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General Information
Symbol
Dmel\mir-6-1
Species
D. melanogaster
Name
mir-6-1 stem loop
Annotation Symbol
CR43047
Feature Type
FlyBase ID
FBgn0262464
Gene Model Status
Stock Availability
Also Known As
miR-6, dme-mir-6-1
Key Links
Genomic Location
Cytogenetic map
Sequence location
2R:19,661,003..19,661,084 [-]
Recombination map
2-90
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
-
Protein Signatures (InterPro)
    -
    Molecular Function (GO)
    [Detailed GO annotations]
    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-6-1 or the JBrowse view of Dmel\mir-6-1 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)
    FBtr0304531
    22
    FBtr0472707
    22
    FBtr0304530
    82
    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-6-1 using the Feature Mapper tool.

    External Data
    Crossreferences
    Linkouts
    Gene Ontology (1 term)
    Molecular Function (0 terms)
    Terms Based on Experimental Evidence (0 terms)
    Terms Based on Predictions or Assertions (0 terms)
    Biological Process (1 term)
    Terms Based on Experimental Evidence (1 term)
    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
    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
    in situ
    Stage
    Tissue/Position (including subcellular localization)
    Reference
    organism | ubiquitous
    nucleus

    Comment: probe reflects expression of primary transcript encompassing 8 mir genes between CG15125 and CG11018

    organism | 10-90% egg length
    nucleus

    Comment: probe reflects expression of primary transcript encompassing 8 mir genes between CG15125 and CG11018

    organism | restricted

    Comment: along anterior-posterior axis

    organism | striped

    Comment: restricted dorsally late stage 5

    dorsal ectoderm | striped
    nucleus

    Comment: probe reflects expression of primary transcript encompassing 8 mir genes between CG15125 and CG11018

    northern blot
    Stage
    Tissue/Position (including subcellular localization)
    Reference
    Additional Descriptive Data
    mir-6-1 transcript is ubquitously expressed in precellular embryos. At stage 5, transcript expression is repressed, first at the posterior pole of the embryo, then in a dorsal patch at the anterior of the embryo. Late in stage 5, transcript expression begins to be lost in the mesoderm and neural ectoderm in ventral and lateral regions. By late embryonic stage 5, expression is refined to transient stripes in the dorsal ectoderm These stripes become further refined to a single central band by embryonic stage 7. Expression is essentially lost by the onset of germband elongation, except for residual expression at the anterior tip of the embryo, and in the dorsal ectoderm. mir-6-1 transcript is localized to the nucleus at all stages.
    Expression has a broad peak from the fourth hour until the end of embryonic development. Probe
    Northern analysis of 24 microRNAs showed that the expression of mir-4, mir-5, mir-124 and mir-6 isoforms (mir-6-1, mir-6-2 and mir-6-3) is restricted to embryogenesis and the first larval instar with levels decreasing during the latter part of the first larval stage.
    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-6-1 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, and Transgenic Constructs
    Classical and Insertion Alleles ( 1 )
    For All Classical and Insertion Alleles Show
     
    Other relevant insertions
    Transgenic Constructs ( 9 )
    For All Alleles Carried on Transgenic Constructs Show
    Transgenic constructs containing/affecting coding region of mir-6-1
    Transgenic constructs containing regulatory region of mir-6-1
    Deletions and Duplications ( 1 )
    Phenotypes
    For more details about a specific phenotype click on the relevant allele symbol.
    Lethality
    Allele
    Other Phenotypes
    Allele
    Phenotype manifest in
    Allele
    Orthologs
    Human Orthologs (via DIOPT v7.1)
    Homo sapiens (Human) (0)
    No records found.
    Model Organism Orthologs (via DIOPT v7.1)
    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
    Paralogs (via DIOPT v7.1)
    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 ( 1 )
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
     
    Disease Associations of Human Orthologs (via DIOPT v7.1 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:
    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
    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)
    2R
    Recombination map
    2-90
    Cytogenetic map
    Sequence location
    2R:19,661,003..19,661,084 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    56E1-56E1
    Limits computationally determined from genome sequence between P{PZ}sm05338&P{PZ}emm1 and P{lacW}l(2)k08002k08002
    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 (19)
     
    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 database merge of
              Additional comments
              The annotation for mir-6-1 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 CR33004 to CR43047 to reflect this change.
              Other Comments
              mir-3, mir-4, mir-5, mir-6-1, mir-6-2 and mir-6-3 sequences are clustered within 900bp in 56D7-56E3.
              New annotation (CR33004) in release 3 of the genome annotation.
              Origin and Etymology
              Discoverer
              Etymology
              Identification
              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.
              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
              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
              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.
              Synonyms and Secondary IDs (13)
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              References (71)