Open Close
General Information
Symbol
Dmel\Root
Species
D. melanogaster
Name
Rootletin
Annotation Symbol
CG6129
Feature Type
FlyBase ID
FBgn0039152
Gene Model Status
Stock Availability
Gene Snapshot
Rootletin (Root) encodes the major structural component of the ciliary rootlet. It is expressed in sensory neurons and is required for ciliary-transmitted sensory functions including hearing, touch and taste. [Date last reviewed: 2018-11-08]
Key Links
Genomic Location
Cytogenetic map
Sequence location
3R:24,113,286..24,128,193 [+]
Recombination map

3-83

RefSeq locus
NT_033777 REGION:24113286..24128193
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
    Summary (Interactive Fly)

    structural component of base of cilia - organizes rootlets at the base of primary cilia in sensory neurons - essential for sensory neuron functions, including negative geotaxis, taste, touch response, and hearing - rootlet assembly requires centrioles

    Gene Model and Products
    Number of Transcripts
    3
    Number of Unique Polypeptides
    1

    Please see the GBrowse view of Dmel\Root or the JBrowse view of Dmel\Root 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

    Low-frequency RNA-Seq exon junction(s) not annotated.

    Gene model reviewed during 5.49

    Sequence Ontology: Class of Gene
    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    Assoc. CDS (aa)
    FBtr0304161
    6731
    2048
    FBtr0339244
    7040
    2048
    FBtr0339245
    7005
    2048
    Additional Transcript Data and Comments
    Reported size (kB)
    Comments
    External Data
    Crossreferences
    Polypeptide Data
    Annotated Polypeptides
    Name
    FlyBase ID
    Predicted MW (kDa)
    Length (aa)
    Theoretical pI
    RefSeq ID
    GenBank
    FBpp0293091
    232.7
    2048
    6.13
    FBpp0308351
    232.7
    2048
    6.13
    FBpp0308352
    232.7
    2048
    6.13
    Polypeptides with Identical Sequences

    The group(s) of polypeptides indicated below share identical sequence to each other.

    2048 aa isoforms: Root-PD, Root-PE, Root-PF
    Additional Polypeptide Data and Comments
    Reported size (kDa)
    Comments
    External Data
    Crossreferences
    Linkouts
    Sequences Consistent with the Gene Model
    Mapped Features

    Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Root using the Feature Mapper tool.

    External Data
    Crossreferences
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    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 (5 terms)
    Terms Based on Experimental Evidence (5 terms)
    CV Term
    Evidence
    References
    Terms Based on Predictions or Assertions (0 terms)
    Cellular Component (1 term)
    Terms Based on Experimental Evidence (1 term)
    CV Term
    Evidence
    References
    inferred from direct assay
    colocalizes_with ciliary rootlet
    inferred from direct assay
    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
    Additional Descriptive Data

    Root is expressed in a dynamic pattern corresponding to developing sensory neuron lineages. Starting in stage 12 it is expressed in all precursor and progeny cells of type I sensory lineages of all sensory modalities (including olfactory, external sensory (mechanosensory and gustatory), and chordotonal (auditory and proprioceptive) neurons. Expression continues in these lineages but appears to become restricted to chordotonal neurons. Expression appears to occur exclusively and transiently in the lineages leading to cells that differentiate a cilium.

    Marker for
     
    Subcellular Localization
    CV Term
    Polypeptide Expression
    immunolocalization
    Stage
    Tissue/Position (including subcellular localization)
    Reference
    mass spectroscopy
    Stage
    Tissue/Position (including subcellular localization)
    Reference
    western blot
    Stage
    Tissue/Position (including subcellular localization)
    Reference
    Additional Descriptive Data

    Root-protein is detected in the ciliary rootlet of scolopidial neurons as well as in neurons of external sensory organs.

    Marker for
     
    Subcellular Localization
    CV Term
    Evidence
    References
    inferred from direct assay
    colocalizes_with ciliary rootlet
    inferred from direct assay
    Expression Deduced from Reporters
    High-Throughput Expression Data
    Associated Tools

    GBrowse - Visual display of RNA-Seq signals

    View Dmel\Root 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
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    Flygut - An atlas of the Drosophila adult midgut
    Images
    Alleles, Insertions, and Transgenic Constructs
    Classical and Insertion Alleles ( 16 )
    For All Classical and Insertion Alleles Show
     
    Other relevant insertions
    Transgenic Constructs ( 10 )
    For All Alleles Carried on Transgenic Constructs Show
    Transgenic constructs containing/affecting coding region of Root
    Transgenic constructs containing regulatory region of Root
    Deletions and Duplications ( 1 )
    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
    Orthologs
    Human Orthologs (via DIOPT v7.1)
    Homo sapiens (Human) (6)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Alignment
    Complementation?
    Transgene?
    11 of 15
    Yes
    Yes
    7 of 15
    No
    Yes
    2 of 15
    No
    Yes
    1 of 15
    No
    Yes
    1 of 15
    No
    Yes
    1 of 15
    No
    Yes
    Model Organism Orthologs (via DIOPT v7.1)
    Mus musculus (laboratory mouse) (5)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Alignment
    Complementation?
    Transgene?
    11 of 15
    Yes
    Yes
    6 of 15
    No
    Yes
    3 of 15
    No
    Yes
    1 of 15
    No
    Yes
    1 of 15
    No
    Yes
    Rattus norvegicus (Norway rat) (2)
    11 of 13
    Yes
    Yes
    3 of 13
    No
    Yes
    Xenopus tropicalis (Western clawed frog) (4)
    5 of 12
    Yes
    Yes
    2 of 12
    No
    Yes
    1 of 12
    No
    Yes
    1 of 12
    No
    Yes
    Danio rerio (Zebrafish) (5)
    11 of 15
    Yes
    Yes
    1 of 15
    No
    Yes
    1 of 15
    No
    Yes
    Caenorhabditis elegans (Nematode, roundworm) (2)
    6 of 15
    Yes
    Yes
    1 of 15
    No
    No
    Arabidopsis thaliana (thale-cress) (3)
    1 of 9
    Yes
    No
    1 of 9
    Yes
    Yes
    1 of 9
    Yes
    Yes
    Saccharomyces cerevisiae (Brewer's yeast) (1)
    1 of 15
    Yes
    No
    Schizosaccharomyces pombe (Fission yeast) (3)
    1 of 12
    Yes
    No
    1 of 12
    Yes
    No
    1 of 12
    Yes
    No
    Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091900EP )
    Organism
    Common Name
    Gene
    AAA Syntenic Ortholog
    Multiple Dmel Genes in this Orthologous Group
    Drosophila melanogaster
    fruit fly
    Drosophila suzukii
    Spotted wing Drosophila
    Drosophila suzukii
    Spotted wing Drosophila
    Drosophila simulans
    Drosophila sechellia
    Drosophila erecta
    Drosophila yakuba
    Drosophila ananassae
    Drosophila pseudoobscura pseudoobscura
    Drosophila persimilis
    Drosophila willistoni
    Drosophila virilis
    Drosophila mojavensis
    Drosophila grimshawi
    Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150094 )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Musca domestica
    House fly
    Glossina morsitans
    Tsetse fly
    Lucilia cuprina
    Australian sheep blowfly
    Mayetiola destructor
    Hessian fly
    Aedes aegypti
    Yellow fever mosquito
    Anopheles darlingi
    American malaria mosquito
    Anopheles darlingi
    American malaria mosquito
    Anopheles gambiae
    Malaria mosquito
    Culex quinquefasciatus
    Southern house mosquito
    Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W01W7 )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Bombyx mori
    Silkmoth
    Danaus plexippus
    Monarch butterfly
    Heliconius melpomene
    Postman butterfly
    Apis florea
    Little honeybee
    Apis mellifera
    Western honey bee
    Bombus impatiens
    Common eastern bumble bee
    Bombus terrestris
    Buff-tailed bumblebee
    Linepithema humile
    Argentine ant
    Megachile rotundata
    Alfalfa leafcutting bee
    Nasonia vitripennis
    Parasitic wasp
    Dendroctonus ponderosae
    Mountain pine beetle
    Dendroctonus ponderosae
    Mountain pine beetle
    Dendroctonus ponderosae
    Mountain pine beetle
    Dendroctonus ponderosae
    Mountain pine beetle
    Tribolium castaneum
    Red flour beetle
    Tribolium castaneum
    Red flour beetle
    Pediculus humanus
    Human body louse
    Rhodnius prolixus
    Kissing bug
    Rhodnius prolixus
    Kissing bug
    Cimex lectularius
    Bed bug
    Acyrthosiphon pisum
    Pea aphid
    Zootermopsis nevadensis
    Nevada dampwood termite
    Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X01TU )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Strigamia maritima
    European centipede
    Ixodes scapularis
    Black-legged tick
    Stegodyphus mimosarum
    African social velvet spider
    Stegodyphus mimosarum
    African social velvet spider
    Daphnia pulex
    Water flea
    Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G034H )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Strongylocentrotus purpuratus
    Purple sea urchin
    Strongylocentrotus purpuratus
    Purple sea urchin
    Strongylocentrotus purpuratus
    Purple sea urchin
    Strongylocentrotus purpuratus
    Purple sea urchin
    Strongylocentrotus purpuratus
    Purple sea urchin
    Ciona intestinalis
    Vase tunicate
    Ciona intestinalis
    Vase tunicate
    Ciona intestinalis
    Vase tunicate
    Ciona intestinalis
    Vase tunicate
    Gallus gallus
    Domestic chicken
    Gallus gallus
    Domestic chicken
    Gallus gallus
    Domestic chicken
    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 ( 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 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-protein
      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.
      InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      External Data
      Linkouts
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      3R
      Recombination map

      3-83

      Cytogenetic map
      Sequence location
      3R:24,113,286..24,128,193 [+]
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      95E1-95E1
      Limits computationally determined from genome sequence between P{PZ}Syx1A06737&P{PZ}Syx1A10660 and P{PZ}crb07207&P{PZ}BRWD305842
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (9)
      Genomic Clones (18)
       
      cDNA Clones (20)
       

      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)
        Other clones
        RNAi and Array Information
        Linkouts
        DRSC - Results frm RNAi screens
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        Antibody Information
        Laboratory Generated Antibodies
         

        polyclonal

        Commercially Available Antibodies
         
        Other Information
        Relationship to Other Genes
        Source for database identify of

        Source for identity of: Rootletin CG6129

        Source for identity of: Root Rootletin

        Source for database merge of
        Additional comments
        Other Comments

        Root is essential for ciliary rootlet formation and for cohesion of basal bodies, but the structure of the cilium appears normal in mutant neurons. Root is required for normal neuron sensory perception.

        Origin and Etymology
        Discoverer
        Etymology

        The name "Rootletin" is based on sequence homology.

        Identification
        External Crossreferences and Linkouts ( 33 )
        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.
        GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
        RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
        UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
        Other crossreferences
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        KEGG Genes - Molecular building blocks of life in the genomic space.
        modMine - A data warehouse for the modENCODE project
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
        FlyMine - An integrated database for Drosophila genomics
        Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Synonyms and Secondary IDs (5)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (39)