FlyBase Gene Report: Dmel\lncRNA:bxd

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

produces non-coding RNA that may mediate or counteract epigenetic silencing - bxd RNA mediates recruitment of Ash1 to stimulates gene expression (Interactive Fly, lncRNA:bxd )

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Red Book
Interactive Fly

Also Known As

bxd

Key Links

Genomic Location

Cytogenetic map

89E1-89E1

Sequence location

3R:16,742,125..16,773,189 [-]

Recombination map

3-59

RefSeq locus

NT_033777 REGION:16742125..16773189

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (3 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in negative regulation of DNA-templated transcription

inferred from expression pattern

(Petruk et al., 2006)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in heterochromatin formation

inferred from electronic annotation with Rfam:RF01930

(RNAcentral, 2018-)

inferred from electronic annotation with Rfam:RF01930, Rfam:RF01931, Rfam:RF01932, Rfam:RF01933

(RNAcentral, 2018-)

inferred from electronic annotation with Rfam:RF01929

(RNAcentral, 2018-)

inferred from electronic annotation with Rfam:RF01930, Rfam:RF01934, Rfam:RF01935

(RNAcentral, 2018-)

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)

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)

produces non-coding RNA that may mediate or counteract epigenetic silencing - bxd RNA mediates recruitment of Ash1 to stimulates gene expression

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

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

Experimentally Determined Structures

Crossreferences

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

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

FBtr0083342

1258

FBtr0083343

1587

FBtr0083344

1755

FBtr0083341

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

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

NA

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

JBrowse - Visual display of RNA-Seq signals

View Dmel\lncRNA:bxd in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\lncRNA:bxd

View exonic expression by tissue for Dmel\lncRNA:bxd

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

3772220/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0020556

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0020556

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)Ubx^pbx-1

(Petruk et al., 2006)

Df(3R)Ubx^pbx-2

(Petruk et al., 2006)

Inferred from location ( 5 )

Variants

Variant Molecular Consequences

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 v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (0)

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (0)

Mus musculus (laboratory mouse) (0)

Xenopus tropicalis (Western clawed frog) (0)

Danio rerio (Zebrafish) (0)

Caenorhabditis elegans (Nematode, roundworm) (0)

Anopheles gambiae (African malaria mosquito) (0)

Arabidopsis thaliana (thale-cress) (0)

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:lncRNA:bxd. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (0)

Human Disease Associations

FlyBase Human Disease Model Reports

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 v9.1 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

Interaction Browsers

Summary of Genetic Interactions

Interaction Browsers

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

FlyBase

External Links

External Data

Linkouts

Class of Gene

lncRNA_gene

nuclear_gene

(FlyBase Genome Annotators, 2002-2003)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-59

Cytogenetic map

89E1-89E1

Sequence location

3R:16,742,125..16,773,189 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

89E1-89E1

Limits computationally determined from genome sequence between P{lacW}CSN5^L4032 and P{EP}MESK4^EP1015

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)

(Martin et al., 1995)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (4)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

63770

w¹¹¹⁸; PBac{IT.GAL4}lncRNA:bxd^0744-G4

79924

y¹ sc^* v¹ sev²¹; P{TOE.GS02193}attP40

77526

w¹¹¹⁸; PBac{IT.GAL4}lncRNA:bxd^0182-G4/TM6B, Tb¹

57550

y¹ sc^* v¹ sev²¹; P{TRiP.HMC04867}attP40

Genomic Clones (30)

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

SD07683

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

FBgn0020556

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

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)

Relationship to Other Genes

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)

Nomenclature History

Source for database identify of

Source for identity of: lncRNA:bxd bxd

(FlyBase, 2009-)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CR31273

(Ni et al., 2010.12.1)

CR31277

bxd

(Chetverina et al., 2022, Yue et al., 2022, Erokhin et al., 2021, Cang and Nie, 2020, Li et al., 2019, Kang et al., 2018, Liu et al., 2017, Transgenic RNAi Project members, 2017-, Clandinin and Owens, 2016-, Kahn et al., 2016, Garaulet and Lai, 2015, Fedoseeva and Tchurikov, 2013, Fujioka et al., 2013, Mallo and Alonso, 2013, McKay and Lieb, 2013, Pease et al., 2013, Saunders et al., 2013, Cunningham et al., 2010, Margueron et al., 2009, Tariq et al., 2009, Hauenschild et al., 2008, Davis et al., 2007, Holohan et al., 2007, Mito et al., 2007, Pease and Bender, 2007, Prasanth and Spector, 2007, Ringrose and Paro, 2007, Schuettengruber et al., 2007, Schwartz and Pirrotta, 2007, Gilfillan et al., 2006, Klymenko et al., 2006, Lemons and McGinnis, 2006, Mohd-Sarip et al., 2006, Petruk et al., 2006, Petruk et al., 2006, Schwartz et al., 2006, Mohd-Sarip et al., 2005, Schwartz et al., 2005, Zhimulev et al., 2003, Dellino et al., 2002, Huang et al., 2002, Rank et al., 2002, Hodgson et al., 2001)

bxd RNA

(Bender and Lucas, 2013)

lncRNA-bxd

(Li et al., 2019)

lncRNA:bxd

Name Synonyms

bithoraxoid

(Mallo and Alonso, 2013, McKay and Lieb, 2013, Pease et al., 2013, Lee et al., 2010, Davis et al., 2007, Petruk et al., 2006, Huang et al., 2002)

bxd

Secondary FlyBase IDs

FBgn0051273
FBgn0051277

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 28 )

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.

3772220

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

3772220/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0020556

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0020556

FlyMine - An integrated database for Drosophila genomics

FBgn0020556

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CR31273

MARRVEL_MODEL - MARRVEL (model organism gene)

3772220

Linkouts

DRSC - Results frm RNAi screens

FBgn0020556

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0020556

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

References (87)

The following external sites may use different assemblies or annotations than FlyBase.

NA

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