FB2020_06, released Dec 22, 2020

Gene: Dmel\scaRNA:MeU5-G38

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General Information
Symbol
Dmel\scaRNA:MeU5-G38
Species
D. melanogaster
Name
small Cajal body-specific RNA : MeU5-G38
Annotation Symbol
CR43572
Feature Type
snoRNA_gene
FlyBase ID
FBgn0261455
Gene Model Status
Current
Stock Availability
None publicly available
Other Summaries
Also Known As

mgU5-38, scaRNA:mgU5-38

Key Links
Genomic Location
Cytogenetic map
Sequence location
3R:22,036,343..22,036,443 [+]
Recombination map

3-74

RefSeq locus
NT_033777 REGION:22036343..22036443
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
GO Summary Ribbons
Gene Ontology (GO) Annotations (1 term)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
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 (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in Cajal body
inferred from direct assay
(Deryusheva and Gall, 2009)
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
    1
    Number of Unique Polypeptides
    0

    Please see the JBrowse view of Dmel\scaRNA:MeU5-G38 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
    Sequence Ontology: Class of Gene
    nuclear_gene
    (Tycowski et al., 2009)
    snoRNA_gene
    (Tycowski et al., 2009)
    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    scaRNA:MeU5-G38-RA
    FBtr0309756
    NR_048460
    101
    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\scaRNA:MeU5-G38 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
    located_in Cajal body
    inferred from direct assay
    (Deryusheva and Gall, 2009)
    Expression Deduced from Reporters
    High-Throughput Expression Data
    Associated Tools

    GBrowse - Visual display of RNA-Seq signals

    View Dmel\scaRNA:MeU5-G38 in GBrowse 2
    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
    Alleles, Insertions, and Transgenic Constructs
    Classical and Insertion Alleles ( 0 )
    For All Classical and Insertion Alleles Show
     
    Other relevant insertions
    Transgenic Constructs ( 0 )
    For All Alleles Carried on Transgenic Constructs Show
    Transgenic constructs containing/affecting coding region of scaRNA:MeU5-G38
    Transgenic constructs containing regulatory region of scaRNA:MeU5-G38
    Deletions and Duplications ( 0 )
    Phenotypes
    For more details about a specific phenotype click on the relevant allele symbol.
    Phenotype manifest in
    Allele
    Orthologs
    Downloads
    Download All DIOPT Orthologs
    Download All OrthoDB 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
    Downloads
    Download All DIOPT 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
      View in Interactions Browser
      Please see the Physical Interaction reports below for full details
      RNA-protein
      Physical Interaction
      Assay
      References
      scaRNA:MeU5-G38 - WDR79
      affinity chromatography technology, Identification by mass spectrometry, nucleic acid uv cross-linking assay, autoradiography
      (Tycowski et al., 2009)
      Summary of Genetic Interactions
      esyN Network Diagram
      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)
      3R
      Recombination map

      3-74

      Cytogenetic map
      94A1-94A1
      Sequence location
      3R:22,036,343..22,036,443 [+]
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      94A1-94A1
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location

      3-74

      (FlyBase, 2016)

      3-76.0

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (0)
      Genomic Clones (18)
       

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

      cDNA Clones (0)
       

      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
              Other clones
                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: scaRNA:MeU5-G38 scaRNA:mgU5-38

                (FlyBase, 2009-)
                Source for database merge of
                Additional comments

                scaRNA:mgU5-38 is encoded in an intron of pit.

                (Graveley et al., 2011)

                Renamed to make consistent with the naming convention of other guide RNAs in FlyBase. (Modified base is given in FBrf0209497.)

                (FlyBase, 2009-)
                Other Comments

                New annotation (CR43572) in release 5.41 of the genome annotation.

                (FlyBase Genome Annotators, 2011)

                scaRNA:mgU5-38 is a Cajal body-specific RNA (scaRNA) that is predicted to modify U5 snRNA.

                (Tycowski et al., 2009)
                Origin and Etymology
                Discoverer
                Etymology
                Identification
                External Crossreferences and Linkouts ( 6 )
                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
                GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
                KEGG Genes - Molecular building blocks of life in the genomic space.
                Synonyms and Secondary IDs (5)
                Reported As
                Symbol Synonym
                mgU5-38
                (Deryusheva and Gall, 2013, Deryusheva and Gall, 2009, Tycowski et al., 2009)
                scaRNA:MeU5-G38
                scaRNA:mgU5-38
                (FlyBase Genome Annotators, 2011)
                scaRNA:pit-a
                (Graveley et al., 2011)
                Name Synonyms
                small Cajal body-specific RNA : MeU5-G38
                Secondary FlyBase IDs
                  Datasets (0)
                  Study focus (0)
                  Experimental Role
                  Project
                  Project Type
                  Title
                  References (8)