FlyBase Gene Report: Dmel\CG42541

General Information

Symbol

Dmel\CG42541

Species

D. melanogaster

Name

Annotation Symbol

CG42541

Feature Type

protein_coding_gene

FlyBase ID

FBgn0260658

Gene Model Status

Current

Stock Availability

8 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

3F4-3F7

Sequence location

X:3,891,497..3,930,578 [-]

Recombination map

1-5

RefSeq locus

NC_004354 REGION:3891497..3930578

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 (4 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables calcium channel regulator activity

inferred from biological aspect of ancestor with PANTHER:PTN000632293

(GO Reference Genome Project, 2011-)

enables GTP binding

inferred from biological aspect of ancestor with PANTHER:PTN000632293

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR001806

(InterPro Project Members, 2004-)

enables GTPase activity

inferred from electronic annotation with InterPro:IPR001806

(InterPro Project Members, 2004-)

Biological Process (0 terms)

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 (1 term)

CV Term

Evidence

References

is_active_in plasma membrane

inferred from biological aspect of ancestor with PANTHER:PTN000632293

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

RAS GTPASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

GTPase activity
RHEA 19669:

Summaries

Gene Group (FlyBase)

RAS GTPASES -: The Ras family are members of the Ras superfamily of small GTPases. Ras proteins act in signal transduction cascades, generally the activated GTPase recruits and activates downstream effectors. Members this family are typically membrane-associated via isoprenylation of a CaaX motif in the C-terminus. (Adapted from PMID:15731001).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\CG42541 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

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q7KVX6)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

merge of CG15240 and CG32776

Gene model reviewed during 5.45

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

CG42541-RC

FBtr0301099

NM_206622

6157

1418

CG42541-RD

FBtr0301100

NM_001038740

8817

1417

CG42541-RE

FBtr0332388

NM_001272295

9704

1417

CG42541-RF

FBtr0332389

NM_001272296

8763

1399

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

CG42541-PC

FBpp0290321

155.5

1418

7.84

FBpp0290322

155.4

1417

7.84

FBpp0304662

155.4

1417

7.84

FBpp0304663

153.3

1399

7.94

M9PJ04

NP_001259225

AGB95071

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\CG42541 using the Feature Mapper tool.

External Data

Crossreferences

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

CG42541_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).

-0.65

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\CG42541 in JBrowse

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

View exonic expression by developmental stage for Dmel\CG42541

View exonic expression by tissue for Dmel\CG42541

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

FBgn0260658

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

31344/tissue=All

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

FBgn0260658

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

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

FBgn0260658

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

CG32776

Flygut - An atlas of the Drosophila adult midgut

FBgn0260658

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 3 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 6 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of CG42541

Transgenic constructs containing regulatory region of CG42541

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 8 )

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

viable, with Scer\GAL4^Mef2.PR

viable, with Scer\GAL4^pnr-MD237

Other Phenotypes

Allele

visible, with Scer\GAL4^pnr-MD237

CG42541^GD8953

Phenotype manifest in

Allele

chaeta | increased number, with Scer\GAL4^pnr-MD237

CG42541^GD8953

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) (50)

Hsap\GEM

4 of 14

Yes

Hsap\REM1

4 of 14

Yes

Hsap\REM2

4 of 14

Yes

Hsap\RRAD

4 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

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) (38)

Rnor\Rem1

5 of 14

Yes

Rnor\Rem2

5 of 14

Yes

Rnor\Rrad

5 of 14

Yes

4 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (42)

Mmus\Gem

5 of 14

Yes

Mmus\Rem2

5 of 14

Yes

Mmus\Rrad

5 of 14

Yes

4 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (37)

Xtro\gem

3 of 13

Yes

2 of 13

1 of 13

1 of 13

1 of 13

Yes

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

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

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (42)

Drer\gem

4 of 14

Yes

Drer\rem1

4 of 14

Yes

Drer\rrad

4 of 14

Yes

3 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

Drer\si:dkeyp-59c12.1

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

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) (31)

Cele\Y52B11A.4

5 of 14

Yes

Cele\F20D6.8

3 of 14

Yes

Cele\W04C9.5

3 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Cele\D1081.12

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (24)

Agam\AgaP_AGAP007615

5 of 12

Yes

3 of 12

3 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (18)

Atha\AT5G59840

1 of 13

Yes

Atha\ATFP8

1 of 13

Yes

Atha\RAB1A

1 of 13

Yes

Atha\RAB1C

1 of 13

Yes

Atha\RAB8

1 of 13

Yes

Atha\RAB11c

1 of 13

Yes

Atha\RAB18

1 of 13

Yes

Atha\RABA1d

1 of 13

Yes

Atha\RABA1g

1 of 13

Yes

Atha\RABA1i

1 of 13

Yes

Atha\RABA5d

1 of 13

Yes

Atha\RABB1a

1 of 13

Yes

Atha\RABE1c

1 of 13

Yes

Atha\RABE1e

1 of 13

Yes

Atha\RABG3E

1 of 13

Yes

Atha\RABH1c

1 of 13

Yes

Atha\RABH1d

1 of 13

Yes

Atha\RABH1e

1 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (8)

Scer\RAS1

2 of 13

Yes

Scer\RAS2

2 of 13

Yes

Scer\RHB1

2 of 13

Yes

Scer\RSR1

2 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\ras1

2 of 12

Yes

Spom\rhb1

2 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:CG42541. 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) (22)

7 of 13

6 of 13

5 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

Ric

2 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 ( 1 )

Allele

Disease

Interaction

References

CG42541^KK109685

exacerbates atypical teratoid rhabdoid tumor

modeled by Snr1^KK101602

(Tegeder et al., 2019)

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?

GEM; GTP binding protein overexpressed in skeletal muscle

4 of 14

600164

REM1; RRAD and GEM like GTPase 1

4 of 14

610388

REM2; RRAD and GEM like GTPase 2

4 of 14

616955

RRAD; RRAD, Ras related glycolysis inhibitor and calcium channel regulator

4 of 14

179503

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

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

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Snr1

suppressible

CG42541

(Tegeder et al., 2019)

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0260658

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-5

Cytogenetic map

3F4-3F7

Sequence location

X:3,891,497..3,930,578 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

3F4-3F7

Limits computationally determined from genome sequence between P{EP}CG2930^EP1352 and P{EP}EP425;

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-5

(FlyBase, 2016)

1-4.9

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (8)

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

Bloomington

58345

y¹ v¹; P{TRiP.HMJ22476}attP40/CyO

22039

w^67c23 P{Mae-UAS.6.11}CG42541^GG01713

37350

y¹ w^* Mi{MIC}CG42541^MI03613

97565

y¹ w^* TI{CRIMIC.TG4.1}CG42541^{CR02684-TG4.1}

NIG-Fly

16828R-2

P{NIG.16828R}2

HMJ22476

y¹ v¹; P{TRiP.HMJ22476}attP40/CyO

VDRC

v100179

P{KK105178}VIE-260B

v104518

P{KK109685}VIE-260B

Genomic Clones (21)

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

cDNA Clones (13)

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.

FBgn0260658

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0260658

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

S2 cells treated with dsRNA generated against this gene show reduced phagocytosis of Candida albicans compared to untreated cells.

(Stroschein-Stevenson et al., 2006)

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: CG15240 CG32776

(FlyBase Genome Annotators, 2009)

Source for merge of: CG32776 BcDNA:RH43809

(FlyBase, 1996-)

Source for merge of: CG16828 CG16829

(FlyBase Genome Annotators, 2002-2003)

Additional comments

Annotations CG15240 and CG32776 merged as CG42541 in release 5.15 of the genome annotation.

(FlyBase Genome Annotators, 2009)

Annotations CG16828 and CG16829 merged as CG32776 in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Source for merge of CG32776 BcDNA:RH43809 was a shared cDNA ( date:030728 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (6)

Reported As

Symbol Synonym

BcDNA:RH43809

CG15240

(Keleman et al., 2009.8.5, Gilfillan et al., 2006)

CG16828

(Boutros et al., 2004)

CG16829

CG32776

(Vaque et al., 2013, Japanese National Institute of Genetics, 2012.5.21, Diez et al., 2011, Keleman et al., 2009.8.5, Gilfillan et al., 2006, Stroschein-Stevenson et al., 2006)

CG42541

(Corthals et al., 2023, Sun et al., 2020, Tegeder et al., 2019, Croset et al., 2018, Gene Disruption Project members, 2018-, Vernes, 2014, Ni et al., 2010.12.1, FlyBase Genome Annotators, 2009)

Name Synonyms

CG15240

CG32776

Secondary FlyBase IDs

FBgn0029682
FBgn0029683
FBgn0062938
FBgn0029684
FBgn0052776

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 49 )

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.

31344

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.

Q7KVX6

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.

Q7KVX6

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0260658

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

31344/tissue=All

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

FBgn0260658

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

FBgn0260658

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

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

dme:Dmel_CG42541

MARRVEL_MODEL - MARRVEL (model organism gene)

31344

Linkouts

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

FBgn0260658

DroID - A comprehensive database of gene and protein interactions.

FBgn0260658

DRSC - Results frm RNAi screens

FBgn0260658

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

CG42541_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0260658

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

CG32776

Flygut - An atlas of the Drosophila adult midgut

FBgn0260658

References (38)

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

-0.65

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