FlyBase Gene Report: Dmel\lncRNA:CR46499

General Information

Symbol

Dmel\lncRNA:CR46499

Species

D. melanogaster

Name

long non-coding RNA:CR46499

Annotation Symbol

CR46499

Feature Type

lncRNA_gene

FlyBase ID

FBgn0288701

Gene Model Status

Current

Stock Availability

5 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Also Known As

lncRNA:CR45484 , lincRNA.947

Key Links

Genomic Location

Cytogenetic map

4C2-4C2

Sequence location

X:4,373,271..4,383,220 [+]

Recombination map

1-8

RefSeq locus

NC_004354 REGION:4373271..4383220

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 (0 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

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:CR46499 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

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry M9NFW1)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Gene model reviewed during 5.56

Supported by strand-specific RNA-Seq data.

Gene model reviewed during 6.46

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

Gene model reviewed during 6.03

Gene model reviewed during 5.51

Gene model reviewed during 5.40

Gene model reviewed during 5.54

Gene model may be incomplete.

Gene model based on FBrf0251019.

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

lncRNA:CR46499-RD

FBtr0481675

NR_182250

5852

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:CR46499 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

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\lncRNA:CR46499 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:CR46499

View exonic expression by tissue for Dmel\lncRNA:CR46499

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

19835710/tissue=All

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

FBgn0288701

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

FBgn0288701

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 3 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 3 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of lncRNA:CR46499

Transgenic constructs containing regulatory region of lncRNA:CR46499

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 13 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

lncRNA:CR46499^GD15314

viable, with Scer\GAL4^Mef2.PR

lncRNA:CR46499^GD15314

viable, with Scer\GAL4^pnr-MD237

lncRNA:CR46499^GD15314

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:CR46499. 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

Other Interaction Browsers

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

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

lncRNA_gene

(FlyBase Genome Annotators, 2022)

nuclear_gene

(FlyBase Genome Annotators, 2014)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-8

Cytogenetic map

4C2-4C2

Sequence location

X:4,373,271..4,383,220 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

4C2-4C2

Limits computationally determined from genome sequence between P{EP}CG2930^EP1352 and P{EP}EP425

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-8

(FlyBase, 2016)

1-6.6

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (5)

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

Bloomington

63824

w¹¹¹⁸ PBac{IT.GAL4}lncRNA:CR46499^0802-G4

41023

y¹ w^* Mi{MIC}lncRNA:CR46499^MI01862

94388

w^* TI{CRIMIC.TG4.0}lncRNA:CR46499^{CR60343-TG4.0}

VDRC

v103348

P{KK112958}VIE-260B

v29878

w¹¹¹⁸; P{GD15314}v29878

Genomic Clones (13)

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

cDNA Clones (0)

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

New annotation (CR45484) in release 5.56 of the genome annotation.

(FlyBase Genome Annotators, 2014)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG12688 lncRNA:CR45484

(FlyBase Genome Annotators, 2022)

Additional comments

Annotations CG12688 and CR45484 merged as CR46499 in release 6.46 of the genome annotation; merge based on NCBI Gnomon analysis.

(FlyBase Genome Annotators, 2022)

Nomenclature History

Source for database identify of

Source for identity of: lncRNA:CR45484 CR45484

(FlyBase, 2009-)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (9)

Reported As

Symbol Synonym

CG12688

(Murphy, 2021.9.2, Murphy, 2021.9.2, Gene Disruption Project members, 2018-, Keleman et al., 2009.8.5, Lin and Kellis, 2006.12.15, Negre et al., 2006)

CR45484

(Clandinin and Owens, 2016-, FlyBase Genome Annotators, 2014)

CR46499

(FlyBase Genome Annotators, 2022)

FBgn0029707

(Heames et al., 2020)

lincRNA.947

(FlyBase Genome Annotators, 2014, Young et al., 2012)

lncRNA:CR45484

(Murphy, 2021.9.2, Murphy, 2021.9.2)

lncRNA:CR46499

Name Synonyms

long non-coding RNA:CR45484

long non-coding RNA:CR46499

Secondary FlyBase IDs

FBgn0029707
FBgn0267040

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.

19835710

GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

NR_182250

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

URS000234A4A6_7227

UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

M9NFW1

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

M9NFW1

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

19835710/tissue=All

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

FBgn0288701

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

FBgn0288701

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

dme:Dmel_CR46499

MARRVEL_MODEL - MARRVEL (model organism gene)

19835710

Linkouts

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0288701

References (25)

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

NA

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