FB2025_01 , released February 20, 2025
Gene: Dmel\lncRNA:SMRG
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General Information
Symbol
Dmel\lncRNA:SMRG
Species
D. melanogaster
Name
Scutellar Macrochaetes Regulatory Gene
Annotation Symbol
CR46390
Feature Type
lncRNA_gene
FlyBase ID
FBgn0286868
Gene Model Status
Current
Stock Availability
None publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

SMRG

Key Links
Genomic Location
Cytogenetic map
11B10-11B10
Sequence location
Recombination map
1-39
RefSeq locus
NC_004354 REGION:12680687..12682560
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 (4 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
enables RNA polymerase II-specific DNA-binding transcription factor binding
inferred from direct assay
(Xu et al., 2019)
enables transcription corepressor activity
inferred from mutant phenotype
(Xu et al., 2019)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
acts_upstream_of_negative_effect chaeta development
inferred from mutant phenotype
(Xu et al., 2019)
involved_in negative regulation of transcription by RNA polymerase II
inferred from mutant phenotype
(Xu et al., 2019)
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
    1
    Number of Unique Polypeptides
    0

    Please see the JBrowse view of Dmel\lncRNA:SMRG 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

    This lncRNA overlaps and may be derived from the long 3' UTR of the upstream gene.

    Supported by FBrf0241584.

    Gene model reviewed during 6.27

    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    lncRNA:SMRG-RA
    FBtr0475041
    NR_167813
    1874
    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:SMRG 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
    RT-PCR
    Stage
    Tissue/Position (including subcellular localization)
    Reference
    adult stage
    adult head
    (Xu et al., 2019)
    adult abdomen
    (Xu et al., 2019)
    Additional Descriptive Data

    Quantitative RT-PCR shows that lncRNA:SMRG is found mainly in the adult head and thorax but not the abdomen.

    (Xu et al., 2019)
    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:SMRG 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 ( 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 lncRNA:SMRG
    Transgenic constructs containing regulatory region of lncRNA:SMRG
    Aberrations (Deficiencies and Duplications) ( 1 )
    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
    Other Phenotypes
    Allele
    visible | adult stage | dominant
    Phenotype manifest in
    Allele
    scutellar bristle | increased number
    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:SMRG. 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:SMRG - E(spl)mβ-HLH
      anti bait coimmunoprecipitation, quantitative reverse transcription pcr
      (Xu et al., 2019)
      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
      lncRNA:SMRG
      suppressible
      sc
      (Xu et al., 2019)
      lncRNA:SMRG
      enhanceable
      sc
      (Xu et al., 2019)
      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)
      X
      Recombination map
      1-39
      Cytogenetic map
      11B10-11B10
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      11B10-11B10
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location

      1-39

      (FlyBase, 2016)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (0)
      Genomic Clones (11)
       

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

      cDNA Clones (7)
       

      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 (CR46390) in release 6.27 of the genome annotation.

                    (FlyBase Genome Annotators, 2019)
                    Relationship to Other Genes
                    Source for database merge of
                    Additional comments
                    Nomenclature History
                    Source for database identify of

                    Source for identity of: lncRNA:SMRG CR46390

                    (Xu et al., 2019)
                    Nomenclature comments
                    Etymology
                    Synonyms and Secondary IDs (5)
                    Reported As
                    Symbol Synonym
                    CR46390
                    (FlyBase Genome Annotators, 2019)
                    SMRG
                    (Li et al., 2019, Xu et al., 2019)
                    lncRNA-SMRG
                    (Li et al., 2019)
                    lncRNA:SMRG
                    Name Synonyms
                    Scutellar Macrochaetes Regulatory Gene
                    (Xu et al., 2019)
                    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 (4)