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General Information
Symbol
Dmel\mir-9a
Species
D. melanogaster
Name
mir-9a stem loop
Annotation Symbol
CR42891
Feature Type
FlyBase ID
FBgn0262373
Gene Model Status
Stock Availability
Gene Summary
a microRNA that regulates maternal-to-zygotic transition, muscle-tendon attachments, production of sensory bristles and wing development (Interactive Fly, mir-9a )
Contribute a Gene Snapshot for this gene.
Also Known As

miR-9, dme-miR-9a

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
3-45
RefSeq locus
NT_037436 REGION:19565131..19565208
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (9 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (0 terms)
Biological Process (7 terms)
Terms Based on Experimental Evidence (7 terms)
CV Term
Evidence
References
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
    Summary (Interactive Fly)

    a microRNA that regulates maternal-to-zygotic transition, muscle-tendon attachments, production of sensory bristles and wing development

    Gene Model and Products
    Number of Transcripts
    3
    Number of Unique Polypeptides
    0

    Please see the JBrowse view of Dmel\mir-9a 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

    Locations and structures of miRNA models as mapped by miRBase (FBrf0220601).

    Conserved: found throughout the Drosophila genus (FBrf0230987).

    Sequence Ontology: Class of Gene
    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    FBtr0304197
    23
    FBtr0472710
    22
    FBtr0304196
    78
    Additional Transcript Data and Comments
    Reported size (kB)
    Comments
    External Data
    Crossreferences
    miRBase - A searchable database of published miRNA sequences and annotation.
    Rfam - A collection of RNA sequence families of structural RNAs including non-coding RNA genes as well as cis-regulatory elements
    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\mir-9a 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
    northern blot
    Stage
    Tissue/Position (including subcellular localization)
    Reference
    organism

    Comment: expression starts at 2 hr AEL

    Additional Descriptive Data

    Expression is weak, with a broad peak from 6 hours of embryonic development through the first larval instar.

    Northern analysis of 24 microRNAs showed that a number of them were expressed constituitively throughout development.

    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

    GBrowse - Visual display of RNA-Seq signals

    View Dmel\mir-9a in GBrowse 2
    RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
    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
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
    Images
    Alleles, Insertions, Transgenic Constructs, and Aberrations
    Classical and Insertion Alleles ( 6 )
    For All Classical and Insertion Alleles Show
     
    Other relevant insertions
    Transgenic Constructs ( 12 )
    For All Alleles Carried on Transgenic Constructs Show
    Transgenic constructs containing/affecting coding region of mir-9a
    Transgenic constructs containing regulatory region of mir-9a
    Aberrations (Deficiencies and Duplications) ( 0 )
    Inferred from experimentation ( 0 )
    Inferred from location ( 0 )
    Alleles Representing Disease-Implicated Variants
    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
    wing margin bristle | ectopic & anterior wing margin
    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
    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

    Please see the Physical Interaction reports below for full details
    RNA-RNA
    Physical Interaction
    Assay
    References
    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
    DroID - A comprehensive database of gene and protein interactions.
    MIST (genetic) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3L
    Recombination map
    3-45
    Cytogenetic map
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    76B7-76B7
    Limits computationally determined from genome sequence between P{EP}MESR6EP3142 and P{lacW}l(3)L3809L3809
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (3)
    Genomic Clones (13)
     

    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: mir-9a mir-9

              Source for database merge of
              Additional comments

              The annotation for mir-9a has been changed in release 5.31 of the genome annotation, so that instead of representing a mature miRNA it now represents the precursor stem loop pre-miRNA. The symbol of the annotation has been changed from CR33063 to CR42891 to reflect this change.

              Other Comments

              mir-9a minimises the phenotypic impact of genomic diversity on determination of sensory cell fate by buffering the level of sens protein.

              mir-9a ensures the precise specification of sensory organ precursors by down-regulating the expression of sens through its 3' untranslated region.

              New annotation (CR33063) in release 3 of the genome annotation.

              Origin and Etymology
              Discoverer
              Etymology
              Identification
              External Crossreferences and Linkouts ( 21 )
              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
              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
              FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
              FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
              FlyMine - An integrated database for Drosophila genomics
              GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
              KEGG Genes - Molecular building blocks of life in the genomic space.
              MARRVEL_MODEL - MARRVEL (model organism gene)
              miRBase - A searchable database of published miRNA sequences and annotation.
              modMine - A data warehouse for the modENCODE project
              Rfam - A collection of RNA sequence families of structural RNAs including non-coding RNA genes as well as cis-regulatory elements
              Linkouts
              DroID - A comprehensive database of gene and protein interactions.
              Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
              MIST (genetic) - An integrated Molecular Interaction Database
              Synonyms and Secondary IDs (14)
              Reported As
              Symbol Synonym
              dme-miR-9a-5p
              transfrag 22
              Name Synonyms
              mir-9a
              mir-9a stem loop
              Secondary FlyBase IDs
              • FBgn0067680
              • FBgn0046813
              • FBgn0262184
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              References (108)