FlyBase Gene Report: Dmel\vex

General Information

Symbol

Dmel\vex

Species

D. melanogaster

Name

vexed

Annotation Symbol

CG42339

Feature Type

protein_coding_gene

FlyBase ID

FBgn0259241

Gene Model Status

Current

Stock Availability

5 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

9F13-10A3

Sequence location

X:10,967,722..11,039,901 [-]

Recombination map

1-33

RefSeq locus

NC_004354 REGION:10967722..11039901

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\vex 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 Q9VZ43)

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

Gene model reviewed during 5.45

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

vex-RA

FBtr0299861

NM_144209

656

113

vex-RB

FBtr0299862

NM_132446

2354

395

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

vex-PA

FBpp0289139

12.2

113

8.22

FBpp0289140

43.9

395

6.30

Q9VZ43

NP_572674

AAF47985

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\vex 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).

-0.56

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\vex in JBrowse

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

View exonic expression by developmental stage for Dmel\vex

View exonic expression by tissue for Dmel\vex

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

FBgn0259241

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

32033/tissue=All

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

FBgn0259241

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0259241

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

FBgn0259241

Flygut - An atlas of the Drosophila adult midgut

FBgn0259241

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 5 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 3 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of vex

Transgenic constructs containing regulatory region of vex

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(1)BSC540

(Davis et al., 2022)

Inferred from location ( 9 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Other Phenotypes

Allele

decreased cell number | adult stage, with Scer\GAL4^GMR54H02

vex^HMC06376

decreased cell number | adult stage, with Scer\GAL4^GMR77A03

vex^HMC06376

decreased cell number | adult stage, with Scer\GAL4^repo

vex^HMC06376

decreased cell number | adult stage, with Scer\GAL4^αTub84B.PL

vex^HMC06376

decreased cell number | adult stage | progressive (with Df(1)BSC540)

decreased cell number | adult stage | progressive | recessive

decreased rate of adult locomotory behavior | progressive (with Df(1)BSC540)

decreased rate of adult locomotory behavior | progressive | recessive

decreased rate of adult locomotory behavior | recessive, with Scer\GAL4^GMR54H02

vex^HMC06376

decreased rate of adult locomotory behavior | recessive, with Scer\GAL4^GMR77A03

vex^HMC06376

decreased rate of adult locomotory behavior | recessive, with Scer\GAL4^repo

vex^HMC06376

decreased rate of adult locomotory behavior | recessive, with Scer\GAL4^αTub84B.PL

vex^HMC06376

Phenotype manifest in

Allele

adult brain

vex^MI01691

adult dopaminergic neuron | decreased number

adult dopaminergic neuron | decreased number, with Scer\GAL4^GMR54H02

vex^HMC06376

adult dopaminergic neuron | decreased number, with Scer\GAL4^GMR77A03

vex^HMC06376

adult dopaminergic neuron | decreased number, with Scer\GAL4^repo

vex^HMC06376

adult dopaminergic neuron | decreased number, with Scer\GAL4^αTub84B.PL

vex^HMC06376

adult dopaminergic neuron | decreased number (with Df(1)BSC540)

dopaminergic PPL1 neuron | adult stage | decreased number

dopaminergic PPL1 neuron | adult stage | decreased number, with Scer\GAL4^GMR54H02

vex^HMC06376

dopaminergic PPL1 neuron | adult stage | decreased number, with Scer\GAL4^GMR77A03

vex^HMC06376

dopaminergic PPL1 neuron | adult stage | decreased number, with Scer\GAL4^repo

vex^HMC06376

dopaminergic PPL1 neuron | adult stage | decreased number, with Scer\GAL4^αTub84B.PL

vex^HMC06376

dopaminergic PPL1 neuron | adult stage | decreased number (with Df(1)BSC540)

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) (16)

Hsap\SBSPON

10 of 14

Yes

3 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) (15)

Rnor\Sbspon

9 of 14

Yes

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

Mus musculus (laboratory mouse) (17)

Mmus\Sbspon

8 of 14

Yes

3 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

Yes

Mmus\Thsd7b

1 of 14

Yes

Mmus\Tinagl1

1 of 14

Mmus\Tinag

1 of 14

Xenopus tropicalis (Western clawed frog) (10)

Xtro\LOC100492479

8 of 13

Yes

Xtro\sbspon

8 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Xtro\rspo2

1 of 13

Yes

Xtro\spon2

1 of 13

Xtro\thsd7a

1 of 13

Yes

Xtro\thsd7b

1 of 13

Yes

Danio rerio (Zebrafish) (20)

Drer\si:dkey-178e17.3

9 of 14

Yes

Drer\sbspon

8 of 14

Yes

Drer\si:dkey-7k24.5

8 of 14

Yes

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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Drer\thsd7ab

1 of 14

Yes

Drer\thsd7ba

1 of 14

Yes

Drer\thsd7bb

1 of 14

Yes

Drer\tinagl1

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\sbsp-1

8 of 14

Yes

Cele\spon-1

2 of 14

Anopheles gambiae (African malaria mosquito) (7)

Agam\AgaP_AGAP010795

6 of 12

Yes

Agam\AgaP_AGAP010796

2 of 12

Yes

2 of 12

2 of 12

2 of 12

1 of 12

1 of 12

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:vex. 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) (6)

2 of 13

2 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?

SBSPON; somatomedin B and thrombospondin type 1 domain containing

10 of 14

621005

SPON1; spondin 1

3 of 14

604989

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

vex

suppressible

Nos

(Davis et al., 2022)

vex

suppressible

Rel

(Davis et al., 2022)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0259241

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.

O-glycosylation of TSR domain-containing proteins

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-33

Cytogenetic map

9F13-10A3

Sequence location

X:10,967,722..11,039,901 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

9F13-10A3

Limits computationally determined from genome sequence between P{EP}EP1321^EP1321&P{EP}CG2061^EP1537 and P{EP}CG11756^EP1610

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Cytogenetic location of 10A1--10A2 based on known data for C901, v and sev, previous data described in FBrf0073632, and comparison with the physical map (Release 5.8).

(Babenko et al., 2009)

10A1-10A2

(Babenko et al., 2009)

Experimentally Determined Recombination Data

Location

1-33

(FlyBase, 2016)

1-34.4

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (5)

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

Bloomington

32773

y¹ w^* Mi{MIC}vex^MI01691

51278

y¹ w^* Mi{MIC}vex^MI09347

57935

y¹ w^* Mi{MIC}vex^MI12354

59652

y¹ w^* Mi{MIC}vex^MI13384

67273

y¹ sc^* v¹ sev²¹; P{TRiP.HMC06376}attP40

Genomic Clones (44)

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

cDNA Clones (10)

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.

FBgn0259241

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0259241

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Relationship to Other Genes

Source for database merge of

Source for merge of: CG12626 CG15204

(FlyBase Genome Annotators, 2008)

Additional comments

Annotations CG12626 and CG15204 merged as CG42339 in release 5.9 of the genome annotation.

(FlyBase Genome Annotators, 2008)

Nomenclature History

Source for database identify of

Source for identity of: vex CG42339

(Davis et al., 2022)

Nomenclature comments

Etymology

Named as 'vexed' based on the mutant phenotype of a progressive loss of DA neurons and locomotor dysfunction.

(Davis et al., 2022)

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

CG12626

(Babenko et al., 2009)

CG15204

(Babenko et al., 2009)

CG42339

(Davis et al., 2022, Davis et al., 2021, Meltzer et al., 2019, Lopez et al., 2018, Duff et al., 2015, Vernes, 2014, Zhimulev et al., 2014, Perkins et al., 2009, FlyBase Genome Annotators, 2008)

vex

(Davis et al., 2022)

Name Synonyms

CG12626

CG15204

vexed

(Shweta et al., 2024, Davis et al., 2022)

Secondary FlyBase IDs

FBgn0040851
FBgn0030256

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 34 )

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.

32033

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.

Q9VZ43

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.

Q9VZ43

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0259241

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

32033/tissue=All

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

FBgn0259241

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

FBgn0259241

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

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

dme:Dmel_CG42339

MARRVEL_MODEL - MARRVEL (model organism gene)

32033

Linkouts

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

FBgn0259241

DroID - A comprehensive database of gene and protein interactions.

FBgn0259241

DRSC - Results frm RNAi screens

FBgn0259241

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0259241

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0259241

Flygut - An atlas of the Drosophila adult midgut

FBgn0259241

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

FBgn0259241

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

TC034735

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

O-glycosylation of TSR domain-containing proteins

References (23)

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

-0.56

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