FB2022_03, released June 9, 2022

Gene: Dmel\lncRNA:bxd

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General Information
Symbol
Dmel\lncRNA:bxd
Species
D. melanogaster
Name
bithoraxoid
Annotation Symbol
CR31273
Feature Type
lncRNA_gene
FlyBase ID
FBgn0020556
Gene Model Status
Current
Stock Availability
4 publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

bxd

Key Links
Genomic Location
Cytogenetic map
89E1-89E1
Sequence location
Recombination map
3-59
RefSeq locus
NT_033777 REGION:16742125..16773189
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 (2 terms)
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
involved_in negative regulation of transcription, DNA-templated
inferred from expression pattern
(Petruk et al., 2006)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
(Petruk et al., 2006)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
    -
    Summaries
    Phenotypic Description (Red Book; Lindsley and Zimm 1992)
    bxd: bithoraxoid (E.B. Lewis)
    thumb
    bxd: bithoraxoid
    From Bridges and Morgan, 1923, Carnegie Inst. Washington Publ. No. 327: 225.
    Homozygotes show transformation of the anterior first abdominal segment (A1) to the corresponding region of the third thoracic segment (T3). In addition, bxd homozygotes have posterior T3 and posterior A1 transformed toward posterior T2. Hemizygotes for the stronger bxd alleles show (with variable expression) formation of one or a pair of well-developed thoracic legs and, rarely, an extra haltere on A1; the frequency of these abdominal halteres is greatly enhanced in hemizygotes for bxd9 iab2K. The A1 legs in bxd hemizygotes contain underdeveloped posterior compartments, indicating that posterior A1 is partially transformed toward thorax.
    pbx: postbithorax
    Adult homozygotes and hemizygotes have posterior region of third thoracic segment (T3) transformed toward corresponding region of the second (T2).
    Summary (Interactive Fly)
    Gene Model and Products
    Number of Transcripts
    4
    Number of Unique Polypeptides
    0

    Please see the JBrowse view of Dmel\lncRNA:bxd 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 New Section
    Comments on Gene Model

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

    Gene model based on GenBank accessions for bxd and FBrf0046282

    Gene model reviewed during 5.54

    Sequence Ontology: Class of Gene
    lncRNA_gene
    nuclear_gene
    (FlyBase Genome Annotators, 2002-2003)
    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    lncRNA:bxd-RA
    FBtr0083342
    NR_002034
    1258
    lncRNA:bxd-RB
    FBtr0083343
    NR_002033
    1587
    lncRNA:bxd-RC
    FBtr0083344
    NR_002032
    1755
    lncRNA:bxd-RD
    FBtr0083341
    NR_002035
    1124
    Additional Transcript Data and Comments
    Reported size (kB)
    Comments
    External Data
    Crossreferences
    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\lncRNA:bxd using the Feature Mapper tool.

    External Data
    Crossreferences
    Linkouts
    Expression Data
    Expression Summary Ribbons
    Colored tiles in ribbon indicate that the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:
     low
    high 
    Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.
    Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
    Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:
     low
    high 
    as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
    Transcript Expression
    Additional Descriptive Data
    Marker for
     
    Subcellular Localization
    CV Term
    Polypeptide Expression
    Additional Descriptive Data
    Marker for
     
    Subcellular Localization
    CV Term
    Evidence
    References
    located_in nucleus
    inferred from direct assay
    (Petruk et al., 2006)
    Expression Deduced from Reporters
    High-Throughput Expression Data
    Associated Tools

    GBrowse - Visual display of RNA-Seq signals

    View Dmel\lncRNA:bxd in GBrowse 2
    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
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    Images
    FlyBase Wiki
    Image Based Resources
    Alleles, Insertions, Transgenic Constructs, and Aberrations
    Classical and Insertion Alleles ( 4 )
    For All Classical and Insertion Alleles Show
     
    Other relevant insertions
    Transgenic Constructs ( 2 )
    For All Alleles Carried on Transgenic Constructs Show
    Transgenic constructs containing/affecting coding region of lncRNA:bxd
    Transgenic constructs containing regulatory region of lncRNA:bxd
    Aberrations (Deficiencies and Duplications) ( 2 )
    Inferred from experimentation ( 2 )
    Gene partially disrupted in
    Df(3R)Ubxpbx-1
    (Petruk et al., 2006)
    Df(3R)Ubxpbx-2
    (Petruk et al., 2006)
    Inferred from location ( 0 )
    Alleles Representing Disease-Implicated Variants
    Phenotypes
    For more details about a specific phenotype click on the relevant allele symbol.
    Phenotype manifest in
    Allele
    Orthologs
    Downloads
    Download All DIOPT 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.
    Other Organism Orthologs (via OrthoDB)
    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
      esyN Network Diagram
      Interactions Browser
      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
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      External Data
      Linkouts
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      3R
      Recombination map
      3-59
      Cytogenetic map
      89E1-89E1
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      89E1-89E1
      Limits computationally determined from genome sequence between P{lacW}CSN5L4032 and P{EP}MESK4EP1015
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      89E2-89E2
      (Martin et al., 1995)
      Based on proximity to Ubx.
      (Martin et al., 1995)
      Experimentally Determined Recombination Data
      Location

      3-59

      (FlyBase, 2016)

      3-58.8

      (Comeron et al., 2012)

      3-

      (Martin et al., 1995)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (4)
      Genomic Clones (30)
      cDNA Clones (50)
       

      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
          DRSC - Results frm RNAi screens
          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: lncRNA:bxd bxd

          (FlyBase, 2009-)
          Source for database merge of
          Additional comments

          The "CG31275" annotation (FBgn0051275) is located within an intron of "bxd" (FBgn0020556). "CG31275" corresponds to the transcript in GenBank accession M27999 described as the "late bithoraxoid transcript" in FBrf0046282.

          (FlyBase Genome Annotators, 2002-2003)
          Other Comments

          dsRNA made from templates generated with primers directed against this gene has no effect on Ubx expression.

          (Petruk et al., 2006)

          Transcription of bxd, acting in cis, represses transcription of Ubx.

          (Petruk et al., 2006)

          dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology.

          (Kiger et al., 2003)

          New annotation (CR31273) in release 3 of the genome annotation.

          (FlyBase Genome Annotators, 2002-2003)

          The transcription unit that produces the noncoding bxd transcript has been identified.

          (Lewis et al., 1995)

          Non-coding RNA regulating Ubx.

          (Martin et al., 1995)
          Origin and Etymology
          Discoverer
          Etymology
          Identification
          External Crossreferences and Linkouts ( 30 )
          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
          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
          Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
          GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
          KEGG Genes - Molecular building blocks of life in the genomic space.
          MARRVEL_MODEL - MARRVEL (model organism gene)
          modMine - A data warehouse for the modENCODE project
          Linkouts
          DRSC - Results frm RNAi screens
          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
          Synonyms and Secondary IDs (7)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          References (85)