FlyBase Gene Report: Dmel\Vajk4

General Information

Symbol

Dmel\Vajk4

Species

D. melanogaster

Name

Annotation Symbol

CG30101

Feature Type

protein_coding_gene

FlyBase ID

FBgn0050101

Gene Model Status

Current

Stock Availability

4 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

vajk-4

Key Links

Genomic Location

Cytogenetic map

54B7-54B7

Sequence location

2R:17,408,258..17,410,204 [-]

Recombination map

2-82

RefSeq locus

NT_033778 REGION:17408258..17410204

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 (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables chitin binding

inferred from direct assay

(Cinege et al., 2017)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables chitin binding

inferred from biological aspect of ancestor with PANTHER:PTN008719865

(GO Reference Genome Project, 2011-)

enables structural constituent of chitin-based cuticle

inferred from sequence or structural similarity with UniProtKB:Q9V3G8

(Cinege et al., 2017)

Biological Process (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in chitin-based cuticle development

inferred from sequence or structural similarity with UniProtKB:Q9V3G8

(Cinege et al., 2017)

Cellular Component (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in chitin-based extracellular matrix

inferred from direct assay

(Cinege et al., 2017)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in chitin-based extracellular matrix

inferred from biological aspect of ancestor with PANTHER:PTN008719865

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

CPLCP CUTICLE PROTEIN FAMILY

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

CPLCP CUTICLE PROTEIN FAMILY -: The CPLCP family are low complexity cuticle proteins with a highly repetitive, proline-rich region. (Adapted from PMID:19754739.)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Vajk4 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 Q7K0W4)

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

Apparent introns not annotated: probable artifacts due to repetitive sequence.

Gene model reviewed during 5.50

Low-frequency RNA-Seq exon junction(s) not annotated.

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Vajk4-RA

FBtr0086963

NM_137361

1545

328

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

Vajk4-PA

FBpp0086118

38.1

328

8.89

Q7K0W4

NP_611205

AAF57876

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q7K0W4

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Vajk4 using the Feature Mapper tool.

External Data

Crossreferences

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

CG30101_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).

-0.22

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 11 -- 12

ventral epidermis primordium

(Fisher et al., 2012)

embryonic stage 12 -- 16

embryonic/larval tracheal section

(Chung et al., 2011)

oogenesis stage S9 -- S10

border follicle cell

(Borghese et al., 2006)

Additional Descriptive Data

In situ hybridization shows that Vajk4 is enriched in border follicle cells relative to follicle cells in stage S9 or S10 egg chambers.

(Borghese et al., 2006)

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

located_in chitin-based extracellular matrix

inferred from direct assay

(Cinege et al., 2017)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Vajk4 in JBrowse

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

View exonic expression by developmental stage for Dmel\Vajk4

View exonic expression by tissue for Dmel\Vajk4

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

FBgn0050101

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

36950/tissue=All

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

FBgn0050101

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0050101

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

FBgn0050101

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

CG30101

Flygut - An atlas of the Drosophila adult midgut

FBgn0050101

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\Vajk4

Stages(s) 11-12
Stages(s) 13-16

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 1 )

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 Vajk4

Transgenic constructs containing regulatory region of Vajk4

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(2R)Exel7147

(Ryder, 2004.4.26)

Inferred from location ( 3 )

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

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

Vajk4^GD5292

partially lethal, with Scer\GAL4^tin.CΔ4

Vajk4^GD5292

viable

Vajk4^f05583

viable, with Scer\GAL4^Mef2.PR

Vajk4^GD5292

viable, with Scer\GAL4^pnr-MD237

Vajk4^GD5292

Sterility

Allele

fertile

Vajk4^f05583

Other Phenotypes

Allele

short lived | heat sensitive, with Scer\GAL4^tin.CΔ4

Vajk4^GD5292

some die during pupal stage, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Vajk4^GD5292

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) (7)

Hsap\ZNF512B

2 of 14

Yes

Hsap\COL27A1

1 of 14

Yes

Hsap\GGN

1 of 14

Yes

Hsap\MUC19

1 of 14

Hsap\NEFH

1 of 14

Yes

Hsap\TPRX1

1 of 14

Hsap\ZNF512

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) (7)

Rnor\Zfp512b

2 of 14

Yes

Rnor\Ggn

1 of 14

Yes

Rnor\Gp1ba

1 of 14

Rnor\Nefh

1 of 14

Yes

Rnor\Selplg

1 of 14

Rnor\Sprr3

1 of 14

Yes

Rnor\Zfp512

1 of 14

Yes

Mus musculus (laboratory mouse) (7)

Mmus\Zfp512b

2 of 14

Yes

Mmus\Ggn

1 of 14

Yes

Mmus\Magel2

1 of 14

Mmus\Nefh

1 of 14

Yes

Mmus\Rtl1

1 of 14

Yes

Mmus\Zan

1 of 14

Mmus\Zfp512

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (5)

Xtro\ccdc88b

1 of 13

Yes

Xtro\hhat

1 of 13

Yes

Xtro\iws1

1 of 13

Yes

Xtro\LOC101734362

1 of 13

Yes

Xtro\rrbp1

1 of 13

Yes

Danio rerio (Zebrafish) (6)

Drer\si:ch73-366l1.5

3 of 14

Yes

Drer\LOC101886064

1 of 14

Yes

Drer\rrbp1b

1 of 14

Drer\ttn.1

1 of 14

Drer\znf512b

1 of 14

Yes

Drer\znf512

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (7)

Cele\clec-85

1 of 14

Yes

Cele\D1086.9

1 of 14

Yes

Cele\H39E23.3

1 of 14

Yes

Cele\K06A9.1

1 of 14

Yes

Cele\ttn-1

1 of 14

Yes

Cele\W05F2.4

1 of 14

Yes

Cele\ZK84.1

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (15)

Agam\AgaP_AGAP008817

7 of 12

Yes

Agam\AgaP_AGAP009759

5 of 12

Yes

Agam\AgaP_AGAP008893

2 of 12

Yes

Agam\AgaP_AGAP009758

2 of 12

Agam\AgaP_AGAP012355

2 of 12

Yes

Agam\AgaP_AGAP012356

2 of 12

Yes

Agam\AgaP_AGAP012498

2 of 12

Agam\AgaP_AGAP012676

2 of 12

Yes

Agam\AgaP_AGAP013465

2 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

Yes

Agam\AgaP_AGAP007563

1 of 12

Agam\AgaP_AGAP012947

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:Vajk4. 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) (18)

4 of 13

3 of 13

3 of 13

2 of 13

2 of 13

2 of 13

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

dpy

1 of 13

Muc55B

1 of 13

nahoda

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

BioGRID - A database of protein and genetic interactions.

62644

DroID - A comprehensive database of gene and protein interactions.

FBgn0050101

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

2-82

Cytogenetic map

54B7-54B7

Sequence location

2R:17,408,258..17,410,204 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

54B7-54B7

Limits computationally determined from genome sequence between P{EP}EP1061&P{EP}cnk^EP576 and P{EP}l(2)k01209^EP2177&P{lacW}k11012a

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-82

(FlyBase, 2016)

2-85.9

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (4)

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

Bloomington

18887

w¹¹¹⁸; PBac{WH}Vajk4^f05583

36642

y¹ v¹; P{TRiP.GL00602}attP2/TM6C, Sb¹ Tb¹

NIG-Fly

2RG-0706

y² VhaAC39-1^cho-1 v¹; P{U6-Vajk4.NIG.sgRNA}attP40/CyO

VDRC

v15514

w¹¹¹⁸; P{GD5292}v15514

Genomic Clones (19)

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

cDNA Clones (17)

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

LD27203

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.

FBgn0050101

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0050101

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Cinege et al., 2017)

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: CG15901 CG6564

(BDGP Project Members, 2000-)

Source for merge of: CG6564 CG15901

(FlyBase, 1996-)

Additional comments

Annotations CG15901, CG6564 merged as CG30101 in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Source for merge of CG6564 CG15901 was a shared cDNA ( date:010720 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Source for identity of: Vajk4 CG30101

(Somogyi et al., 2010)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (6)

Reported As

Symbol Synonym

CG15901

(Borghese et al., 2006, Hekmat-Scafe et al., 2005)

CG30101

(National Institute of Genetics Fly Stocks, 2022-, Ashwal-Fluss et al., 2014, Chung et al., 2011, Ni et al., 2011.7.19, Herranz et al., 2010, Lebo et al., 2009, Liu et al., 2006)

CG6564

FBgn0050101

(Lehmann et al., 2010)

Vajk4

(Li et al., 2024, Pignataro et al., 2024)

vajk-4

(Cinege et al., 2017, Somogyi et al., 2010)

Name Synonyms

Secondary FlyBase IDs

FBgn0034211
FBgn0034212

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 30 )

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.

36950

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.

Q7K0W4

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

Q7K0W4

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.

Q7K0W4

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0050101

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

36950/tissue=All

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

FBgn0050101

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

FBgn0050101

FlyMine - An integrated database for Drosophila genomics

FBgn0050101

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

dme:Dmel_CG30101

MARRVEL_MODEL - MARRVEL (model organism gene)

36950

Linkouts

BioGRID - A database of protein and genetic interactions.

62644

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

FBgn0050101

DroID - A comprehensive database of gene and protein interactions.

FBgn0050101

DRSC - Results frm RNAi screens

FBgn0050101

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

CG30101_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0050101

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0050101

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

CG30101

Flygut - An atlas of the Drosophila adult midgut

FBgn0050101

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

TC010154

References (41)

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

-0.22

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