FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\mir-279
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General Information
Symbol
Dmel\mir-279
Species
D. melanogaster
Name
mir-279 stem loop
Annotation Symbol
CR43015
Feature Type
miRNA_gene
FlyBase ID
FBgn0262448
Gene Model Status
Current
Stock Availability
5 publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

dme-miR-279, miR279

Key Links
Genomic Location
Cytogenetic map
99A1-99A1
Sequence location
Recombination map
3-98
RefSeq locus
NT_033777 REGION:29215585..29215684
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
Gene Ontology (GO) Annotations (15 terms)
Molecular Function (2 terms)
Biological Process (13 terms)
Terms Based on Experimental Evidence (13 terms)
CV Term
Evidence
References
involved_in brain morphogenesis
inferred from mutant phenotype
(Yamamoto et al., 2008)
involved_in locomotion involved in locomotory behavior
inferred from mutant phenotype
(Yamamoto et al., 2008)
involved_in locomotor rhythm
inferred from mutant phenotype
(Luo and Sehgal, 2012)
involved_in miRNA-mediated gene silencing by mRNA destabilization
inferred from direct assay
(Laneve et al., 2013, Zekri et al., 2013, Djuranovic et al., 2012, Hartl et al., 2011, Cayirlioglu et al., 2008, Eulalio et al., 2008)
involved_in miRNA-mediated post-transcriptional gene silencing
inferred from direct assay
(Duan et al., 2018, Kavaler et al., 2018, Sanfilippo et al., 2016, Sun et al., 2015, Barrio et al., 2014, Luo and Sehgal, 2012, Yoon et al., 2011, Kuzin et al., 2007, Robins et al., 2005)
involved_in negative regulation of epidermal growth factor receptor signaling pathway
inferred from genetic interaction with FLYBASE:aos; FB:FBgn0004569,FLYBASE:mir-996; FB:FBgn0262404
(Duan et al., 2018)
involved_in negative regulation of neuroblast proliferation
inferred from mutant phenotype
(Hartl et al., 2011)
involved_in negative regulation of neuron differentiation
inferred from mutant phenotype
(Sun et al., 2015, Cayirlioglu et al., 2008)
involved_in negative regulation of receptor signaling pathway via JAK-STAT
inferred from direct assay
(Yoon et al., 2011)
inferred from mutant phenotype
(Luo and Sehgal, 2012)
involved_in positive regulation of Notch signaling pathway
inferred from mutant phenotype
(Kavaler et al., 2018)
inferred from genetic interaction with FLYBASE:insb; FB:FBgn0034224
(Kavaler et al., 2018)
involved_in regulation of locomotor rhythm
inferred from mutant phenotype
(Sun et al., 2015)
involved_in startle response
inferred from mutant phenotype
(Yamamoto et al., 2008)
involved_in wing disc dorsal/ventral pattern formation
inferred from genetic interaction with FLYBASE:Bx; FB:FBgn0265598,FLYBASE:ap; FB:FBgn0267978
(Bejarano et al., 2008)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in miRNA-mediated post-transcriptional gene silencing
inferred from electronic annotation with Rfam:RF00754
(RNAcentral, 2018-)
Cellular Component (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Pathway (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
    -
    Summaries
    Pathway (FlyBase)
    NEGATIVE REGULATORS OF JAK-STAT SIGNALING PATHWAY -
    Negative regulators of JAK-STAT signaling down-regulate the pathway, attenuating transcriptional control by Stat92E.
    NEGATIVE REGULATORS OF EGFR SIGNALING PATHWAY -
    Negative regulators of Epidermal Growth Factor Receptor signaling down-regulate the pathway, suppressing the activation of ERK kinase (rl) or acting on downstream effectors.
    POSITIVE REGULATORS OF NOTCH SIGNALING PATHWAY -
    The Notch receptor signaling pathway is activated by the binding of the transmembrane receptor Notch (N) to transmembrane ligands, Dl or Ser, presented on adjacent cells. This results in the proteolytic cleavage of N, releasing the intracellular domain (NICD). NICD translocates into the nucleus, interacting with Su(H) and mam to form a transcription complex, which up-regulates transcription of Notch-responsive genes. Positive regulators of the pathway enhance the signal from the sending cell or the response in the receiving cell. (Adapted from FBrf0225731 and FBrf0192604).
    Gene Model and Products
    Number of Transcripts
    3
    Number of Unique Polypeptides
    0

    Please see the JBrowse view of Dmel\mir-279 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

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

    Conserved: found throughout the Drosophila genus (FBrf0230987).

    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    mir-279-RA
    FBtr0304463
    NR_048509
    22
    mir-279-RB
    FBtr0472724
    26
    mir-279-RM
    FBtr0304462
    NR_048508
    100
    Additional Transcript Data and Comments
    Reported size (kB)
    Comments
    External Data
    Crossreferences
    miRBase - A searchable database of published miRNA sequences and annotation.
    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-279 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
      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\mir-279 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 ( 6 )
      For All Classical and Insertion Alleles Show
       
      Other relevant insertions
      Transgenic Constructs ( 13 )
      For All Alleles Carried on Transgenic Constructs Show
      Transgenic constructs containing/affecting coding region of mir-279
      Transgenic constructs containing regulatory region of mir-279
      Aberrations (Deficiencies and Duplications) ( 2 )
      Inferred from experimentation ( 2 )
      Gene disrupted in
      Df(3R)3450
      (Szeged Stock Center, 1998-)
      Df(3R)ex15C
      (Sun et al., 2015)
      Inferred from location ( 6 )
      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
      lethal
      lethal, with Scer\GAL4Act5C.PU
      lethal, with Scer\GAL4Bx-MS1096
      lethal (with Df(3R)Exel6212)
      lethal | recessive
      viable
      viable, with Scer\GAL4Tub.PU
      Other Phenotypes
      Allele
      abnormal auditory perception | adult stage
      abnormal behavior
      abnormal locomotor behavior | adult stage
      abnormal locomotor rhythm
      abnormal locomotor rhythm, with Scer\GAL4mir-279.PC
      abnormal locomotor rhythm, with Scer\GAL4tim.PE
      abnormal locomotor rhythm | adult stage, with Scer\GAL4tim.PU
      abnormal locomotor rhythm | adult stage | recessive | conditional
      abnormal locomotor rhythm | RU486 conditional, with Scer\GAL4elav.Switch.PO
      abnormal neuroanatomy
      abnormal neuroanatomy | adult stage | somatic clone
      abnormal neurophysiology
      abnormal neurophysiology | recessive
      decreased cell number | P-stage
      decreased cell number | P-stage (with Df(3R)ex15C)
      decreased cell number | P-stage (with mir-279ex36)
      decreased cell number | P-stage (with mir-279ex117)
      short lived
      some die during embryonic stage (with Df(3R)Exel6212)
      some die during embryonic stage | recessive
      uncoordinated | adult stage (with Df(3R)ex15C)
      visible, with Scer\GAL4sd-SG29.1
      Phenotype manifest in
      Allele
      adult olfactory receptor neuron Gr21a/63a | ectopic | somatic clone
      carbon dioxide sensitive neuron | ectopic | somatic clone
      follicle cell, with Scer\GAL4mir-279.PC
      Johnston organ | P-stage
      Johnston organ | P-stage (with Df(3R)ex15C)
      Johnston organ | P-stage (with mir-279ex36)
      Johnston organ | P-stage (with mir-279ex117)
      maxillary palp
      maxillary palp | somatic clone
      maxillary palp basiconic sensillum
      scolopale cell | P-stage
      scolopale cell | P-stage | decreased number (with Df(3R)ex15C)
      scolopale cell | P-stage | decreased number (with mir-279ex36)
      scolopale cell | P-stage | decreased number (with mir-279ex117)
      wing, with Scer\GAL4Bx-MS1096
      wing, with Scer\GAL4sd-SG29.1
      wing margin bristle, with Scer\GAL4sd-SG29.1
      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:mir-279. 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
        Summary of Genetic Interactions
        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
        mir-279
        suppressible
        mir-996
        (Sun et al., 2015)
        mir-279
        suppressible
        pros
        (Hartl et al., 2011)
        mir-279
        suppressible
        upd1
        (Luo and Sehgal, 2012)
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        ap|Bx
        suppressible
        mir-279
        (Bejarano et al., 2008)
        pros
        suppressible
        mir-279
        (Hartl et al., 2011)
        External Data
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        FlyBase
        External Links
        External Data
        Linkouts
        Class of Gene
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3R
        Recombination map
        3-98
        Cytogenetic map
        99A1-99A1
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        99A1-99A1
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        98F-98F
        (determined by in situ hybridisation)
        (Szeged Stock Center, 1998-, Deak et al., 1997)
        Experimentally Determined Recombination Data
        Location

        3-98

        (FlyBase, 2016)

        3-94.8

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (5)
        Genomic Clones (16)
         

        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 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

                      pros and mir-279 are required to prevent the formation of a CO[[2]] olfactory receptor neuron (ORN) within Or59c and Or42a ORN-containing maxillary palp sensilla.

                      (Hartl et al., 2011)

                      New annotation (CR33590) in release 4.1 of the genome annotation.

                      (FlyBase Genome Annotators, 2005)
                      Relationship to Other Genes
                      Source for database merge of

                      Source for merge of: mir-279 l(3)S096207

                      (Cayirlioglu et al., 2008)
                      Additional comments

                      The annotation for mir-279 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 CR33590 to CR43015 to reflect this change.

                      (FlyBase Genome Annotators, 2010)
                      Nomenclature History
                      Source for database identify of
                      Nomenclature comments
                      Etymology
                      Synonyms and Secondary IDs (21)
                      Reported As
                      Symbol Synonym
                      0962/07
                      (Deak et al., 1997)
                      279
                      (Han et al., 2011)
                      CR33590
                      (FlyBase Genome Annotators, 2005)
                      CR43015
                      (FlyBase Genome Annotators, 2010)
                      MIR-279
                      (Ylla et al., 2016)
                      MiR-279
                      (Yang et al., 2009)
                      Mir-279
                      (Robins et al., 2005)
                      dme-miR-279
                      (Volin et al., 2018, Dhahbi et al., 2016, Lucas et al., 2015, Towler et al., 2015, Esslinger et al., 2013)
                      dme-miR-279-3p
                      (Chandra et al., 2015)
                      dme-mir-279
                      (He et al., 2022, miRBase, 2013, Gesellchen and Boutros, 2004)
                      l(3)S096207
                      miR
                      (Berdnik et al., 2008)
                      miR-279
                      (Hiers et al., 2025, Jang et al., 2024, Khoodoruth et al., 2024, Li et al., 2024, Chan et al., 2023, Anna and Kannan, 2021, Galagali and Kim, 2020, King and Sehgal, 2020, Li et al., 2020, Lim et al., 2020, Shi et al., 2020, Reichholf et al., 2019, Church et al., 2017, Li et al., 2017, Mendoza-Viveros et al., 2017, Shu et al., 2017, Green et al., 2016, Monahan and Starz-Gaiano, 2016, Rainey et al., 2016, Fulga et al., 2015, Suh et al., 2015, Barrio et al., 2014, Kong et al., 2014, Laneve and Giangrande, 2014, Bartok et al., 2013, Cande et al., 2013, Laneve et al., 2013, Lucas and Raikhel, 2013, Nesler et al., 2013, Pancratov et al., 2013, Zekri et al., 2013, Djuranovic et al., 2012, Liu et al., 2012, Luo and Sehgal, 2012, Brochtrup and Hummel, 2011, Hartl et al., 2011, Liu et al., 2011, Yoon et al., 2011, Büssing et al., 2010, Fernandez-Valverde et al., 2010, Czech et al., 2009, Eulalio et al., 2009, Eulalio et al., 2009, Kadener et al., 2009, Zekri et al., 2009, Cayirlioglu et al., 2008, Eulalio et al., 2008, Ibáñez-Ventoso et al., 2008, Kawamura et al., 2008, Zhao et al., 2008, Grunwald Kadow et al., 2007, Kuzin et al., 2007, Okamura et al., 2007, Ruby et al., 2007, Rehwinkel et al., 2006, Leaman, 2005, Stark et al., 2005, Lai et al., 2003, Stark et al., 2003, Stark et al., 2003)
                      miR-279-3p
                      (Lim et al., 2018)
                      miR279
                      (Zhang et al., 2010, Kadener et al., 2009)
                      miRNA-279
                      (Ma et al., 2020)
                      mir-279
                      (Örkenby et al., 2023, Hanyu-Nakamura et al., 2019, Redmond et al., 2019, Kavaler et al., 2018, Pan et al., 2017, Mohammed and Lai, 2016.2.8, Sanfilippo et al., 2016, Sun et al., 2015, Chen et al., 2014, Fricke et al., 2014, Mohammed et al., 2014, Wang et al., 2014, Yeh et al., 2014, Zhou et al., 2014, Daneshvar et al., 2013, Monahan and Starz-Gaiano, 2013, Bejarano et al., 2012, Bejarano et al., 2012, Schertel et al., 2012, Szuplewski et al., 2012, Enderle et al., 2011, Smibert et al., 2011, Arancio et al., 2010, FlyBase Genome Annotators, 2010, Herranz et al., 2010, Martin et al., 2009, Okamura et al., 2009, Yamamoto et al., 2009, Neumuller et al., 2008, Yamamoto et al., 2008, Kuzin et al., 2007, Liu et al., 2007, Stark et al., 2007, Stark et al., 2007, Burgler and Macdonald, 2005)
                      mir-279a
                      (Bejarano et al., 2008)
                      mir279
                      (Saadin and Starz-Gaiano, 2016)
                      Name Synonyms
                      lethal (3) S096207
                      miR-279
                      (Westholm et al., 2014)
                      mir-279
                      mir-279 stem loop
                      Secondary FlyBase IDs
                      • FBgn0260633
                      • FBgn0067714
                      • FBgn0028049
                      • FBgn0262308
                      Datasets (0)
                      Study focus (0)
                      Experimental Role
                      Project
                      Project Type
                      Title
                      Study result (0)
                      Result
                      Result Type
                      Title
                      External Crossreferences and Linkouts ( 14 )
                      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)
                      miRBase - A searchable database of published miRNA sequences and annotation.
                      Linkouts
                      DroID - A comprehensive database of gene and protein interactions.
                      FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
                      References (140)