FlyBase Gene Report: Dmel\Lcp1Ψ

General Information

Symbol

Dmel\Lcp1Ψ

Species

D. melanogaster

Name

Larval cuticle protein 1 pseudogene

Annotation Symbol

CR30367

Feature Type

pseudogene

FlyBase ID

FBgn0011812

Gene Model Status

Current

Stock Availability

None publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Also Known As

Ψ1, LcpΨ

Key Links

Genomic Location

Cytogenetic map

44C6-44C6

Sequence location

2R:8,432,886..8,433,384 [-]

Recombination map

2-58

RefSeq locus

NT_033778 REGION:8432886..8433384

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\Lcp1Ψ 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 5.46

Pseudogene similar to Lcp1; proximate; created by tandem duplication.

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Lcp1Ψ-RA

FBtr0088762

NR_001387

456

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\Lcp1Ψ 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).

-0.19

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\Lcp1Ψ in JBrowse

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

View exonic expression by developmental stage for Dmel\Lcp1Ψ

View exonic expression by tissue for Dmel\Lcp1Ψ

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

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

FBgn0011812

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

FBgn0011812

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 ( 1 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Lcp1Ψ

Transgenic constructs containing regulatory region of Lcp1Ψ

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(2R)Exel6058

(Ryder, 2004.4.26)

Inferred from location ( 5 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

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:Lcp1Ψ. 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

nuclear_gene

pseudogene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-58

Cytogenetic map

44C6-44C6

Sequence location

2R:8,432,886..8,433,384 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

44C6-44C6

Limits computationally determined from genome sequence between P{lacW}Rs1^k09514&P{lacW}l(2)k03110^k03110 and P{lacW}Vps25^k08904&P{lacW}ptc^k02507

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-58

(FlyBase, 2016)

2-57.6

(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 (17)

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

DRSC - Results frm RNAi screens

FBgn0011812

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

New annotation (CR30367) in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Estimates of heterozygosity per nucleotide are lower that the average for many functional loci, this may be explained as the Lcp genes lie in a region of relatively low recombination. Low levels of within species polymorphism were unexpected due to the large number of nonsynonymous and synonymous substitutions between the pseudogene and parental genes. It is suggested that this low level of polymorphism results from genetic hitchiking due to directional selection at linked loci or from background selection against slightly deleterious alleles at linked sites.

(Schaeffer and Pritchard, 1995)

The chromatin structure of the larval cuticle gene cluster at 44D (Lcp1, Lcp1Ψ, Lcp2, Lcp3 and Lcp4) has been characterised in embryos.

(Eissenberg et al., 1984)

The structure of and absence of detectable transcript from Lcp1Ψ suggest it is non-functional. Sequence comparisons indicate that it arose by an unequal crossing-over event involving Lcp1 and Lcp2.

(Snyder et al., 1982)

Overall orientation not stated. Located in a group of four genes clustered within 7.9kb DNA. The order of the genes is Lcp1 Lcp1Ψ Lcp2 Lcp3 Lcp4.

(Snyder et al., 1982)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

CG30367

CR30367

Lcp1Psi

(Cornman, 2009, Purugganan, 1998)

Lcp1Ψ

(FlyBase Genome Annotators, 2012)

LcpΨ

(Petrov et al., 1998, Pritchard and Schaeffer, 1997)

Ψ1

(Steinemann and Steinemann, 1990, Kimbrell et al., 1989, Snyder et al., 1982)

ΨI

(Eissenberg et al., 1984)

ΨLcp

(Balakirev and Ayala, 2003)

Name Synonyms

Larval cuticle protein 1 pseudogene

Ψgene I

(Snyder et al., 1982)

Secondary FlyBase IDs

FBgn0050367

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 18 )

Sequence Crossreferences

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_001387

Other crossreferences

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

FBgn0011812

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

FBgn0011812

FlyMine - An integrated database for Drosophila genomics

FBgn0011812

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

dme:Dmel_CR30367

Linkouts

DRSC - Results frm RNAi screens

FBgn0011812

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0011812

References (22)

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

-0.19

Report Sections