FlyBase Gene Report: Dmel\lncRNA:CR32652

General Information

Symbol

Dmel\lncRNA:CR32652

Species

D. melanogaster

Name

long non-coding RNA:CR32652

Annotation Symbol

CR32652

Feature Type

lncRNA_gene

FlyBase ID

FBgn0052652

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

Also Known As

NEST:bs14f06 , bs27e03.y1, bs14d08.y1, bs16e05.y1, bs24h05.y1

Key Links

Genomic Location

Cytogenetic map

11A9-11A9

Sequence location

X:12,411,018..12,412,181 [-]

Recombination map

1-38

RefSeq locus

NC_004354 REGION:12411018..12412181

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:CR32652 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.

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

Gene model reviewed during 6.02

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

lncRNA:CR32652-RB

FBtr0347270

NR_133521

888

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:CR32652 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).

3.59

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:CR32652 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:CR32652

View exonic expression by tissue for Dmel\lncRNA:CR32652

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

FBgn0052652

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

26067086/tissue=All

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

FBgn0052652

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0052652

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

FBgn0052652

Flygut - An atlas of the Drosophila adult midgut

FBgn0052652

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 lncRNA:CR32652

Transgenic constructs containing regulatory region of lncRNA:CR32652

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 37 )

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:CR32652^GD17196

viable, with Scer\GAL4^Mef2.PR

lncRNA:CR32652^GD17196

viable, with Scer\GAL4^pnr-MD237

lncRNA:CR32652^GD17196

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:CR32652. 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.

FBgn0052652

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

lncRNA_gene

nuclear_gene

(FlyBase Genome Annotators, 2014)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-38

Cytogenetic map

11A9-11A9

Sequence location

X:12,411,018..12,412,181 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

11A9-11A9

Limits computationally determined from genome sequence between P{EP}EP1451&P{EP}EP1629 and P{EP}CG11138^EP1313

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-38

(FlyBase, 2016)

1-38.9

(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

VDRC

v46894

w¹¹¹⁸; P{GD17196}v46894

v50030

w¹¹¹⁸; P{GD17196}v50030/TM3

Genomic Clones (22)

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

cDNA Clones (23)

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.

FBgn0052652

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0052652

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Annotation CG32652 renamed CR32652 in release 6.02 of the genome annotation.

(FlyBase Genome Annotators, 2014)

New annotation (CG32652) in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG32652 NEST:bs02c02 NEST:bs23h05 NEST:bs29d03 NEST:bs30c01 NEST:bs13e06 NEST:bs08g03

(Rana, 2004.7.8)

Source for merge of: CG32652 NEST:bs14f06

(FlyBase Genome Annotators, 2005)

Source for merge of: CG32652 NEST:bs16e05 NEST:bs24h05 NEST:bs27e03

(FlyBase, 1996-)

Source for merge of: CG32652 NEST:bs14d08

(FlyBase, 1996-)

Source for merge of: CG32652 NEST:bs27g02

(FlyBase, 1996-)

Additional comments

Source for merge of CG32652 NEST:bs14d08 was sequence comparison ( date:031022 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Source for identity of: lncRNA:CR32652 CR32652

(FlyBase, 2009-)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (26)

Reported As

Symbol Synonym

CG32652

(Hosono et al., 2015, Fukuoh et al., 2014, Chen et al., 2012, Artieri and Singh, 2010, Zhang et al., 2010)

CR32652

(FlyBase Genome Annotators, 2014)

NEST:bs02c02

NEST:bs08g03

NEST:bs13e06

NEST:bs14f06

(Rana, 2004.7.8)

NEST:bs16e05

NEST:bs23h05

NEST:bs24h05

NEST:bs27e03

NEST:bs27g02

NEST:bs29d03

NEST:bs30c01

bs02c02.y1

(Oliver, 2001.8.16)

bs08g03.y1

(Andrews et al., 2000)

bs13e06.y1

(Andrews et al., 2000)

bs14d08.y1