FlyBase Gene Report: Dmel\Tsp29Fa

General Information

Symbol

Dmel\Tsp29Fa

Species

D. melanogaster

Name

Tetraspanin 29Fa

Annotation Symbol

CG9494

Feature Type

protein_coding_gene

FlyBase ID

FBgn0032074

Gene Model Status

Current

Stock Availability

3 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

29F4-29F4

Sequence location

2L:8,933,962..8,936,096 [+]

Recombination map

2-34

RefSeq locus

NT_033779 REGION:8933962..8936096

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

Help me choose

Other Genome Views

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

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (2 terms)

Molecular Function (0 terms)

There is no information supporting a Molecular Function term for this gene. (Based on a review of available data on: 2011-06-30 )

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (0 terms)

There is no information supporting a Biological Process term for this gene. (Based on a review of available data on: 2021-01-27 )

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

located_in integral component of membrane

inferred from sequence model

(Fradkin et al., 2002)

is_active_in integral component of plasma membrane

inferred from biological aspect of ancestor with PANTHER:PTN001060286

(assigned by GO_Central )

(Gaudet et al., 2011)

Gene Group (FlyBase)

TETRASPANINS

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

TETRASPANINS -: Tetraspanins (TSP) have four transmembrane domains and two extracellular loops containing specific short motifs, including highly conserved cysteine residues. TSPs are thought to function as scaffolds that bring multiple proteins - including other TSPs, membrane-associated proteins, extracellular and cytosolic proteins - into single membrane region. These regions are called tetraspanin-enriched microdomains. (Adapted from FBrf0227776 and FBrf0152316).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Tsp29Fa 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 New Section

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q9VLH1)

If you don't see the viewer to the right, 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.

Comments on Gene Model

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Gene model reviewed during 5.50

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Tsp29Fa-RA

FBtr0079754

NM_078791

963

248

Tsp29Fa-RB

FBtr0300289

NM_001169444

1247

248

Tsp29Fa-RC

FBtr0340261

NM_001298838

1052

248

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

RefSeq ID

GenBank

Tsp29Fa-PA

FBpp0079355

26.6

248

5.62

NP_523515

AAF52719

Tsp29Fa-PB

FBpp0289517

26.6

248

5.62

NP_001162915

ACZ94205

Tsp29Fa-PC

FBpp0309228

26.6

248

5.62

NP_001285767

AHN54281

Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

248 aa isoforms: Tsp29Fa-PA, Tsp29Fa-PB, Tsp29Fa-PC

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

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Tsp29Fa 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

Expression Summary Ribbons

Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

embryonic/larval midgut

(Hernández de Madrid and Casanova, 2018)

embryonic stage 13 -- 16

embryonic midgut chamber

(Fisher et al., 2012)

embryonic/larval midgut

(Fisher et al., 2012)

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

GBrowse - Visual display of RNA-Seq signals

View Dmel\Tsp29Fa in GBrowse 2

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

View exonic expression by developmental stage for Dmel\Tsp29Fa

View exonic expression by tissue for Dmel\Tsp29Fa

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

FBgn0032074

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

34211/tissue=All

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

FBgn0032074

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0032074

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

FBgn0032074

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

CG9494

Flygut - An atlas of the Drosophila adult midgut

FBgn0032074

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\Tsp29Fa

Stages(s) 13-16

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 ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Tsp29Fa

Transgenic constructs containing regulatory region of Tsp29Fa

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(2L)Exel7040

(Ryder, 2004.4.26)

Inferred from location ( 0 )

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

Tsp29Fa^GD1017

viable, with Scer\GAL4^Mef2.PR

Tsp29Fa^GD1017

viable, with Scer\GAL4^pnr-MD237

Tsp29Fa^GD1017

viable, with Scer\GAL4^tin.CΔ4

Tsp29Fa^GD1017

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (5)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\CD63

8 of 15

Yes

3 of 15

3 of 15

1 of 15

1 of 15

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (5)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Cd63

8 of 15

Yes

3 of 15

2 of 15

1 of 15

1 of 15

Rattus norvegicus (Norway rat) (3)

Rnor\Cd63

7 of 13

Yes

Rnor\Tspan6

3 of 13

Rnor\Tspan7

2 of 13

Yes

Xenopus tropicalis (Western clawed frog) (5)

Xtro\cd63

5 of 12

Yes

Xtro\tspan6

3 of 12

Xtro\LOC100497410

2 of 12

Yes

Xtro\tspan7

2 of 12

Yes

Xtro\cd151

1 of 12

Danio rerio (Zebrafish) (7)

Drer\cd63

8 of 15

Yes

Drer\tspan7b

3 of 15

Yes

3 of 15

2 of 15

2 of 15

2 of 15

1 of 15

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\tsp-7

7 of 15

Yes

Arabidopsis thaliana (thale-cress) (4)

Atha\AT2G20230

1 of 9

Yes

Atha\AT2G20740

1 of 9

Yes

Atha\AT4G28770

1 of 9

Yes

Atha\TOM2A

1 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (0)

No records found.

Schizosaccharomyces pombe (Fission yeast) (0)

No records found.

Other Organism Orthologs (via OrthoDB)

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (34)

Gene Symbol

Score

Source

Alignment

5 of 10

4 of 10

3 of 10

3 of 10

3 of 10

2 of 10

lbm

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

2 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Model Summary Ribbon

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 v8.0 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?

CD63; CD63 molecule

8 of 15

155740

TSPAN6; tetraspanin 6

3 of 15

300191

TSPAN7; tetraspanin 7

3 of 15

300096

INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED 58; XLID58

non-syndromic X-linked intellectual disability 58

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

Interactions Browser

Summary of Genetic Interactions

esyN Network Diagram

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.

FBgn0032074

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

Lysosome

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

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-34

Cytogenetic map

29F4-29F4

Sequence location

2L:8,933,962..8,936,096 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

29F4-29F4

Limits computationally determined from genome sequence between P{lacW}l(2)k04003^k04003 and P{PZ}tai⁰¹³⁵¹

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

29F-29F

(Todres, 2000.6.1)

Experimentally Determined Recombination Data

Location

2-34

(FlyBase, 2016)

2-29.6

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (3)

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

Bloomington

40829

y¹ v¹; P{TRiP.HMS01995}attP40

VDRC

v105839

P{KK102968}VIE-260B

v44876

w¹¹¹⁸; P{GD1017}v44876

Genomic Clones (13)

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

cDNA Clones (36)

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 GBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

RE39366

Other clones

IP17824

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.

FBgn0032074

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0032074

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

34211

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: Tsp29Fa CG9494

(FlyBase, 1996-)

Source for database merge of

Additional comments

Source for identity of Tsp29Fa CG9494 was sequence comparison ( date:000815 ).

(FlyBase, 1996-)

Other Comments

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 46 )

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.

34211

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.

Q9VLH1

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

Q9VLH1

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.

Q9VLH1

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0032074

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

FBgn0032074

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

34211/tissue=All

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

FBgn0032074

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0032074

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

FBgn0032074

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

CG9494

Flygut - An atlas of the Drosophila adult midgut

FBgn0032074

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

34211

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

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

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

Dmel_CG9494

MARRVEL_MODEL - MARRVEL (model organism gene)

34211

modMine - A data warehouse for the modENCODE project

FBgn0032074

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0032074

DRSC - Results frm RNAi screens

FBgn0032074

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0032074

FlyMine - An integrated database for Drosophila genomics

FBgn0032074

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

Lysosome

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

Synonyms and Secondary IDs (4)

Reported As

Symbol Synonym

CG9494

(Meadows et al., 2010, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Fradkin et al., 2002, Todres et al., 2000)

Dm.Tsp29Fa

(Todres et al., 2000)

Tsp29Fa

(Xu et al., 2019, Hernández de Madrid and Casanova, 2018, Fox and Andrew, 2015, Jeibmann et al., 2015, Japanese National Institute of Genetics, 2012.5.21, Okumura et al., 2007, Senger et al., 2006)

Name Synonyms

Tetraspanin 29Fa

(Jeibmann et al., 2015, Todres, 2000.6.1)

Secondary FlyBase IDs

Datasets (6)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (6)

Result

Result Type

Title

scRNAseq_2020_Cho_NI72LG_seq_clustering

cell clustering analysis

Clustering analysis of lymph gland cells from non-infested larvae at 72 h after egg-laying

scRNAseq_2020_Cho_NI96LG_seq_clustering

cell clustering analysis

Clustering analysis of lymph gland cells from non-infested larvae at 96 h after egg-laying

scRNAseq_2020_Cho_NI120LG_seq_clustering

cell clustering analysis

Clustering analysis of lymph gland cells from non-infested larvae at 120 h after egg-laying

scRNAseq_2020_Cho_WI96LG_seq_clustering

cell clustering analysis

Clustering analysis of lymph gland cells from wasp-infested larvae at 96 h after egg-laying

scRNAseq_2020_Cho_NI96HL_seq_clustering

cell clustering analysis

Clustering analysis of circulating hemocytes from non-infested larvae at 96 h after egg-laying

scRNAseq_2020_Cho_NI120HL_seq_clustering

cell clustering analysis

Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying

References (30)

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

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