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
Also Known As
miR-9, dme-miR-9a, CR33063
Genomic Location
Cytogenetic map
Sequence location
3L:19,565,131..19,565,208 [+]
Recombination map
3-45
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
GO Summary Ribbons
Families, Domains and Molecular Function
Gene Group Membership (FlyBase)
Protein Family (UniProt, Sequence Similarities)
-
Protein Domains/Motifs
Molecular Function (see GO section for details)
Experimental Evidence
-
Predictions / Assertions
-
Summaries
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
0

Please see the GBrowse view of Dmel\mir-9a or 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
Gene Ontology (6 terms)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (6 terms)
Terms Based on Experimental Evidence (6 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)
Expression Data
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
Alleles, Insertions, Transgenic Constructs and Phenotypes
Classical and Insertion Alleles ( 6 )
Transgenic Constructs ( 12 )
Deletions and Duplications ( 0 )
Summary of 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 v7.1)
Homo sapiens (Human) (0)
No orthologs reported.
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (0)
No orthologs reported.
Rattus norvegicus (Norway rat) (0)
No orthologs reported.
Xenopus tropicalis (Western clawed frog) (0)
No orthologs reported.
Danio rerio (Zebrafish) (0)
No orthologs reported.
Caenorhabditis elegans (Nematode, roundworm) (0)
No orthologs reported.
Arabidopsis thaliana (thale-cress) (0)
No orthologs reported.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No orthologs reported.
Schizosaccharomyces pombe (Fission yeast) (0)
No orthologs reported.
Orthologs 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
Human Disease Model Data
FlyBase Human Disease Model Reports
Alleles Reported to Model Human Disease (Disease Ontology)
Download
Models ( 0 )
Allele
Disease
Evidence
References
Interactions ( 0 )
Allele
Disease
Interaction
References
Comments ( 0 )
 
Human Orthologs (via DIOPT v7.1)
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
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 look at the Interaction Group reports for full details of the physical interactions
RNA-RNA
Interacting group
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.
Pathways
Gene Group - Pathway Membership (FlyBase)
External Data
Linkouts
Genomic Location and Detailed Mapping Data
Chromosome (arm)
3L
Recombination map
3-45
Cytogenetic map
Sequence location
3L:19,565,131..19,565,208 [+]
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 sequences
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 ( 15 )
            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
            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
            Linkouts
            DroID - A comprehensive database of gene and protein interactions.
            FlyMine - An integrated database for Drosophila genomics
            GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
            Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
            KEGG Genes - Molecular building blocks of life in the genomic space.
            modMine - A data warehouse for the modENCODE project
            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 (91)