FB2025_01 , released February 20, 2025
Gene: Dmel\sisRNA:4
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General Information
Symbol
Dmel\sisRNA:4
Species
D. melanogaster
Name
stable intronic sequence RNA 4
Annotation Symbol
CR46356
Feature Type
lncRNA_gene
FlyBase ID
FBgn0285969
Gene Model Status
Current
Stock Availability
1 publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

sisR-4

Key Links
Genomic Location
Cytogenetic map
44C2-44C2
Sequence location
Recombination map
2-58
RefSeq locus
NT_033778 REGION:8230532..8231065
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
Function
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 (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in positive regulation of transcription by RNA polymerase II
inferred from mutant phenotype
(Tay and Pek, 2017)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in cytosol
inferred from direct assay
(Tay and Pek, 2017)
is_active_in nucleus
inferred from direct assay
(Tay and Pek, 2017)
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\sisRNA:4 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

    Postulated sisRNA derived from the corresponding intron of the dpn gene (FBrf0235195); not independently transcribed.

    Locations of termini approximate.

    Gene model reviewed during 6.19

    Annotated transcripts for this gene are not independently transcribed, but are proposed to derive from precursors generated by transcription of the overlapping gene, dpn.

    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    sisRNA:4-RA
    FBtr0473388
    NR_163207
    534
    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\sisRNA:4 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).

      NA

      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 cytosol
      inferred from direct assay
      (Tay and Pek, 2017)
      is_active_in nucleus
      inferred from direct assay
      (Tay and Pek, 2017)
      Expression Deduced from Reporters
      High-Throughput Expression Data
      Associated Tools

      JBrowse - Visual display of RNA-Seq signals

      View Dmel\sisRNA:4 in JBrowse
      RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
      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 ( 1 )
      For All Classical and Insertion Alleles Show
       
      Other relevant insertions
      Transgenic Constructs ( 1 )
      For All Alleles Carried on Transgenic Constructs Show
      Transgenic constructs containing/affecting coding region of sisRNA:4
      Transgenic constructs containing regulatory region of sisRNA:4
      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.
      Other Phenotypes
      Allele
      majority die during embryonic stage | maternal effect
      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:sisRNA:4. 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
        Other Interaction Browsers
        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
        sisRNA:4
        suppressible
        dpn
        (Tay and Pek, 2017)
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        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)
        2R
        Recombination map
        2-58
        Cytogenetic map
        44C2-44C2
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        44C2-44C2
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        2-58

        (FlyBase, 2016)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (1)
        Genomic Clones (20)
        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 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 (CR46356) in release 6.19 of the genome annotation.

                      (FlyBase Genome Annotators, 2017)

                      Located at the 3' end of the second intron of the dpn gene.

                      (Tay and Pek, 2017)
                      Relationship to Other Genes
                      Source for database merge of
                      Additional comments
                      Nomenclature History
                      Source for database identify of
                      Nomenclature comments
                      Etymology
                      Synonyms and Secondary IDs (3)
                      Reported As
                      Symbol Synonym
                      sisR-4
                      (Chan et al., 2023, Voo et al., 2021, Chan and Pek, 2019, Pek, 2018, Tay and Pek, 2017)
                      sisRNA:4
                      (FlyBase Genome Annotators, 2017)
                      Name Synonyms
                      stable intronic sequence RNA 4
                      Secondary FlyBase IDs
                        Datasets (0)
                        Study focus (0)
                        Experimental Role
                        Project
                        Project Type
                        Title
                        Study result (0)
                        Result
                        Result Type
                        Title
                        External Crossreferences and Linkouts ( 9 )
                        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
                        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
                        References (7)