FlyBase Gene Report: Dmel\asRNA:CR11538

General Information

Symbol

Dmel\asRNA:CR11538

Species

D. melanogaster

Name

antisense RNA:CR11538

Annotation Symbol

CR11538

Feature Type

antisense_lncRNA_gene

FlyBase ID

FBgn0017424

Gene Model Status

Current

Stock Availability

None publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Pathway
Interactive Fly

Also Known As

lncRNA-CR11538, anon-68Ed

Key Links

Genomic Location

Cytogenetic map

68F5-68F5

Sequence location

3L:12,129,103..12,131,488 [-]

Recombination map

3-38

RefSeq locus

NT_037436 REGION:12129103..12131488

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 (6 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

enables protein sequestering activity

inferred from physical interaction with FLYBASE:Rel; FB:FBgn0014018

(Huang et al., 2024)

inferred from physical interaction with FLYBASE:Dif; FB:FBgn0011274,FLYBASE:dl; FB:FBgn0260632

(Zhou et al., 2021)

enables transcription regulator inhibitor activity

inferred from direct assay

(Zhou et al., 2021)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (3 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

involved_in negative regulation of antimicrobial peptide production

inferred from mutant phenotype

(Zhou et al., 2021)

involved_in negative regulation of peptidoglycan recognition protein signaling pathway

inferred from mutant phenotype

(Huang et al., 2024)

involved_in negative regulation of Toll signaling pathway

inferred from mutant phenotype

(Zhou et al., 2021)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

is_active_in nucleus

inferred from direct assay

(Zhou et al., 2021)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

Pathway (FlyBase)

Negative Regulators of Toll-NF-κB Signaling Pathway

Negative Regulators of Imd Signaling Pathway

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Pathway (FlyBase)

Negative Regulators of Toll-NF-κB Signaling Pathway -: In Drosophila, the canonical Toll signaling pathway is initiated by the binding of a spatzle ligand to Toll (Tl) or a Toll-like receptor leading to the nuclear localization of the NF-κB (dl or Dif) transcription factor. Negative regulators of Toll-NF-κB Signaling lead to the increased cytosolic retention of the NF-κB proteins dl or Dif and/or repression of target gene transcription. (Adapted from FBrf0091014 and FBrf0223077).
Negative Regulators of Imd Signaling Pathway -: Negative regulators of the immune deficiency (Imd) pathway result in the decreased activity of the NFκB-like transcription factor Rel in the nucleus. Negative regulators are important in preventing damage to the host from over-activation of the pathway; preventing inappropriate triggering or terminating the response. (Adapted from FBrf0224587 and FBrf0238555.)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\asRNA:CR11538 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 6.02

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

Antisense: overlaps Lsp2 on opposite strand.

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

asRNA:CR11538-RC

FBtr0347179

NR_133226

2386

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\asRNA:CR11538 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).

5.20

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

is_active_in nucleus

inferred from direct assay

(Zhou et al., 2021)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\asRNA:CR11538 in JBrowse

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

View exonic expression by developmental stage for Dmel\asRNA:CR11538

View exonic expression by tissue for Dmel\asRNA:CR11538

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

26067081/tissue=All

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

FBgn0017424

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0017424

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

FBgn0017424

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 0 )

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 asRNA:CR11538

Transgenic constructs containing regulatory region of asRNA:CR11538

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3L)Exel6116

(Ryder, 2004.4.26)

Inferred from location ( 7 )

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 immune response | adult stage

asRNA:CR11538^UAS.cZa

increased mortality | adult stage | conditional

asRNA:CR11538^UAS.cZa

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:asRNA:CR11538. 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

esyN Network Diagram

Show neighbor-neighbor interactions:

Off

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

Select Layout:

Force Directed

Circle

Concentric

Legend:

Protein

RNA

Selected Interactor(s)

Other Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

RNA-protein

Physical Interaction

Assay

References

asRNA:CR11538 - Dif

anti tag coimmunoprecipitation, quantitative reverse transcription pcr

(Zhou et al., 2021)

asRNA:CR11538 - Rel

anti tag coimmunoprecipitation, quantitative reverse transcription pcr

(Huang et al., 2024)

asRNA:CR11538 - dl

anti tag coimmunoprecipitation, quantitative reverse transcription pcr

(Zhou et al., 2021)

Summary of Genetic Interactions

esyN Network Diagram

Other Interaction Browsers

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.

FBgn0017424

Pathways

Signaling Pathways (FlyBase)

Negative Regulators of Toll-NF-κB Signaling Pathway
Negative Regulators of Imd Signaling Pathway

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

antisense_lncRNA_gene

(FlyBase Genome Annotators, 2015)

nuclear_gene

(FlyBase Genome Annotators, 2015)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-38

Cytogenetic map

68F5-68F5

Sequence location

3L:12,129,103..12,131,488 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

68F5-68F5

Limits computationally determined from genome sequence between P{PZ}rols⁰⁸²³²&P{lacW}l(3)j2D3^j2D3 and P{PZ}l(3)05088⁰⁵⁰⁸⁸

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-38

(FlyBase, 2016)

3-30.9

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (0)

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

Genomic Clones (11)

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

cDNA Clones (1)

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

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Annotation CG11538 restored as CR11538 in release 6.02 of the genome annotation.

(FlyBase Genome Annotators, 2014)

Annotation CG11538 eliminated in release 5.13 of the genome annotation.

(FlyBase Genome Annotators, 2008)

A 684 amino acid open reading frame included within Lsp2 but from the opposite strand.

Relationship to Other Genes

Source for database merge of

Source for merge of: anon-68Ed CG11538

(Misra, 2000.4.14)

Additional comments

Annotation Lsp2 on opposite strand represents correct CDS.

(FlyBase Genome Annotators, 2008)

Nomenclature History

Source for database identify of

Source for identity of: asRNA:CR11538 CR11538

(FlyBase, 2009-)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CG11538

(FlyBase Genome Annotators, 2008, Reiter et al., 2007, Lin and Kellis, 2006.12.15, Stanyon et al., 2004)

CR11538

(Pang et al., 2021, FlyBase Genome Annotators, 2015, FlyBase Genome Annotators, 2014)

LncRNA-CR11538

(Zhou et al., 2021)

anon-68Ed

(Burmester, 2000.3.29)

asRNA:CR11538

lncRNA-CR11538

(Huang et al., 2024, Huang et al., 2024)

Name Synonyms

antisense RNA:CR11538

Secondary FlyBase IDs

FBgn0036252

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 13 )

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.

26067081

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.

NR_133226

RNAcentral - A comprehensive ncRNA sequence collection representing all ncRNA types from a broad range of organisms

URS00009D92B3_7227

Other crossreferences

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

26067081/tissue=All

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

FBgn0017424

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

FBgn0017424

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

dme:Dmel_CR11538

MARRVEL_MODEL - MARRVEL (model organism gene)

26067081

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0017424

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0017424

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0017424

References (22)

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

5.20

Report Sections