FB2024_03 , released June 25, 2024
Gene: Dmel\Trs20
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General Information
Symbol
Dmel\Trs20
Species
D. melanogaster
Name
TRAPP subunit 20
Annotation Symbol
CG5161
Feature Type
protein_coding_gene
FlyBase ID
FBgn0266724
Gene Model Status
Current
Stock Availability
14 publicly available
Gene Summary
May play a role in vesicular transport from endoplasmic reticulum to Golgi. Involved in dsRNA uptake. (UniProt, Q9VUZ1)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

l(3)72Dh, E(smoDN)B-left

Key Links
Genomic Location
Cytogenetic map
72D9-72D9
Sequence location
Recombination map
3-44
RefSeq locus
NT_037436 REGION:16131001..16131632
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (9 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in dsRNA transport
inferred from mutant phenotype
(Saleh et al., 2006)
involved_in spermatogenesis
inferred from mutant phenotype
(Lindsley et al., 2013)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport
inferred from biological aspect of ancestor with PANTHER:PTN000274300
(GO Reference Genome Project, 2011-)
inferred from electronic annotation with InterPro:IPR006722
(InterPro Project Members, 2004-)
inferred from sequence or structural similarity with SGD:S000000458
(Gene Ontology Curators, 2002-)
involved_in Golgi vesicle transport
inferred by curator from GO:1990071,GO:1990072
(Riedel et al., 2018)
Cellular Component (5 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
part_of TRAPPII protein complex
inferred from direct assay
(Riedel et al., 2018)
part_of TRAPPIII protein complex
inferred from direct assay
(Riedel et al., 2018)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
is_active_in cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN000274300
(GO Reference Genome Project, 2011-)
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000274300
(GO Reference Genome Project, 2011-)
part_of TRAPP complex
inferred from sequence or structural similarity with SGD:S000000458
(Gene Ontology Curators, 2002-)
inferred from biological aspect of ancestor with PANTHER:PTN000274300
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the TRAPP small subunits family. Sedlin subfamily. (Q9VUZ1)
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
TRAPPII COMPLEX -
The TRAPPII complex is a Rab guanine nucleotide-exchange factor complex involved in ER-Golgi and intra-Golgi trafficking. (Adapted from FBrf0238107.)
TRAPPIII COMPLEX -
The TRAPPIII complex is a Rab guanine nucleotide-exchange factor complex involved in ER-Golgi and intra-Golgi trafficking. (Adapted from FBrf0238107.)
Protein Function (UniProtKB)
May play a role in vesicular transport from endoplasmic reticulum to Golgi. Involved in dsRNA uptake.
(UniProt, Q9VUZ1)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Trs20 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 Q9VUZ1)

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
PDB - An information portal to biological macromolecular structures
Comments on Gene Model

Gene model reviewed during 5.46

Gene model reviewed during 6.02

Sequence Ontology: Class of Gene
gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Trs20-RA
FBtr0075491
NM_140584
575
139
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
Trs20-PA
FBpp0075246
16.6
139
9.24
Q9VUZ1
NP_648841
AAF49531
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
Subunit Structure (UniProtKB)

Part of the multisubunit TRAPP (transport protein particle) complex.

(UniProt, Q9VUZ1)
Crossreferences
InterPro - A database of protein families, domains and functional sites
PDB - An information portal to biological macromolecular structures
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\Trs20 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).

0.29

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of TRAPPII protein complex
inferred from direct assay
(Riedel et al., 2018)
part_of TRAPPIII protein complex
inferred from direct assay
(Riedel et al., 2018)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Trs20 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 9 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 8 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Trs20
Transgenic constructs containing regulatory region of Trs20
Aberrations (Deficiencies and Duplications) ( 9 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (4)
Hsap\TRAPPC2
14 of 14
Yes
Yes
Hsap\TRAPPC2B
11 of 14
No
Yes
Hsap\TRAPPC2L
2 of 14
No
No
Hsap\TRAPPC4
1 of 14
No
No
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (4)
Rnor\Trappc2
14 of 14
Yes
Yes
Rnor\Trappc2b
11 of 14
No
Yes
Rnor\Trappc2l
2 of 14
No
No
Rnor\Trappc4
1 of 14
No
No
Mus musculus (laboratory mouse) (4)
Mmus\Trappc2
14 of 14
Yes
Yes
Mmus\0610009B22Rik
12 of 14
No
Yes
Mmus\Trappc2l
2 of 14
No
No
Mmus\Trappc4
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (3)
Xtro\trappc2
11 of 13
Yes
Yes
Xtro\trappc2l
2 of 13
No
No
Xtro\trappc4
1 of 13
No
No
Danio rerio (Zebrafish) (3)
Drer\trappc2
12 of 14
Yes
Yes
Drer\trappc2l
2 of 14
No
No
Drer\trappc4
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (3)
Cele\sedl-1
13 of 14
Yes
Yes
Cele\T10F2.5
2 of 14
No
No
Cele\trpp-4
1 of 14
No
No
Anopheles gambiae (African malaria mosquito) (2)
Agam\AgaP_AGAP002528
12 of 12
Yes
Yes
Agam\AgaP_AGAP013488
2 of 12
No
No
Arabidopsis thaliana (thale-cress) (2)
Atha\AT1G80500
13 of 13
Yes
Yes
Atha\AT2G20930
2 of 13
No
No
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\TRS20
12 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\trs20
12 of 12
Yes
Yes
Spom\SPAC15A10.12c
2 of 12
No
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Trs20. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (2)
CG9067
3 of 13
Trs23
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 )
    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?
    TRAPPC2; trafficking protein particle complex subunit 2
    14 of 14
    300202
    TRAPPC2B; trafficking protein particle complex subunit 2B
    11 of 14
    620472
        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
        Summary of Genetic Interactions
        esyN Network Diagram
        Show/hide secondary interactors 
        (data from AllianceMine provided by esyN)
        esyN Network Key:
        Suppression
        Enhancement
        Other 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
        smo
        enhanceable
        Trs20
        (Collins, 2005.7.7, Collins and Cohen, 2005)
        External Data
        Subunit Structure (UniProtKB)
        Part of the multisubunit TRAPP (transport protein particle) complex.
        (UniProt, Q9VUZ1 )
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        MIST (genetic) - An integrated Molecular Interaction Database
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Linkouts
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3L
        Recombination map
        3-44
        Cytogenetic map
        72D9-72D9
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        72D9-72D9
        Limits computationally determined from genome sequence between P{lacW}SsRβs1939 and P{lacW}l(3)72Dnj5A4
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Mapped by male specific recombination.
        (Collins, 2005.7.7)
        72D6-72D9
        (Collins, 2005.7.7)
        Experimentally Determined Recombination Data
        Location

        3-44

        (FlyBase, 2016)

        3-38.4

        (Comeron et al., 2012)

        3-

        (Collins, 2005.7.7, Collins and Cohen, 2005)

        3-[43]

        Left of (cM)
        (Collins, 2005.7.7)
        Right of (cM)
        (Collins, 2005.7.7)
        Notes
        Stocks and Reagents
        Stocks (14)
        Genomic Clones (13)
         

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

        cDNA Clones (57)
         

        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.

          cDNA Clones, End Sequenced (ESTs)
          BDGP DGC clones
            Other clones
            RNAi and Array Information
            Linkouts
            Antibody Information
            Laboratory Generated Antibodies
             
            Commercially Available Antibodies
             
            Cell Line Information
            Publicly Available Cell Lines
             
              Other Stable Cell Lines
               
                Other Comments

                The l(3)72Dh complementation group comprises 2 EMS-induced mutant alleles.

                (Cooper and Kennison, 2011)

                dsRNA made from templates generated with primers directed against CG5161 that is transfected into S2 treated with Listeria monocytogenes reveals CG5161 to be involved in Listeria monocytogenes entry.

                (Cheng et al., 2005)
                Relationship to Other Genes
                Source for database merge of

                Source for merge of: CG5161 BcDNA:RE62842

                (FlyBase, 1996-)

                Source for merge of: l(3)72Dh CG5161

                (Cooper and Kennison, 2011)

                Source for merge of: l(3)72Dh E(smoDN)B-left

                (Cooper and Kennison, 2011)

                Source for merge of: Trs20 l(3)72Dh

                (Robinett et al., 2009)
                Additional comments

                Source for merge of CG5161 BcDNA:RE62842 was a shared cDNA ( date:030728 ).

                (FlyBase, 1996-)
                Nomenclature History
                Source for database identify of
                Nomenclature comments
                Etymology

                Named "Trs20" after the S. cerevisiae ortholog.

                (FlyBase, 2009-)
                Synonyms and Secondary IDs (13)
                Reported As
                Symbol Synonym
                BcDNA:RE62842
                CG5161
                (Hosono et al., 2015, Gillingham et al., 2014, Japanese National Institute of Genetics, 2012.5.21, Cooper and Kennison, 2011, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Perkins et al., 2009, Robinett et al., 2009, Gandhi et al., 2007, Saleh et al., 2006)
                E(smoDN)B-left
                (Cooper and Kennison, 2011)
                Group B-left
                (Collins and Cohen, 2005)
                TRAPP2C
                (Otsuka et al., 2019)
                TRAPPC2
                (Riedel et al., 2018)
                Trs20
                (Song et al., 2022, Transgenic RNAi Project members, 2017-, Bischof and FlyORF project members, 2014.6.20)
                Trs20p
                (Littleton, 2000)
                l(3)72Dh
                (Lindsley et al., 2013, Cooper and Kennison, 2011)
                Name Synonyms
                Enhancer of smoDN group B-left
                (Collins, 2005.7.7)
                TRAPP subunit 20
                TRAPP subunit 20 ortholog
                lethal (3) 72Dh
                Secondary FlyBase IDs
                • FBgn0044807
                • FBgn0263604
                • FBgn0005540
                • FBgn0036573
                • FBgn0047077
                • FBgn0083255
                Datasets (0)
                Study focus (0)
                Experimental Role
                Project
                Project Type
                Title
                Study result (0)
                Result
                Result Type
                Title
                External Crossreferences and Linkouts ( 36 )
                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.
                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.
                UniProt/Swiss-Prot - Manually annotated and reviewed 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.
                DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
                EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
                FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
                InterPro - A database of protein families, domains and functional sites
                KEGG Genes - Molecular building blocks of life in the genomic space.
                MARRVEL_MODEL - MARRVEL (model organism gene)
                PDB - An information portal to biological macromolecular structures
                Linkouts
                Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
                DroID - A comprehensive database of gene and protein interactions.
                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
                Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
                FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
                iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
                MIST (genetic) - An integrated Molecular Interaction Database
                MIST (protein-protein) - An integrated Molecular Interaction Database
                Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                References (49)