FB2025_01 , released February 20, 2025
Gene: Dmel\Use1
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General Information
Symbol
Dmel\Use1
Species
D. melanogaster
Name
Unconventional SNARE in the ER 1
Annotation Symbol
CG14181
Feature Type
protein_coding_gene
FlyBase ID
FBgn0035965
Gene Model Status
Current
Stock Availability
5 publicly available
Gene Summary
SNARE that may be involved in targeting and fusion of Golgi-derived retrograde transport vesicles with the ER (By similarity). Required for protein secretion. (UniProt, Q9VSU7)
Contribute a Gene Snapshot for this gene.
All Summaries
Key Links
Genomic Location
Cytogenetic map
67A1-67A1
Sequence location
Recombination map
3-28
RefSeq locus
NT_037436 REGION:9135709..9137181
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 (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables SNAP receptor activity
inferred from biological aspect of ancestor with PANTHER:PTN000990443
(GO Reference Genome Project, 2011-)
inferred from sequence or structural similarity with UniProtKB:P53146
(Gene Ontology Curators, 2002-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in Golgi organization
inferred from mutant phenotype
(Bard et al., 2006)
involved_in protein secretion
inferred from mutant phenotype
(Bard et al., 2006)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
inferred from sequence or structural similarity with SGD:S000003066
(Gene Ontology Curators, 2002-)
inferred from biological aspect of ancestor with PANTHER:PTN000990443
(GO Reference Genome Project, 2011-)
Cellular Component (4 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)
located_in endoplasmic reticulum
inferred from direct assay
(Bard et al., 2006)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
located_in cytoplasmic side of endoplasmic reticulum membrane
inferred from sequence or structural similarity with SGD:S000003066
(Gene Ontology Curators, 2002-)
is_active_in endoplasmic reticulum
inferred from biological aspect of ancestor with PANTHER:PTN000990443
(GO Reference Genome Project, 2011-)
located_in endoplasmic reticulum
inferred from sequence or structural similarity with UniProtKB:P53146
(Gene Ontology Curators, 2002-)
part_of SNARE complex
inferred from sequence or structural similarity with SGD:S000003066
(Gene Ontology Curators, 2002-)
inferred from biological aspect of ancestor with PANTHER:PTN000990443
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the USE1 family. (Q9VSU7)
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
Qc-SNAREs -
Q-SNAREs are members of the SNARE (soluble N-ethylmaleimide-sensitive factor-attachment protein (SNAP) receptor) family that mediate vesicle-fusion. SNAREs are cytoplasmic, membrane-anchored proteins that contain a 60 amino acid SNARE domain. Three Q-SNAREs domains from the target membrane and one R-SNARE domain from the vesicle interact to form a four four-helix bundle that pulls the two membranes in close proximity and promotes fusion. After fusion, the complexes are dissembled by NSF (N-ethylmaleimide-sensitive factor) and SNAPs (Soluble NSF Attachment Proteins). Q-SNAREs are named from their contribution of a conserved Glutamine (Q) residue to the helix bundle. Q-SNARE domains are designated a, b or c, depending on their position within the helix bundle. (Adapted from PMID:15893389 and FBrf0216182).
Protein Function (UniProtKB)
SNARE that may be involved in targeting and fusion of Golgi-derived retrograde transport vesicles with the ER (By similarity). Required for protein secretion.
(UniProt, Q9VSU7)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Use1 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 Q9VSU7)

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 5.40

Gene model reviewed during 5.45

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Use1-RA
FBtr0076537
NM_140032
980
250
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
Use1-PA
FBpp0076264
28.3
250
10.02
Q9VSU7
NP_648289
AAF50314
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
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\Use1 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).

0.74

Transcript Expression
Additional Descriptive Data
Marker for
 
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)
located_in endoplasmic reticulum
inferred from direct assay
(Bard et al., 2006)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Use1 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
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 2 )
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 Use1
Transgenic constructs containing regulatory region of Use1
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
Inferred from location ( 6 )
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\USE1
13 of 14
Yes
Yes
1  
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\Use1
13 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Use1
12 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\use1
6 of 13
Yes
Yes
Xtro\mat2a
1 of 13
No
No
Danio rerio (Zebrafish) (1)
Drer\use1
13 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\use-1
11 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP005893
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (2)
Atha\AT1G54110
3 of 13
Yes
Yes
Atha\AT3G55600
3 of 13
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\USE1
3 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\SPAC17G6.07c
8 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Use1. 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?
    USE1; unconventional SNARE in the ER 1
    13 of 14
    610675
         
        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)
        Other Interaction Browsers
        View in FlyBase Interactions Browser   View in MIST tool (external link)
        Please see the Physical Interaction reports below for full details
        protein-protein
        Physical Interaction
        Assay
        References
        Use1 - Bet1
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Gos28
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Membrin
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Nsf2
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Sec20
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Sec22
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Seipin
        anti tag coimmunoprecipitation, peptide massfingerprinting
        (Bi et al., 2014)
        Use1 - Slh
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Snap24
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Snap29
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Syb
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Syx13
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Syx18
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Syx1A
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Syx5
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Syx7
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Syx8
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Vamp7
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Vti1a
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - Ykt6
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - koko
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - αSnap
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - γSnap1
        experimental knowledge based
        (Guruharsha et al., 2011)
        Use1 - γSnap2
        experimental knowledge based
        (Guruharsha et al., 2011)
        Summary of Genetic Interactions
        esyN Network Diagram
        Other Interaction Browsers
        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.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        FlyBase
        External Links
        External Data
        Linkouts
        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Class of Gene
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3L
        Recombination map
        3-28
        Cytogenetic map
        67A1-67A1
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        67A1-67A1
        Limits computationally determined from genome sequence between P{PZ}l(3)0162901629&P{PZ}mRpL1210534 and P{EP}Hsp26EP3336&P{EP}Hsp26EP3315
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        3-28

        (FlyBase, 2016)

        3-21.9

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (5)
        Genomic Clones (17)
         

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

        cDNA Clones (5)
         

        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

                dsRNA directed against this gene has been used in a screen for genes required for constitutive protein secretion.

                (Bard et al., 2006)

                dsRNA directed against Use1 inhibits protein secretion in S2 cells and results in fusion of Golgi membranes with the endoplasmic reticulum in more than 50% of the treated cells.

                (Bard et al., 2006)
                Relationship to Other Genes
                Source for database merge of
                Additional comments
                Nomenclature History
                Source for database identify of

                Source for identity of: Use1 CG14181

                (Bard et al., 2006)
                Nomenclature comments
                Etymology

                Named "Use1" after the S. cerevisiae ortholog.

                (FlyBase, 2009-)
                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 ( 29 )
                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
                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
                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
                Flygut - An atlas of the Drosophila adult midgut
                FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
                iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
                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
                Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                References (39)