FB2024_02 , released April 23, 2024
Gene: Dmel\Trp1
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General Information
Symbol
Dmel\Trp1
Species
D. melanogaster
Name
Translocation protein 1
Annotation Symbol
CG4758
Feature Type
protein_coding_gene
FlyBase ID
FBgn0011584
Gene Model Status
Current
Stock Availability
10 publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

Dtrp1

Key Links
Genomic Location
Cytogenetic map
30F5-30F5
Sequence location
Recombination map
2-38
RefSeq locus
NT_033779 REGION:10009381..10013170
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 (8 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables protein transmembrane transporter activity
inferred from genetic interaction with SGD:S000006015
(Noel and Cartwright, 1994)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables protein transmembrane transporter activity
inferred from sequence or structural similarity with SGD:S000006015
(Gene Ontology Curators, 2002-)
Biological Process (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in post-translational protein targeting to membrane, translocation
inferred from genetic interaction with SGD:S000006015
(Noel and Cartwright, 1994)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in post-translational protein targeting to membrane, translocation
inferred from biological aspect of ancestor with PANTHER:PTN000278138
(GO Reference Genome Project, 2011-)
inferred from sequence or structural similarity with SGD:S000006015
(Gene Ontology Curators, 2002-)
involved_in protein transport
inferred from electronic annotation with InterPro:IPR004728
(InterPro Project Members, 2004-)
Cellular Component (5 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in endomembrane system
inferred from high throughput direct assay
(Tan et al., 2009)
part_of Sec62/Sec63 complex
inferred from genetic interaction with SGD:S000006015
(Noel and Cartwright, 1994)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
is_active_in endoplasmic reticulum membrane
inferred by curator from GO:0008320
(Noel and Cartwright, 1994)
located_in endoplasmic reticulum membrane
inferred from electronic annotation with InterPro:IPR004728
(InterPro Project Members, 2004-)
is_active_in endoplasmic reticulum
inferred from biological aspect of ancestor with PANTHER:PTN000278138
(GO Reference Genome Project, 2011-)
located_in endoplasmic reticulum
inferred from sequence or structural similarity with SGD:S000006015
(Gene Ontology Curators, 2002-)
is_active_in membrane
inferred from biological aspect of ancestor with PANTHER:PTN000278138
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
SEC62/SEC63 COMPLEX -
The Sec62/Sec63 complex is a subcomplex of the endoplasmic reticulum Sec complex that is involved in the transmembrane translocation of proteins into the ER. (Adapted from PMID: 29263911.)
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
4

Please see the JBrowse view of Dmel\Trp1 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 Q9VL49)

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

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

Gene model reviewed during 5.52

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Trp1-RA
FBtr0079931
NM_057660
2045
415
Trp1-RB
FBtr0079932
NM_164885
2093
428
Trp1-RC
FBtr0305986
NM_001259031
1532
398
Trp1-RD
FBtr0343741
NM_001298863
1484
385
Additional Transcript Data and Comments
Reported size (kB)

2.2, 1.6 (northern blot)

(Noel and Cartwright, 1994)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
Trp1-PA
FBpp0079521
47.1
415
6.02
Q9VL50
NP_477008
AAF52847
Trp1-PB
FBpp0079522
48.6
428
4.65
Q9VL49
NP_723510
AAF52848
Trp1-PC
FBpp0297128
45.4
398
4.72
C6SV41
NP_001245960
AFH03634
Trp1-PD
FBpp0310307
44.0
385
6.66
X2J9A4
NP_001285792
AHN54306
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)

402 (aa); 46 (kD)

(Noel and Cartwright, 1994)
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\Trp1 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).

-0.24

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 4 -- 6
organism
(Fisher et al., 2012)
embryonic stage 7 -- 8
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 11
salivary gland body primordium
(Abrams and Andrew, 2005)
embryonic stage 11 -- 12
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 13 -- 14
presumptive embryonic salivary gland
(Abrams and Andrew, 2005)
embryonic stage 13 -- 16
organism | ubiquitous
(Fisher et al., 2012)
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage -- adult stage
(Noel and Cartwright, 1994)
adult stage | male
ejaculatory duct
(Noel and Cartwright, 1994)
male accessory gland
(Noel and Cartwright, 1994)
adult stage | female
(Noel and Cartwright, 1994)
oogenesis & adult stage | female
ovary
(Noel and Cartwright, 1994)
spermatogenesis & adult stage
testis
(Noel and Cartwright, 1994)
Additional Descriptive Data

Trp1 2.2kb transcripts are expressed throughout development with peaks in 6-12hr embryos and at 18-30hr post-pupation. They are expressed at low levels in the testis and in accessory glands in males and are also present in the carcass. They at expressed at nearly equal levels in the ovary and carcass in females.

(Noel and Cartwright, 1994)
Marker for
 
salivary gland body primordium
(Abrams and Andrew, 2005)
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
day 7 of adulthood -- day 49 of adulthood
adult heart
(Cammarato et al., 2011)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in endomembrane system
inferred from high throughput direct assay
(Tan et al., 2009)
part_of Sec62/Sec63 complex
inferred from genetic interaction with SGD:S000006015
(Noel and Cartwright, 1994)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Trp1 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
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
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
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 6 )
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 Trp1
Transgenic constructs containing regulatory region of Trp1
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
Inferred from location ( 0 )
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) (1)
Hsap\SEC62
13 of 14
Yes
Yes
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) (1)
Rnor\Sec62
12 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Sec62
12 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\sec62
2 of 13
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\sec62
13 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\C18E9.2
13 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP009788
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
Atha\AT3G20920
6 of 13
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\SEC62
9 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\sec62
8 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Trp1. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
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?
    SEC62; SEC62 homolog, preprotein translocation factor
    13 of 14
    602173
        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
        Show neighbor-neighbor interactions:
        Show/hide secondary interactors 
        (data from AllianceMine provided by esyN)
        Select Layout:
        Legend:
        Protein
        RNA
        Selected Interactor(s)
        Interactions Browser
        View in Interactions Browser
        Please see the Physical Interaction reports below for full details
        MIST Molecular Interaction Search Tool
        View in MIST tool (external link)
        Please see the Physical Interaction reports below for full details
        protein-protein
        Physical Interaction
        Assay
        References
        Trp1 - Atg8a
        pull down, anti tag western blot
        (Wang et al., 2023)
        Trp1 - Hpd
        experimental knowledge based
        (Guruharsha et al., 2011)
        Trp1 - TwdlF
        experimental knowledge based
        (Guruharsha et al., 2011)
        Trp1 - rb
        experimental knowledge based
        (Guruharsha et al., 2011)
        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
        BioGRID - A database of protein and genetic interactions.
        DroID - A comprehensive database of gene and protein interactions.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Linkouts
        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        2L
        Recombination map
        2-38
        Cytogenetic map
        30F5-30F5
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        30F5-30F5
        Limits computationally determined from genome sequence between P{EP}CG4747EP594&P{lacW}l(2)k13305k13305 and P{lacW}l(2)k06324k06324
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        31A-31A
        (Cartwright, 1994.10.12)
        Experimentally Determined Recombination Data
        Location

        2-38

        (FlyBase, 2016)

        2-33.2

        (Comeron et al., 2012)

        2-

        (Cartwright, 1994.10.12)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (10)
        Genomic Clones (14)
         

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

        cDNA Clones (269)
         

        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
        DRSC - Results frm RNAi screens
        Antibody Information
        Laboratory Generated Antibodies
         
        Commercially Available Antibodies
         
        Cell Line Information
        Publicly Available Cell Lines
         
          Other Stable Cell Lines
           
            Other Comments

            Trp1 has been cloned and characterised. Trp1 encodes a protein with a domain of sequence homology to the yeast endoplasmic reticulum membrane-bound translocation protein encoded by Scer\SEC62.

            (Noel and Cartwright, 1994)
            Relationship to Other Genes
            Source for database merge of
            Additional comments
            Nomenclature History
            Source for database identify of
            Nomenclature comments
            Etymology
            Synonyms and Secondary IDs (6)
            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.
            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/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.
            BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
            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
            FlyMine - An integrated database for Drosophila genomics
            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)
            Linkouts
            BioGRID - A database of protein and genetic interactions.
            Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
            DroID - A comprehensive database of gene and protein interactions.
            DRSC - Results frm RNAi screens
            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
            Flygut - An atlas of the Drosophila adult midgut
            KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
            MIST (protein-protein) - An integrated Molecular Interaction Database
            References (54)