FlyBase Gene Report: Dmel\lncRNA:sphinx

General Information

Symbol

Dmel\lncRNA:sphinx

Species

D. melanogaster

Name

long non-coding RNA:sphinx

Annotation Symbol

CR34154

Feature Type

lncRNA_gene

FlyBase ID

FBgn0083990

Gene Model Status

Current

Stock Availability

1 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Also Known As

sphinx, spx

Key Links

Genomic Location

Cytogenetic map

102F4-102F4

Sequence location

4:975,168..977,261 [+]

Recombination map

4-0

RefSeq locus

NC_004353 REGION:975168..977261

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

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

NCBI

UCSC

Ensembl

Function

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 (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in male courtship behavior

inferred from mutant phenotype

(Dai et al., 2008)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in negative regulation of gene expression

inferred from electronic annotation with Rfam:RF02046, Rfam:RF02047

(RNAcentral, 2018-)

Cellular Component (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\lncRNA:sphinx 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

Gene model reviewed during 5.55

Probable lncRNA gene; may encode small polypeptide(s).

Gene model reviewed during 5.47

Gene model reviewed during 6.02

Gene model supported by FBrf0149156.

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

FBtr0111044

891

FBtr0111045

1235

FBtr0111046

643

FBtr0334622

467

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

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\lncRNA:sphinx 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).

-0.19

Transcript Expression

distribution deduced from reporter

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | male

male accessory gland

(Chen et al., 2011)

anterior ejaculatory duct

(Chen et al., 2011)

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | male

male accessory gland

(Dai et al., 2008)

Additional Descriptive Data

lncRNA:sphinx transcript is expressed in the accessory gland, but not in the testis.

(Dai et al., 2008)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

Reporter: P{sphinx-GFP.265}

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

antennal lobe glomerulus VA2

(Chen et al., 2011)

adult medial antennal lobe tract

(Chen et al., 2011)

prothoracic leg taste bristle

(Chen et al., 2011)

chemosensory neuron of anterior wing margin

(Chen et al., 2011)

adult stage | male

male accessory gland main cell

(Chen et al., 2011)

Reporter: P{sphinx-GFP.1067}

Stage

Tissue/Position (including subcellular localization)

Reference

larval stage

terminal organ

(Chen et al., 2011)

adult stage

antennal lobe glomerulus VA2

(Chen et al., 2011)

adult medial antennal lobe tract

(Chen et al., 2011)

prothoracic leg taste bristle

(Chen et al., 2011)

chemosensory neuron of anterior wing margin

(Chen et al., 2011)

adult labral sense organ

(Chen et al., 2011)

adult stage | male

male accessory gland main cell

(Chen et al., 2011)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\lncRNA:sphinx 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:sphinx

View exonic expression by tissue for Dmel\lncRNA:sphinx

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

4379815/tissue=All

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

FBgn0083990

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

FBgn0083990

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 ( 1 )

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:sphinx

Transgenic constructs containing regulatory region of lncRNA:sphinx

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(4)CORL

(Takaesu et al., 2012)

Inferred from location ( 9 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Other Phenotypes

Allele

abnormal courtship behavior | male limited

lncRNA:sphinx^720RW

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:sphinx. 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, 2006)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

4-0

Cytogenetic map

102F4-102F4

Sequence location

4:975,168..977,261 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

102F4-102F4

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

102F8-102F8

(determined by in situ hybridisation)

(Wang et al., 2002)

102F8-102F8

(Wang, 2002.1.30)

Experimentally Determined Recombination Data

Location

4-0

(FlyBase, 2016)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (1)

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

Bloomington

67977

y¹ v¹; P{TRiP.HMS05838}attP2

Genomic Clones (7)

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

cDNA Clones (95)

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

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

FBgn0083990

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

New annotation (CR34154) in release 5.1 of the genome annotation.

(FlyBase Genome Annotators, 2006)

Relationship to Other Genes

Source for database merge of

Additional comments

The sphinx gene appears to have been formed by the insertion of a retroposed sequence of the ATP synthase F-chain gene from chromosome 2 (CG4692) into the 102F region of chromosome 4, recruiting sequences upstream to form a new locus.

(Dai et al., 2008)

The "sphinx" gene (AF479655) had mistakenly been associated with the CG11091 annotation in FlyBase. This was in error, since the CG11091 annotation is on the opposite strand to the "sphinx" gene. A new annotation corresponding to "sphinx", CR34154, has been created in release 5.1 of the genome annotation.

(FlyBase Genome Annotators, 2006)

The sphinx gene on the 4th chromosome appears to be a chimeric gene, with the second exon having all the hallmarks of a retrosequence derived from the CG4692 gene on the 2nd chromosome. In addition, the retroposition process appears to have involved an S-element, leaving a partial S-element fragment attached the CG4692-derived region in the sphinx gene. The retrosequence has recruited a nearby exon and intron in the 4th chromosome, thereby evolving a chimeric gene structure.

(Wang et al., 2002)

Nomenclature History

Source for database identify of

Source for identity of: lncRNA:sphinx sphinx

(FlyBase, 2009-)

Nomenclature comments

Etymology

The "sphinx" gene is a young chimeric RNA gene and is named "sphinx" to invoke an analogy to another chimera, the Sphinx from ancient Greek legend having a lion's body and a human head.

(Wang et al., 2002)

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CR34154

(Ni et al., 2012, Zhan et al., 2011, FlyBase Genome Annotators, 2006)

Sphinx

(Mbodj et al., 2013)

lncRNA-Sphinx

(Li et al., 2019)

lncRNA:sphinx

(Goldsmith et al., 2022)

sphinx

(Dimitriadou et al., 2020, Hall et al., 2019, Li et al., 2019, Tran et al., 2018, Housden et al., 2017, Ni et al., 2012, Takaesu et al., 2012, Chen et al., 2011, Dai et al., 2008, Yang et al., 2008, Podemski et al., 2004, Wang et al., 2002)

spx

(Wang et al., 2004, Wang, 2002.1.30, Wang et al., 2002)

Name Synonyms

Sphinx

(Lindsay and Wasserman, 2014, Kurata, 2010)

long non-coding RNA:sphinx

sphinx

(Chen et al., 2011, Pfeiffer et al., 2008, Yang et al., 2008, Wang, 2002.1.30, Wang et al., 2002)

Secondary FlyBase IDs

FBgn0039931

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 20 )

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.

4379815

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

AF479655

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

4379815/tissue=All

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

FBgn0083990

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

FBgn0083990

FlyMine - An integrated database for Drosophila genomics

FBgn0083990

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

dme:Dmel_CR34154

MARRVEL_MODEL - MARRVEL (model organism gene)

4379815

Linkouts

DRSC - Results frm RNAi screens

FBgn0083990

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0083990

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

References (28)

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

-0.19

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