A Database of Drosophila Genes & Genomes

FB2008_06, released July 3, 2008
 

Gene Dmel\bxd

General Information
SymbolDmel\bxdSpeciesD. melanogaster
NamebithoraxoidAnnotation symbolCR31273
Feature typenon_protein_coding_geneFlyBase IDFBgn0020556
Created / Updated2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)3RRecombination map3-
Cytogenetic map 89E1-89E1 Sequence location3R:12,567,847..12,598,911 [-]
Map ( GBrowse ) detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
The gene bithoraxoid is referred to in FlyBase by the symbol bxd (CR31273, FBgn0020556). It has the cytological map location 89E1. Its sequence location is 3R:12567847..12598911. Its molecular function is described as specific transcriptional repressor activity. The biological processes in which it is involved are not known. 2 alleles are reported. No phenotypic data is available. It has 4 annotated transcripts.

External Summaries

hide Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage
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).
hide Detailed Mapping Data
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
Based on proximity to Ubx.  
(Martin et al., 1995)
Experimentally Determined Recombination Data
Location
3-
(Martin et al., 1995)
Left of (cM)
Right of (cM)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology)
References
In direction of increasing cytology: Fas1+ nonA-l+ Cctγ+ CG14906- CG31217- CG31217- Ubx- bxd- Glut3+ abd-A- iab-4+ CG10349+ Abd-B- Actn3- Ahcy89E-
(Martin et al., 1995)
Gene Order (overall orientation not stated)
References
hide Gene Model & Products
Please see the GBrowse view of Dmel\bxd for information on other features
detailed view FBtr0083346 FBtr0083345 FBpp0082792 FBpp0082791
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
 
bxd-RA
FBtr0083342
 NR_002034
  1258
 
bxd-RB
FBtr0083343
 NR_002033
  1576
 
bxd-RC
FBtr0083344
 NR_002032
  1755
 
bxd-RD
FBtr0083341
 NR_002035
  1124
 
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
 
Name
AY069828
 
AY118756
 
CO194902
 
CO284737
 
CO293279
 
CO295629
 
CO328362
 
CO341389
 
EC063751
 
EC079694
 
EC090417
 
EC212860
 
EC253468
 
M27988
 
M27990
 
M27992
 
M27993
 
M27995
 
M27997
 
M27998
 
 
Maps to
Does NOT map to
Identified with
hide Mapped Features & Mutations
Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here
Type
Symbol & Location
Additional Notes
References
hide External Data
Linkouts
Crossreferences
hide Expression Data
FlyBase-Curated Data
Transcript data Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
hide Summary of Transcript Expression
Stage
Tissue/Position
Reference
Marker for
    Subcellular Localization
    CV Term
    hide External Data & Images
    Linkouts
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    •
    GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies
    •
    hide Alleles & Phenotypes
    hide Summary of Allele Phenotypes
    Phenotype manifest in
    Allele
    hide Classical Alleles ( 2 )
    For All Classical Alleles Show

    Allele of bxdClassMutagenStocksKnown lesion
    bxdpbx-1
      		0 Yes
      bxdpbx-2
        		0 Yes
        hide Alleles Carried on Transgenic Constructs ( 0 )
        For All Alleles Carried on Transgenic Constructs Show

        Allele of bxdClassMutagenStocksKnown lesion
        hide Aneuploid Aberrations
        Useful duplication
         
        Partially disrupted in
        (Petruk et al., 2006)
        (Petruk et al., 2006)
        hide Transgenic Constructs & Insertions
        Transgenic Constructs
        Type of construct
        Name
        Expression data
        Insertions
        Type of insertions
        Name
        Expression data
        hide Related Comments
        Please look at the allele reports for the complete phenotype data
        hide Gene Ontology: Function, Process & Cellular Component ( 2 )
        hide Molecular Function
        CV term
        Evidence
        References
        specific transcriptional repressor activity
        inferred from mutant phenotype
        (Petruk et al., 2006)
        hide Biological Process
        CV term
        Evidence
        References
        hide Cellular Component
        CV term
        Evidence
        References
        colocalizes_with
        chromatin
        inferred from direct assay
        (Sanchez-Elsner et al., 2006)
        hide Sequence Ontology: Class of Gene
        non_protein_coding_gene
        (FlyBase Genome Annotators, 2002-2003)
        nuclear_gene
        (FlyBase Genome Annotators, 2002-2003)
        hide Interactions & Pathways
        hide Summary of Genetic Interactions
        Interacts with
        Please look at the allele data for full details of the genetic interactions
        bxd allele
        Gene
        References
        hide External Data
        Linkouts
        BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions
        •
        hide Orthologs
        Genome-wide drosophilid orthologs
        Curated drosophilid orthologs
         
         
         
         
         
         
        Linkouts
        hide Functional Complementation between Species
        hide Inter-Species Misexpression Data
        Produces phenotype in
        Produces NO phenotype in
        hide Stocks & Reagents
        hide Stocks Listed in FlyBase ( 0 )
        hide Genomic Clones ( 1 )
        hide cDNA Clones ( 8 )
        cDNA Clones, Fully Sequenced
        BDGP DGC clones
        Other clones
        cDNA Clones, End Sequenced (ESTs)
        BDGP DGC clones
        Other clones
        hide RNAi & Array Information
        Affy Oligo
        Linkouts
        DRSC - RNAi screening (Harvard): high-throughput cell culture data and design
        •
        hide Other Information
        hide Discoverer
        hide Etymology
        hide Identification
        hide Position Effect Variegation Data
        hide Relationship to Other Genes
        Source for database identity of
        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)
        hide Comments About Role
        Non-coding RNA regulating Ubx.
        (Martin et al., 1995)
        Transcription of bxd, acting in cis, represses transcription of Ubx.
        (Petruk et al., 2006)
        hide Comments About Molecular Function
        dsRNA made from templates generated with primers directed against this gene has no effect on Ubx expression.
        (Petruk et al., 2006)
        Noncoding bxd transcripts facilitate Ubx transcription by recruiting ash1 protein to the bxd TREs (trithorax response elements).
        (Sanchez-Elsner et al., 2006)
        hide Other Comments
        The transcription unit that produces the noncoding bxd transcript has been identified.
        (Lewis et al., 1995)
        New annotation (CR31273) in release 3 of the genome annotation.
        (FlyBase Genome Annotators, 2002-2003)
        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)
        hide External Crossreferences & Linkouts
        Sequence Crossreferences
        RefSeq (Transcripts)
        •
        DDBJ / EMBL / GenBank
        •
        Other Crossreferences
        Linkouts
        BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions
        •
        DRSC - RNAi screening (Harvard): high-throughput cell culture data and design
        •
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        •
        FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans
        •
        GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies
        •
        Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
        •
        hide Synonyms & Secondary IDs ( 4 )
        Reported As
        Symbol Synonym
        bxd
        (Schwartz and Pirrotta, 2007, Pease and Bender, 2007, Petruk et al., 2006, Petruk et al., 2006, Schuettengruber, 2006, Sanchez-Elsner et al., 2006, Gilfillan et al., 2006, Klymenko et al., 2006, Lemons and McGinnis, 2006, Prasanth and Spector, 2007, Rank et al., 2002, Huang et al., 2002, Hodgson et al., 2001, Mito et al., 2007)
        CR31273
         
        CR31277
         
        Name Synonym
        bithoraxoid
        (Petruk et al., 2006, Huang et al., 2002)
        bxd
         
        Secondary FlyBase IDs
        • FBgn0051273
        • FBgn0051277
        hide References ( 44 )
        Generate a list of
        List References by type
        hide Recent research papers ( 5 )
        Mito et al., 2007, Science 315(5817): 1408--1411
        Histone replacement marks the boundaries of cis-regulatory domains. [FBrf0193797]
        Gilfillan et al., 2006, Genes Dev. 20(7): 858--870
        Chromosome-wide gene-specific targeting of the Drosophila dosage compensation complex. [FBrf0190543]
        Klymenko et al., 2006, Genes Dev. 20(9): 1110--1122
        A Polycomb group protein complex with sequence-specific DNA-binding and selective methyl-lysine-binding activities. [FBrf0190547]
        Petruk et al., 2006, Cell 127(5): 1209--1221
        Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in cis by transcriptional interference. [FBrf0192625]
        Sanchez-Elsner et al., 2006, Science 311(5764): 1118--1123
        Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax. [FBrf0190616]
        Show all research papers ...
        hide Recent reviews ( 4 )
        Prasanth and Spector, 2007, Genes Dev. 21(1): 11--42
        Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. [FBrf0193472]
        Schwartz and Pirrotta, 2007, Nature Rev. Genet. 8(1): 9--22
        Polycomb silencing mechanisms and the management of genomic programmes. [FBrf0193718]
        Lemons and McGinnis, 2006, Science 313(5795): 1918--1922
        Genomic evolution of Hox gene clusters. [FBrf0200009]
        Schuettengruber, 2006, Cell 128(4): 735--745
        Genome regulation by polycomb and trithorax proteins. [FBrf0198664]
        Show all reviews ...