 217bp fragment is sufficient for recruitment and spreading of the MSL complex along the flanking chromatin. This short element is sufficient to activate MSL spreading in the absence of active roX1 transcription.

        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.

        The roX1 gene contains sequences that seem to provide an entry site for the MSL complex to recognize the X chromosome. This site is termed the "roX1 chromatin entry site" (roX1-CES). The roX1-CES provides a nucleation site for extensive spreading (in cis or trans) of the complex into flanking chromatin, even when moved to an autosome.

        roX1 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 yin, a female-specific gene expressed in the ovary.

        The roX1 gene shows a male-specific expression pattern in adult flies, localising specifically to the male X chromosome. roX1 expression is dependent on Sxl, but is independent of tra activity, and is positively regulated by genes of the dosage compensation system such as mle.

        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 37 )
        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
        BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        EMBL-EBI Single Cell Expression Atlas
        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
        modMine - A data warehouse for the modENCODE project
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        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 (17)
        Reported As
        Symbol Synonym
        BcDNA:GH10432
        EG:EG0002.2
        chrX:3706836..3706970
        lncRNA-roX1
        roX1
        (Higareda Alvear et al., 2021, Ota et al., 2021, Valsecchi et al., 2021, Ellison and Bachtrog, 2019, Kopp and Park, 2019, Li et al., 2019, Lv et al., 2019, Prayitno et al., 2019, Tikhonova et al., 2019, Bell et al., 2018, Cheetham and Brand, 2018, Kim et al., 2018, Lucchesi, 2018, Valsecchi et al., 2018, Joshi and Meller, 2017, Liu et al., 2017, Rogoyski et al., 2017, Urban et al., 2017, Kuroda et al., 2016, Kuzu et al., 2016, Quinn et al., 2016, Gallach, 2015, Koya and Meller, 2015, Lakhotia, 2015, Lindehell et al., 2015, Lucchesi and Kuroda, 2015, Ramírez et al., 2015, Ríos-Barrera et al., 2015, Vensko and Stone, 2015, Apte et al., 2014, Ferrari et al., 2014, Figueiredo et al., 2014, Lee et al., 2014, Militti et al., 2014, Quinn et al., 2014, Stern et al., 2014, Chen 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, Larschan et al., 2012, Lim and Kelley, 2012, Menon and Meller, 2012, Prabhakaran and Kelley, 2012, Birchler et al., 2011, Georgiev et al., 2011, Larschan et al., 2011, Morra et al., 2011, Straub and Becker, 2011, Gallach et al., 2010, Gladstein et al., 2010, Park et al., 2010, Prabhakaran and Kelley, 2010, Deng and Meller, 2009, Deng et al., 2009, Hutter, 2009.5.17, Hutter, 2009.6.2, Lebo et al., 2009, Menon and Meller, 2009, Patalano et al., 2009, Alekseyenko et al., 2008, Aratani et al., 2008, Bachtrog, 2008, Hutter, 2008.12.10, Kelley et al., 2008, Kong and Meller, 2008, Li et al., 2008, Morra et al., 2008, Park et al., 2008, Pierre et al., 2008, Semeshin et al., 2008, Spierer et al., 2008, Sural et al., 2008, Bai et al., 2007, Copeland et al., 2007, Larschan et al., 2007, Larschan et al., 2007, Lecuyer et al., 2007, Mendjan and Akhtar, 2007, Park et al., 2007, Prasanth and Spector, 2007, Stark et al., 2007, Straub and Becker, 2007, Biemar et al., 2006, Buscaino et al., 2006, Dahlsveen et al., 2006, Deng and Meller, 2006, Deng and Meller, 2006, Gilfillan et al., 2006, Legube et al., 2006, Mendjan et al., 2006, Pal Bhadra et al., 2006, Schubeler, 2006, Deng et al., 2005, Inagaki et al., 2005, Ray and Fox, 2005, Zhimulev et al., 2003)
        Secondary FlyBase IDs
        • FBgn0015564
        • FBgn0052777
        • FBgn0063259
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (249)