FlyBase Gene Report: Dmel\LysC

General Information

Symbol

Dmel\LysC

Species

D. melanogaster

Name

Lysozyme C

Annotation Symbol

CR9111

Feature Type

pseudogene

FlyBase ID

FBgn0004426

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

Lys C

Key Links

Genomic Location

Cytogenetic map

61F3-61F3

Sequence location

3L:1,210,485..1,210,726 [+]

Recombination map

3-0

RefSeq locus

NT_037436 REGION:1210485..1210726

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\LysC 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 5.41

Gene model reviewed during 5.46

Pseudogene similar to LysD; proximate; partial; deletion of 3' end and intergenic region.

Gene model reviewed during 6.04

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

LysC-RB

FBtr0347605

242

Additional Transcript Data and Comments

Reported size (kB)

0.480 (longest cDNA)

(Daffre et al., 1994)

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\LysC using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

LysC_1

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).

-0.40

Transcript Expression

No Assay Recorded

Stage

Tissue/Position (including subcellular localization)

Reference

larval stage

embryonic/larval midgut

(Daffre et al., 1994)

RNase protection, primer extension, SI map

Stage

Tissue/Position (including subcellular localization)

Reference

larval stage & adult stage

(Daffre et al., 1994)

adult stage

adult midgut

(Daffre et al., 1994)

Additional Descriptive Data

LysC transcripts are detected in the feeding stages (larvae and adults) with maximal expression in third instar larvae. This expression pattern was surmised from RNase protection experiments with a probe from the closely related LysD gene.

(Daffre et al., 1994)

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\LysC in JBrowse

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

View exonic expression by developmental stage for Dmel\LysC

View exonic expression by tissue for Dmel\LysC

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

38126/tissue=All

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

FBgn0004426

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

FBgn0004426

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 LysC

Transgenic constructs containing regulatory region of LysC

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3L)LysB-P-Δ

(Marra et al., 2021)

Inferred from location ( 10 )

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) (8)

Hsap\LALBA

1 of 14

Yes

Hsap\LYZ

1 of 14

Yes

Hsap\LYZL1

1 of 14

Yes

Hsap\LYZL2

1 of 14

Yes

Hsap\LYZL4

1 of 14

Yes

Hsap\LYZL6

1 of 14

Yes

Hsap\SPACA3

1 of 14

Yes

Hsap\SPACA5B

1 of 14

Yes

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (9)

Rnor\Lalba

1 of 14

Yes

Rnor\Lyc2

1 of 14

Yes

Rnor\Lyz2

1 of 14

Yes

Rnor\Lyzl1

1 of 14

Yes

Rnor\Lyzl4

1 of 14

Yes

Rnor\Lyzl6

1 of 14

Yes

Rnor\RGD1306474

1 of 14

Yes

Rnor\Spaca3

1 of 14

Yes

Rnor\Spaca5

1 of 14

Yes

Mus musculus (laboratory mouse) (9)

Mmus\9530003J23Rik

1 of 14

Yes

Mmus\Lalba

1 of 14

Yes

Mmus\Lyz1

1 of 14

Yes

Mmus\Lyz2

1 of 14

Yes

Mmus\Lyzl1

1 of 14

Yes

Mmus\Lyzl4

1 of 14

Yes

Mmus\Lyzl6

1 of 14

Yes

Mmus\Spaca3

1 of 14

Yes

Mmus\Spaca5

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (3)

Xtro\LOC100493330

1 of 13

Yes

Xtro\lyz

1 of 13

Yes

Xtro\MGC89221

1 of 13

Yes

Danio rerio (Zebrafish) (1)

Drer\lyz

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (0)

Anopheles gambiae (African malaria mosquito) (5)

Agam\LYSC1_ANOGA

1 of 12

Yes

Agam\LYSC2

1 of 12

Yes

Agam\LYSC3

1 of 12

Yes

Agam\LYSC5

1 of 12

Yes

Agam\LYSC8

1 of 12

Yes

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:LysC. 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) (12)

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

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.

FBgn0004426

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

gene_with_edited_transcript

(Graveley et al., 2011)

nuclear_gene

pseudogene

(FlyBase Genome Annotators, 2015)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-0

Cytogenetic map

61F3-61F3

Sequence location

3L:1,210,485..1,210,726 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

61F3-61F3

Limits computationally determined from genome sequence between P{PZ}l(3)05967⁰⁵⁹⁶⁷ and P{PZ}l(3)02640⁰²⁶⁴⁰

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

61F-61F

(determined by in situ hybridisation)

(Kylsten et al., 1988)

Experimentally Determined Recombination Data

Location

3-0

(FlyBase, 2016)

3-1.5

(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

64545

y¹ sc^* v¹ sev²¹; P{TRiP.HMC05564}attP40

NIG-Fly

HMJ21466

y¹ v¹; P{TRiP.HMJ21466}attP40/CyO

Genomic Clones (15)

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

FBgn0004426

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Annotation CG9111 renamed CR9111 in release 6.04 of the genome annotation.

(FlyBase Genome Annotators, 2015)

The strain whose genome sequence is reported in FBrf0155827 is mutant at LysC, not LysE as was reported on page 19 of FBrf0155827.

(Misra, 2004.1.7)

FlyBase curator comment: The reference to "LysE" on page 19 is a typographical error - the gene meant is LysC. See Misra, 2004.1.7, personal communication to FlyBase.

(Misra et al., 2002)

Lysozymes are expressed at a high level mainly in the digestive tract, they are not a component of the haemolymph. Lysozyme is not induced by bacteria so is not part of the inducible immune response but instead has been recruited for digestion of symbiotic bacteria in the stomach.

(Daffre et al., 1994)

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 (6)

Reported As

Symbol Synonym

CG9111

(Palu and Thummel, 2016, Meadows, 2014.12.12, Ni et al., 2010.12.1, Li et al., 2009, Perkins et al., 2009)

CR9111

(FlyBase Genome Annotators, 2015)

Lys C

(Burgess et al., 2004, Roxstrom-Lindquist et al., 2004)

LysC

(Liang et al., 2024, Gallo et al., 2022, Marra et al., 2021, Štětina et al., 2019, FlyBase Genome Annotators, 2015, Short and Lazzaro, 2013, Rynes et al., 2012, Findlay et al., 2009, Li et al., 2009, Blanco et al., 2008, Kwon et al., 2008, Yan et al., 2008, Waterhouse et al., 2007)

lysC

(Lemaitre, 2000.12.20)

Name Synonyms

Lysozyme C

(Hurlbut et al., 2009, Rollmann et al., 2008, Roxstrom-Lindquist et al., 2004)

Secondary FlyBase IDs

FBgn0002575

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.

38126

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

Z22226

Other crossreferences

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

38126/tissue=All

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

FBgn0004426

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

FBgn0004426

FlyMine - An integrated database for Drosophila genomics

FBgn0004426

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

dme:Dmel_CR9111

MARRVEL_MODEL - MARRVEL (model organism gene)

38126

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0004426

DRSC - Results frm RNAi screens

FBgn0004426

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

LysC_1

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0004426

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0004426

References (50)

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

-0.40

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