FlyBase Gene Report: Dmel\lncRNA:CR31781

General Information

Symbol

Dmel\lncRNA:CR31781

Species

D. melanogaster

Name

long non-coding RNA:CR31781

Annotation Symbol

CR31781

Feature Type

lncRNA_gene

FlyBase ID

FBgn0051781

Gene Model Status

Current

Stock Availability

2 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

36B3-36B3

Sequence location

2L:16,869,346..16,878,300 [+]

Recombination map

2-53

RefSeq locus

NT_033779 REGION:16869346..16878300

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 (1 term)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in lateral inhibition

inferred from mutant phenotype

(Mummery-Widmer et al., 2009)

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:CR31781 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 5.50

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.40

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

Gene model reviewed during 5.56

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

FBtr0308925

2340

FBtr0308926

2441

FBtr0308927

2563

FBtr0308928

1434

FBtr0308929

2337

FBtr0346590

2557

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:CR31781 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).

-0.44

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 13 -- 16

larval somatic muscle cell

(Fisher et al., 2012)

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:CR31781 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:CR31781

View exonic expression by tissue for Dmel\lncRNA:CR31781

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

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0051781

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

12798248/tissue=All

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

FBgn0051781

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0051781

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

FBgn0051781

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

Flygut - An atlas of the Drosophila adult midgut

FBgn0051781

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\lncRNA:CR31781

Stages(s) 1-3
Stages(s) 9-10
Stages(s) 11-12
Stages(s) 13-16

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 2 )

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:CR31781

Transgenic constructs containing regulatory region of lncRNA:CR31781

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene disrupted in

Df(2L)Exel6039

(Ryder, 2004.4.26)

Df(2L)Exel8036

(Ryder, 2004.4.26)

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.

Lethality

Allele

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

lncRNA:CR31781^GD1715

viable, with Scer\GAL4^pnr-MD237

lncRNA:CR31781^GD1715

Other Phenotypes

Allele

visible, with Scer\GAL4^pnr-MD237

lncRNA:CR31781^GD1715

Phenotype manifest in

Allele

chaeta, with Scer\GAL4^pnr-MD237

lncRNA:CR31781^GD1715

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:CR31781. 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

DroID - A comprehensive database of gene and protein interactions.

FBgn0051781

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

lncRNA_gene

nuclear_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-53

Cytogenetic map

36B3-36B3

Sequence location

2L:16,869,346..16,878,300 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

36B3-36B3

Limits computationally determined from genome sequence between P{lacW}Mhc^k10423&P{lacW}Cas^k03902 and P{lacW}Aac11^k06710

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-53

(FlyBase, 2016)

2-51.3

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (2)

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

Bloomington

53145

y¹ w^*; Mi{MIC}lncRNA:CR31781^MI09653

59431

y¹ w^*; Mi{MIC}lncRNA:CR31781^MI13131

Genomic Clones (16)

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

cDNA Clones (24)

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.

FBgn0051781

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0051781

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Annotation CG31781 renamed CR31781 in release 5.40 of the genome annotation.

(FlyBase Genome Annotators, 2011)

Gene expression is increased in response to the presence of either one or two copies of Scer\GAL4^hs.PB.

(Liu and Lehmann, 2008)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG15132 BcDNA:GH27691

(FlyBase, 1996-)

Source for merge of: CG15131 CG15132

(FlyBase Genome Annotators, 2002-2003)

Source for merge of: CG31781 BcDNA:LP04536

(FlyBase, 1996-)

Additional comments

Annotations CG15131 and CG15132 merged as CG31781 in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Source for merge of CG15132 BcDNA:GH27691 was a shared cDNA ( date:020730 ).

(FlyBase, 1996-)

Source for merge of CG31781 BcDNA:LP04536 was a shared cDNA ( date:030728 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Source for identity of: lncRNA:CR31781 CR31781

(FlyBase, 2009-)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (8)

Reported As

Symbol Synonym

BcDNA:GH27691

BcDNA:LP04536

CG15131

(Arbeitman et al., 2002)

CG15132

CG31781

(Dialynas et al., 2015, Hosono et al., 2015, Herranz et al., 2010, Kim et al., 2010, Keleman et al., 2009.8.5, Lebo et al., 2009, Liu and Lehmann, 2008, Zeitlinger et al., 2007, Lin and Kellis, 2006.12.15)

CR31781

(Stobdan et al., 2019, Yang et al., 2016, FlyBase Genome Annotators, 2011)

lncRNA:CR31781

(Zhang et al., 2023)

Name Synonyms

long non-coding RNA:CR31781

Secondary FlyBase IDs

FBgn0032616
FBgn0032617
FBgn0061422
FBgn0063119

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 33 )

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.

12798248

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

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0051781

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

12798248/tissue=All

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

FBgn0051781

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

FBgn0051781

FlyMine - An integrated database for Drosophila genomics

FBgn0051781

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

dme:Dmel_CR31781

MARRVEL_MODEL - MARRVEL (model organism gene)

12798248

Linkouts

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0051781

DroID - A comprehensive database of gene and protein interactions.

FBgn0051781

DRSC - Results frm RNAi screens

FBgn0051781

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0051781

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0051781

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

Flygut - An atlas of the Drosophila adult midgut

FBgn0051781

References (31)

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

-0.44

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