Open Close
General Information
Symbol
Dmel\lncRNA:Hsrω
Species
D. melanogaster
Name
Heat shock RNA ω
Annotation Symbol
CR31400
Feature Type
FlyBase ID
FBgn0001234
Gene Model Status
Stock Availability
Gene Snapshot
In progress.Contributions welcome.
Also Known As
hsrω, hsr-omega, Hsromega, hsr-ω, er3
Key Links
Genomic Location
Cytogenetic map
Sequence location
3R:21,296,127..21,317,836 [+]
Recombination map
3-71
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
-
Protein Signatures (InterPro)
    -
    Molecular Function (GO)
    [Detailed GO annotations]
    Experimental Evidence
    -
    Predictions / Assertions
    -
    Summaries
    Phenotypic Description (Red Book; Lindsley and Zimm 1992)
    Hsr93D: Heat-shock RNA at 93D
    A sequence that responds to heat shock by generation of a large puff in polytene chromosomes. The 93D region transcribes mRNA that apparently is not translated. Hsr93D is active in almost all cells in Drosophila melanogaster; the activity is greatly increased by heat shock (Bonner and Pardue, 1976) and is induced independently by benzamide (Lakhotia and Mukherjee, 1970, DIS 45: 108). The inducibility of the locus is selectively repressed by a combination of heat shock with another inducer, by rearing larvae at 10, by heterozygous deficiency for 93D or by treating wild-type salivaries with beta-alanine (Lakhotia, 1989). The 93D heat shock mRNA is predominately polyA- in the cytoplasm, whereas nuclear transcripts are both polyA+ and polyA- (Lengyel, Randson, Grahm, and Pardue, 1980, Chromosoma 80: 237-52). Heat-shock response in homozygous deficiencies for Hsr93D is indistinguishable from normal except for the absence of the 93D puff and transcripts.
    Gene Model and Products
    Number of Transcripts
    7
    Number of Unique Polypeptides
    0

    Please see the GBrowse view of Dmel\lncRNA:Hsrω or the JBrowse view of Dmel\lncRNA:Hsrω 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 based, in part, on work in FBrf0213860.
    Gene model reviewed during 5.47
    miRNA(s) located within the transcribed region of this non-coding RNA gene.
    Low-frequency RNA-Seq exon junction(s) not annotated.
    Gene model reviewed during 5.41
    Gene model reviewed during 5.45
    Gene model reviewed during 6.02
    lncRNA ; SO:0001877
    Transcripts contain a putative 27 aa CDS that is conserved, and the transcripts fractionate with mono-ribosomes, but the putative protein encoded could not be detected (Fini et al., 1989. FBrf0050187).
    Sequence Ontology: Class of Gene
    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    FBtr0084058
    14086
    FBtr0332373
    21216
    FBtr0334316
    13374
    Additional Transcript Data and Comments
    Reported size (kB)
    1.9, 1.2 (unknown); 9-10 (northern blot)
    10, 1.9, 1.2 (northern blot)
    2.0, 1.3 (unknown)
    10-12 (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:Hsrω using the Feature Mapper tool.

    External Data
    Crossreferences
    Linkouts
    Gene Ontology (9 terms)
    Molecular Function (0 terms)
    Terms Based on Experimental Evidence (0 terms)
    Terms Based on Predictions or Assertions (0 terms)
    Biological Process (7 terms)
    Terms Based on Experimental Evidence (7 terms)
    CV Term
    Evidence
    References
    inferred from mutant phenotype
    inferred from mutant phenotype
    inferred from genetic interaction with FLYBASE:rpr; FB:FBgn0011706
    inferred from genetic interaction with FLYBASE:grim; FB:FBgn0015946
    inferred from genetic interaction with FLYBASE:Dcp-1; FB:FBgn0010501
    inferred from genetic interaction with FLYBASE:Dronc; FB:FBgn0026404
    inferred from genetic interaction with FLYBASE:Diap1; FB:FBgn0260635
    inferred from mutant phenotype
    inferred from physical interaction with FLYBASE:sqd; FB:FBgn0263396
    Terms Based on Predictions or Assertions (0 terms)
    Cellular Component (2 terms)
    Terms Based on Experimental Evidence (2 terms)
    CV Term
    Evidence
    References
    inferred from direct assay
    inferred from direct assay
    Terms Based on Predictions or Assertions (0 terms)
    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
    Polypeptide Expression
    Additional Descriptive Data
    Marker for
     
    Subcellular Localization
    CV Term
    Evidence
    References
    inferred from direct assay
    inferred from direct assay
    Expression Deduced from Reporters
    High-Throughput Expression Data
    Associated Tools

    GBrowse - Visual display of RNA-Seq signals

    View Dmel\lncRNA:Hsrω 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
    Alleles, Insertions, and Transgenic Constructs
    Classical and Insertion Alleles ( 28 )
    For All Classical and Insertion Alleles Show
     
    Other relevant insertions
    Transgenic Constructs ( 2 )
    For All Alleles Carried on Transgenic Constructs Show
    Transgenic constructs containing/affecting coding region of lncRNA:Hsrω
    Transgenic constructs containing regulatory region of lncRNA:Hsrω
    Deletions and Duplications ( 16 )
    Phenotypes
    For more details about a specific phenotype click on the relevant allele symbol.
    Lethality
    Allele
    Sterility
    Allele
    Other Phenotypes
    Allele
    Phenotype manifest in
    Allele
    Orthologs
    Human Orthologs (via DIOPT v7.1)
    Homo sapiens (Human) (0)
    No records found.
    Model Organism Orthologs (via DIOPT v7.1)
    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.
    Orthologs 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 v7.1)
    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 ( 5 )
    Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
     
    Disease Associations of Human Orthologs (via DIOPT v7.1 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
    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
    Gene Group - Pathway Membership (FlyBase)
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-71
    Cytogenetic map
    Sequence location
    3R:21,296,127..21,317,836 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    93D4-93D5
    Limits computationally determined from genome sequence between P{PZ}Atpα01164 and P{PZ}mod(mdg4)07038&P{lacW}mod(mdg4)L3101
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    93D4-93D7
    (determined by in situ hybridisation)
    93D-93D
    (determined by in situ hybridisation)
    93D4-93D9
    (determined by in situ hybridisation)
    93D6-93D7
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (15)
    Genomic Clones (25)
    cDNA Clones (72)
     

    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 sequences
    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
      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:Hsrω Hsrω
      Source for database merge of
      Additional comments
      Other Comments
      New annotation (CR31400) in release 3 of the genome annotation.
      The amide response elements of Hsrω have been mapped.
      Functional RNA molecules transcribed from Hsrω are an important and polymorphic regulatory component of an insect thermoresistance phenotype. Both molecular allelic variation and expression characteristics are closely associated with knockdown heat resistance and with the hardening response of flies.
      The autosomal "FLP-DFS" technique (using the P{ovoD1-18} P{FRT(whs)} P{hsFLP} chromosomes) has been used to identify the specific maternal effect phenotype for the zygotic lethal mutation. Hsrω is required for germ cell viability or early oogenesis.
      Hsrω cis-acting sequences that regulate developmental activity in different tissues are studied using Ecol\lacZ reporter gene constructs. Hsrω is expressed in almost all tissue types and is expressed in a specific spatial pattern in different cells of a given tissue. Results suggest a region between -346bp and -844bp upstream of the gene contains major regulatory elements for developmental expression of the gene in most larval and adult tissues.
      Hsrω transcript is broadly distributed over the nucleus in both heat shock and control cells. Polyadenylation of Hsrω RNA utilises RNA processing signals typical of pre-mRNA. Levels of Hsrω are regulated by both transcription and turnover, regulation is sensitive to actinomycin D.
      The product of Hsp83 and its homologs shows a specific nuclear localization in different species of Drosophila and Chironomus. Besides being abundant in the cytoplasm, the Hsp83 product is associated with specific chromosomal loci, such as Hsrω and Dhyd\Hsrω, the telomeric Balbiani rings in Chironomus thummi and the heat-induced puff I-1C in C.tentans.
      Nascent chain nuclear run-on assays in KC161 cells reveal different responses to heat shock for different genes. Transcription of His1 is severely inhibited under mild heat shocks, of Act5C decreases proportionally with increasing temperature while that of the core histone genes or the heat shock cognates is repressed only under extreme heat shock. In unshocked cells Hsp83 is moderately transcribed while transcription from the other heat shock genes is undetectable. Engaged but paused RNA molecules are found at the various Hsp70 and Hsp26 genes but not at the other heat shock genes. Increased transcription of the heat shock genes is observed within 1-2 mins of heat shock and maximal rates were reached within 2-5 minutes. Rates of transcription vary over a 20-fold range. Hsrω is transcribed at a very high rate under non-heat shock conditions, and its response to elevated temperatures is different from that of the protein coding heat shock genes.
      Hsrω RNA expression in non-stressed cells during development has been analysed.
      Nuclear and cytoplasmic transcript together play a role in coordinating nuclear and cytoplasmic activity.
      The gene structure, sequence and transcription pattern of Hsrω and Dhyd\Hsrω have been compared.
      A sequence that responds to heat shock by generation of a large puff in polytene chromosomes. The 93D region transcribes mRNA that apparently is not translated. Hsrω is active in almost all cells in D.melanogaster; the activity is greatly increased by heat shock (Bonner and Pardue, 1976) and is induced independently by benzamide (Lakhotia and Mukherjee, 1970). The inducibility of the locus is selectively repressed by a combination of heat shock with another inducer, by rearing larvae at 10oC, by heterozygous deficiency for 93D or by treating wild-type salivaries with β-alanine (Lakhotia, 1989). The 93D heat shock mRNA is predominantly poly(A)- in the cytoplasm, whereas nuclear transcripts are both poly(A)+ and poly(A)- (Lengyel et al., 1980). Heat-shock response in homozygous deficiencies for Hsrω is indistinguishable from normal except for the absence of the 93D puff and transcripts.
      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 46 )
      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.
      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
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      KEGG Genes - Molecular building blocks of life in the genomic space.
      modMine - A data warehouse for the modENCODE project
      Linkouts
      ApoDroso - Functional genomic database for photoreceptor development, survival and function
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      FlyMine - An integrated database for Drosophila genomics
      MIST (genetic) - An integrated Molecular Interaction Database
      Synonyms and Secondary IDs (34)
      Reported As
      Symbol Synonym
      l(3)93De
      l(3)er3
      lncRNA:Hsrω
      Secondary FlyBase IDs
      • FBgn0051400
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (157)