FB2020_03, released Jun 16, 2020

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
Other Summaries
Also Known As

dme-miR-279, miR279

Key Links
Genomic Location
Cytogenetic map
Sequence location
3R:29,215,585..29,215,684 [+]
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
GO Summary Ribbons
Gene Ontology (GO) Annotations (10 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
mRNA binding involved in posttranscriptional gene silencing
inferred from direct assay
(Duan et al., 2018, Luo and Sehgal, 2012)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (9 terms)
Terms Based on Experimental Evidence (9 terms)
CV Term
Evidence
References
brain morphogenesis
inferred from mutant phenotype
(Yamamoto et al., 2008)
gene silencing by miRNA
inferred from direct assay
(Duan et al., 2018, Luo and Sehgal, 2012)
gene silencing by RNA
inferred from direct assay
(Laneve et al., 2013)
locomotion involved in locomotory behavior
inferred from mutant phenotype
(Yamamoto et al., 2008)
locomotor rhythm
inferred from mutant phenotype
(Luo and Sehgal, 2012)
negative regulation of epidermal growth factor-activated receptor activity
inferred from genetic interaction with FLYBASE:aos; FB:FBgn0004569, FLYBASE:mir-996; FB:FBgn0262404
(Duan et al., 2018)
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)
startle response
inferred from mutant phenotype
(Yamamoto et al., 2008)
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 (0 terms)
Cellular Component (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
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.
    Gene Model and Products
    Number of Transcripts
    3
    Number of Unique Polypeptides
    0

    Please see the GBrowse view of Dmel\mir-279 or 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
    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
    gene
    miRNA_gene
    (FlyBase Genome Annotators, 2010, Stark et al., 2003, Stark et al., 2003)
    nuclear_gene
    (FlyBase Genome Annotators, 2010, Stark et al., 2003, Stark et al., 2003)
    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
      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
      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-279 in GBrowse 2
      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
      Alleles, Insertions, and Transgenic Constructs
      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
      Deletions and Duplications ( 2 )
      Phenotypes
      Orthologs
      Downloads
      Download All DIOPT Orthologs
      Download All OrthoDB 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.
      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
      Paralogs
      Downloads
      Download All DIOPT 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
        Summary of Genetic Interactions
        esyN Network Diagram
        esyN Network Key:
        Suppression
        Enhancement
        View in Interactions Browser
        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
        pros
        (Hartl et al., 2011)
        mir-279
        suppressible
        upd1
        (Luo and Sehgal, 2012)
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Bx|ap
        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)
        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.
        Metabolic Pathways
        External Data
        Linkouts
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3R
        Recombination map

        3-98

        Cytogenetic map
        99A1-99A1
        Sequence location
        3R:29,215,585..29,215,684 [+]
        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 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 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)
                  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)
                  Origin and Etymology
                  Discoverer
                  Etymology
                  Identification
                  External Crossreferences and Linkouts ( 12 )
                  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
                  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.
                  miRBase - A searchable database of published miRNA sequences and annotation.
                  modMine - A data warehouse for the modENCODE project
                  Linkouts
                  DroID - A comprehensive database of gene and protein interactions.
                  Synonyms and Secondary IDs (20)
                  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
                  (miRBase, 2013, Gesellchen and Boutros, 2004)
                  l(3)S096207
                  miR
                  (Berdnik et al., 2008)
                  miR-279
                  (Lim 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, 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)
                  mir-279
                  (Hanyu-Nakamura et al., 2019, Redmond et al., 2019, Kavaler et al., 2018, 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
                  References (121)