FB2025_01 , released February 20, 2025
Gene: Dmel\lncRNA:cherub
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General Information
Symbol
Dmel\lncRNA:cherub
Species
D. melanogaster
Name
cherub
Annotation Symbol
CR43283
Feature Type
lncRNA_gene
FlyBase ID
FBgn0262972
Gene Model Status
Current
Stock Availability
1 publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

lincRNA.752, lncRNA:CR43283 , Dm_3R:37919

Key Links
Genomic Location
Cytogenetic map
86D9-86D9
Sequence location
Recombination map
3-50
RefSeq locus
NT_033777 REGION:11247631..11256123
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 (1 term)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables protein-macromolecule adaptor activity
inferred from direct assay
(Landskron et al., 2018)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (0 terms)
Terms Based on Experimental Evidence (0 terms)
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
    3
    Number of Unique Polypeptides
    0

    Please see the JBrowse view of Dmel\lncRNA:cherub 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
    Experimentally Determined Structures
    Crossreferences
    Comments on Gene Model

    Gene model reviewed during 5.55

    Supported by RNA-Seq data.

    Probable lncRNA gene; may encode small polypeptide(s).

    Gene model reviewed during 5.49

    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    lncRNA:cherub-RA
    FBtr0306728
    NR_048372
    3478
    lncRNA:cherub-RB
    FBtr0306729
    NR_048371
    4774
    lncRNA:cherub-RC
    FBtr0345159
    NR_125141
    8311
    Additional Transcript Data and Comments
    Reported size (kB)
    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:cherub using the Feature Mapper tool.

    External Data
    Crossreferences
    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).

    -0.23

    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

    JBrowse - Visual display of RNA-Seq signals

    View Dmel\lncRNA:cherub in JBrowse
    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
    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 ( 3 )
    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:cherub
    Transgenic constructs containing regulatory region of lncRNA:cherub
    Aberrations (Deficiencies and Duplications) ( 0 )
    Inferred from experimentation ( 0 )
    Inferred from location ( 8 )
    Variants
    Variant Molecular Consequences
    Alleles Representing Disease-Implicated Variants
    Phenotypes
    For more details about a specific phenotype click on the relevant allele symbol.
    Lethality
    Allele
    viable
    Sterility
    Allele
    fertile
    Phenotype manifest in
    Allele
    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:lncRNA:cherub. Refer to their site for version information.
    Paralogs
    Downloads
    Download All DIOPT Paralogs
    Paralogs (via DIOPT v9.1)
    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
    esyN Network Diagram
    Show neighbor-neighbor interactions:
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Other Interaction Browsers
    View in FlyBase Interactions Browser   View in MIST tool (external link)
    Please see the Physical Interaction reports below for full details
    RNA-protein
    Physical Interaction
    Assay
    References
    lncRNA:cherub - Syp
    anti bait coimmunoprecipitation, quantitative reverse transcription pcr
    (Landskron et al., 2018)
    lncRNA:cherub - stau
    anti bait coimmunoprecipitation, quantitative reverse transcription pcr
    (Landskron et al., 2018)
    Summary of Genetic Interactions
    esyN Network Diagram
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    esyN Network Key:
    Suppression
    Enhancement
    Other 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
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    brat
    suppressible
    lncRNA:cherub
    (Landskron et al., 2018)
    External Data
    Linkouts
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    FlyBase
    External Links
    External Data
    Linkouts
    Class of Gene
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-50
    Cytogenetic map
    86D9-86D9
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    86D9-86D9
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    3-50

    (FlyBase, 2016)

    3-47.7

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (1)
    Genomic Clones (18)
     

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

    cDNA Clones (11)
     

    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
         
        Commercially Available Antibodies
         
        Cell Line Information
        Publicly Available Cell Lines
         
          Other Stable Cell Lines
           
            Other Comments

            New annotation (CR43283) in release 5.35 of the genome annotation.

            (FlyBase Genome Annotators, 2011)
            Relationship to Other Genes
            Source for database merge of
            Additional comments
            Nomenclature History
            Source for database identify of

            Source for identity of: lncRNA:CR43283 CR43283

            (FlyBase, 2009-)

            Source for identity of: lncRNA:cherub lncRNA:CR43283

            (Landskron et al., 2018)
            Nomenclature comments
            Etymology

            Named 'cherub', the antonym for brat, to indicate its antagonizing activity towards the 'brat' gene.

            (Landskron et al., 2018)
            Synonyms and Secondary IDs (7)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            Study result (0)
            Result
            Result Type
            Title
            External Crossreferences and Linkouts ( 14 )
            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.
            RNAcentral - A comprehensive ncRNA sequence collection representing all ncRNA types from a broad range of organisms
            Other crossreferences
            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
            FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
            References (16)