FlyBase Gene Report: Dmel\lncRNA:CR42862

General Information

Symbol

Dmel\lncRNA:CR42862

Species

D. melanogaster

Name

long non-coding RNA:CR42862

Annotation Symbol

CR42862

Feature Type

lncRNA_gene

FlyBase ID

FBgn0262109

Gene Model Status

Current

Stock Availability

4 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

61B2-61B2

Sequence location

3L:224,106..230,964 [+]

Recombination map

3-1

RefSeq locus

NT_037436 REGION:224106..230964

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 (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (1 term)

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:CR42862 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 5.40

Many additional alternative transcripts (with variable internal introns) supported by cDNA and RNA-Seq junction data; only most prevalent isoforms represented.

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

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

Gene model reviewed during 5.45

Sequence Ontology: Class of Gene

gene_with_edited_transcript

(Rodriguez et al., 2012)

lncRNA_gene

nuclear_gene

(FlyBase Genome Annotators, 2010)

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

FBtr0304059

5480

FBtr0309035

5141

FBtr0309036

5427

FBtr0309037

5429

FBtr0309038

5420

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:CR42862 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).

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Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

organism | ubiquitous

(Schor et al., 2018)

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | intense | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | intense | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | intense | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

amnioserosa

(Fisher et al., 2012)

organism | intense | ubiquitous

(Fisher et al., 2012)

embryonic stage 13 -- 16

amnioserosa

(Fisher et al., 2012)

embryonic dorsal epidermis

(Fisher et al., 2012)

embryonic head epidermis

(Fisher et al., 2012)

embryonic ventral epidermis

(Fisher et al., 2012)

third instar larval stage

optic lobe neuroepithelial cell

(Wang et al., 2013)

Additional Descriptive Data

Expression is in nuclear foci and is ubiquitous.

(Schor et al., 2018)

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:CR42862 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:CR42862

View exonic expression by tissue for Dmel\lncRNA:CR42862

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

FBgn0262109

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

10178964/tissue=All

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

FBgn0262109

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

FBgn0262109

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 ( 13 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 1 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of lncRNA:CR42862

Transgenic constructs containing regulatory region of lncRNA:CR42862

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3L)Exel6084

(Ryder, 2004.4.26)

Inferred from location ( 0 )

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

lncRNA:CR42862^CB03898

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:CR42862. 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

DroID - A comprehensive database of gene and protein interactions.

FBgn0262109

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-1

Cytogenetic map

61B2-61B2

Sequence location

3L:224,106..230,964 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

61B2-61B2

Limits computationally determined from genome sequence between P{PZ}trh¹⁰⁵¹² and P{EP}EP3104^EP3104

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-1

(FlyBase, 2016)

3-0.0

(Comeron et al., 2012)

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

63381

w¹¹¹⁸; PBac{IT.GAL4}CG33229^0527-G4 lncRNA:CR42862^0527-G4

14847

w^*; P{EPgy2}lncRNA:CR42862^EY00429 CG33229^EY00429/TM6B, Tb¹

Kyoto

104071

w^*; P{GawB}lncRNA:CR42862^NP2049 / TM3, Sb¹ Ser¹

NIG-Fly

HMJ22334

y¹ v¹; P{TRiP.HMJ22334}attP40/CyO

Genomic Clones (22)

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

cDNA Clones (273)

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.

FBgn0262109

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0262109

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Annotation CG32477 renamed CR32477 in release 3.2 of the genome annotation.

(FlyBase Genome Annotators, 2004)

Release 2 annotation CG13878 (which was eliminated in release 3 of the genome annotation) overlaps the same region of the genome, on the same strand, as release 3 annotation CG32477 but the intron/exon structure of the two annotations is different.

(FlyBase Genome Annotators, 2002-2003)

Possibly a non-coding RNA.

(FlyBase Genome Annotators, 2002-2003)

Relationship to Other Genes

Source for database merge of

Source for merge of: CR32477 anon- EST:fe1H7

(FlyBase, 1996-)

Source for merge of: CR32477 CG16971

(FlyBase Genome Annotators, 2010)

Additional comments

Annotations CR32477 and CG16971 merged as CR42862 in release 5.30 of the genome annotation.

(FlyBase Genome Annotators, 2010)

The annotation corresponding to CG33229 was erroneously assigned to the CG16971 annotation in release 3.1 of the genome annotation, when it should have been a separate gene. This has been corrected in release 3.2 of the genome annotation so that CG33229 is annotated as a separate gene from CG16971.

(FlyBase Genome Annotators, 2004)

Nomenclature History

Source for database identify of

Source for identity of: lncRNA:CR42862 CR42862

(FlyBase, 2009-)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

BcDNA:GH06422

CG13878

CG16971

(Bartok et al., 2015, Buszczak et al., 2007, Altenhein et al., 2006, Lin and Kellis, 2006.12.15, Wong et al., 2005)

CG32477

(Giot et al., 2003)

CR32477

(Ellis and Carney, 2009, Zúñiga et al., 2009)

CR42862

(National Institute of Genetics Fly Stocks, 2023-, Pang et al., 2021, Clandinin and Owens, 2016-, DeSalvo et al., 2014, Wang et al., 2013, Rodriguez et al., 2012, FlyBase Genome Annotators, 2010)

anon-EST:fe1H7

lncRNA:CR42862

(Brunet Avalos et al., 2019)

Name Synonyms

anon-fast-evolving-1H7

long non-coding RNA:CR42862

Secondary FlyBase IDs

FBgn0052477
FBgn0025239
FBgn0035115
FBgn0046806
FBgn0260457
FBgn0035114

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 39 )

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.

10178964

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

FBgn0262109

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

10178964/tissue=All

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

FBgn0262109

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

FBgn0262109

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

dme:Dmel_CR42862

MARRVEL_MODEL - MARRVEL (model organism gene)

10178964

Linkouts

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

FBgn0262109

DroID - A comprehensive database of gene and protein interactions.

FBgn0262109

DRSC - Results frm RNAi screens

FBgn0262109

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0262109

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

References (38)

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

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