FlyBase Gene Report: Dmel\CG42540

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\CG42540 using the Feature Mapper tool.

External Data

Crossreferences

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

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

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

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\CG42540 in JBrowse

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

View exonic expression by developmental stage for Dmel\CG42540

View exonic expression by tissue for Dmel\CG42540

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

38562/tissue=All

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

FBgn0260657

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

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

FBgn0260657

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

CG32245

Flygut - An atlas of the Drosophila adult midgut

FBgn0260657

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 7 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 5 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of CG42540

Transgenic constructs containing regulatory region of CG42540

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3L)Exel7208

(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.

Lethality

Allele

viable

CG42540^f01008

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

viable, with Scer\GAL4^Mef2.PR

viable, with Scer\GAL4^pnr-MD237

viable, with Scer\GAL4^tin.CΔ4

CG42540^GD4559

Sterility

Allele

fertile

CG42540^f01008

Other Phenotypes

Allele

abnormal circadian rhythm

CG42540^MB01413

visible, with Scer\GAL4^pnr-MD237

CG42540^GD13041

Phenotype manifest in

Allele

trichogen cell, with Scer\GAL4^pnr-MD237

CG42540^GD13041

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) (10)

Hsap\STOM

13 of 14

Yes

Hsap\STOML3

9 of 14

Yes

Hsap\NPHS2

5 of 14

Yes

Hsap\STOML1

3 of 14

Yes

2 of 14

2 of 14

2 of 14

1 of 14

Yes

Hsap\FLOT1

1 of 14

Hsap\FLOT2

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (7)

Rnor\Stom

13 of 14

Yes

Rnor\Nphs2

6 of 14

Yes

Rnor\Stoml3

6 of 14

Yes

Rnor\Stoml1

3 of 14

Yes

Rnor\Stoml2

2 of 14

Rnor\Phb2

1 of 14

Rnor\Phb

1 of 14

Mus musculus (laboratory mouse) (8)

Mmus\Stom

13 of 14

Yes

Mmus\Stoml3

9 of 14

Yes

Mmus\Nphs2

4 of 14

Yes

Mmus\Stoml1

3 of 14

Yes

2 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (11)

Xtro\stom

10 of 13

Yes

3 of 13

2 of 13

2 of 13

2 of 13

Yes

Xtro\stoml1

2 of 13

Yes

Xtro\erlin1

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Danio rerio (Zebrafish) (13)

Drer\stom

13 of 14

Yes

Drer\stoml3b

11 of 14

Yes

Drer\zgc:112408

8 of 14

Yes

Drer\stoml3a

6 of 14

Drer\nphs2

4 of 14

Yes

Drer\stoml1

3 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (13)

Cele\sto-2

11 of 14

Yes

Cele\mec-2

6 of 14

Cele\sto-3

6 of 14

Yes

6 of 14

5 of 14

5 of 14

4 of 14

4 of 14

3 of 14

2 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (6)

Agam\BND7A_ANOGA

11 of 12

Yes

4 of 12

2 of 12

2 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (16)

Atha\AT5G51570

3 of 13

Yes

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

1 of 13

Yes

Atha\AT4G27580

1 of 13

Yes

Atha\AT5G54095

1 of 13

Yes

Atha\PHB6

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\PHB1

2 of 13

Yes

Scer\PHB2

2 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\SPBC16G5.07c

2 of 12

Yes

Spom\phb1

1 of 12

Spom\phb2

1 of 12

Escherichia coli (enterobacterium) (3)

Ecol\hflC

2 of 11

Yes

Ecol\hflK

2 of 11

Yes

Ecol\qmcA

2 of 11

Yes

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:CG42540. 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) (9)

9 of 13

9 of 13

6 of 13

5 of 13

5 of 13

3 of 13

2 of 13

2 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 ( 1 )

Human Ortholog

Disease

Evidence

References

NPHS2; NPHS2 stomatin family member, podocin

model of nephrotic syndrome type 2

IEA

(FlyBase, 2019-)

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?

STOM; stomatin

13 of 14

133090

STOML3; stomatin like 3

9 of 14

608327

NPHS2; NPHS2 stomatin family member, podocin

5 of 14

604766

NEPHROTIC SYNDROME, TYPE 2; NPHS2

nephrotic syndrome type 2

STOML1; stomatin like 1

3 of 14

608326

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

Show neighbor-neighbor interactions:

Off

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

Select Layout:

Force Directed

Circle

Concentric

Legend:

Protein

RNA

Selected Interactor(s)

Other Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

CG42540

fluorescent resonance energy transfer, fluorescence microscopy

(Nil et al., 2019)

CG42540 - CG4676

two hybrid

(Hu et al., 2017.6.13)

CG42540 - ima

two hybrid

(Hu et al., 2017.6.13)

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.

FBgn0260657

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Class of Gene

gene_with_edited_transcript

(Rodriguez et al., 2012, Graveley et al., 2011, Stapleton et al., 2006)

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-12

Cytogenetic map

64B10-64B11

Sequence location

3L:4,556,087..4,592,295 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

64B10-64B11

; Limits computationally determined from genome sequence between P{PZ}l(3)rG166^rG166 and P{PZ}sinu⁰⁶⁵²⁴

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-12

(FlyBase, 2016)

3-10.1

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (10)

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

Bloomington

83128

y¹ v¹; M{WKO.1-D8}ZH-86Fb

18401

w¹¹¹⁸; PBac{WH}CG42540^f01008

35913

y¹ w^*; Mi{MIC}CG42540^MI02962

36973

y¹ w^*; Mi{MIC}CG42540^MI03826

23181

y¹ w^67c23; Mi{ET1}CG42540^MB01413

65975

y¹ sc^* v¹ sev²¹; P{TRiP.HMC06255}attP40

37213

y¹ w^*; Mi{MIC}CG42540^MI03614/TM3, Sb¹ Ser¹

66836

y¹ w^*; Mi{Trojan-GAL4.1}CG42540^{MI03614-TG4.1}/TM3, Sb¹ Ser¹

VDRC

v101372

P{KK108752}VIE-260B

v14017

w¹¹¹⁸; P{GD4559}v14017

Genomic Clones (34)

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

cDNA Clones (43)

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

FI19456

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.

FBgn0260657

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0260657

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R⁺ cells.

(Boutros et al., 2004)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG13719 CG32245

(FlyBase Genome Annotators, 2009)

Source for merge of: CG13718 CG7468

(FlyBase, 1996-)

Additional comments

Annotations CG13719 and CG32245 merged as CG42540 in release 5.15 of the genome annotation.

(FlyBase Genome Annotators, 2009)

Annotations CG13718, CG7468 merged as CG32245 in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Source for merge of CG13718 CG7468 was a shared cDNA ( date:010720 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

CG13718

CG13719

CG32245

(Ashwal-Fluss et al., 2014, Keleman et al., 2009.8.5, Stapleton et al., 2006)

CG42540

(Min et al., 2023, Rounds et al., 2022, Kumar et al., 2021, Pang et al., 2021, Meltzer et al., 2019, Nil et al., 2019, Hu et al., 2017.6.13, Gene Disruption Project members, 2016-, Aradska et al., 2015, White-Grindley et al., 2014, Rodriguez et al., 2012, FlyBase Genome Annotators, 2009, Perkins et al., 2009)

CG7468

(Boutros et al., 2004)

Name Synonyms

CG13719

CG32245

Secondary FlyBase IDs

FBgn0035559
FBgn0035560
FBgn0040700
FBgn0052245

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 83 )

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.

38562

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

GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

Q9VZA4

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q9VZA4

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

Q9VZA4

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

38562/tissue=All

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

FBgn0260657

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

FBgn0260657

InterPro - A database of protein families, domains and functional sites

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

dme:Dmel_CG42540

MARRVEL_MODEL - MARRVEL (model organism gene)

38562

Linkouts

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

FBgn0260657

DroID - A comprehensive database of gene and protein interactions.

FBgn0260657

DRSC - Results frm RNAi screens

FBgn0260657

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0260657

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

CG32245

Flygut - An atlas of the Drosophila adult midgut

FBgn0260657

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

FBgn0260657

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC003971

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

References (54)

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

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