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General Information
Symbol
Dmel\cup
Species
D. melanogaster
Name
cup
Annotation Symbol
CG11181
Feature Type
FlyBase ID
FBgn0000392
Gene Model Status
Stock Availability
Gene Snapshot
In progress.Contributions welcome.
Also Known As

fs(2)cup, fs(1)cup

Key Links
Genomic Location
Cytogenetic map
Sequence location
2L:6,663,664..6,674,780 [+]
Recombination map

2-21

RefSeq locus
NT_033779 REGION:6663664..6674780
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
-
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
Predictions / Assertions
Summaries
Protein Function (UniProtKB)
Adapter protein that plays a central role in localization of transcripts in the oocyte and in young embryos (PubMed:9118812). Maintains RNA targets in a repressed state by promoting their deadenylation and protects deadenylated mRNAs from further degradation (PubMed:21937713). Binds to and recruits eIF-4E to the 3'-UTR of some mRNA targets which prevents interaction between eIF4E1 and eIF4G (PubMed:14685270, PubMed:15465908, PubMed:21081899). This may contribute to translational repression but does not appear to be necessary for it to occur (PubMed:21081899). Can promote translational repression independently of deadenylation and eIF4E1 binding (PubMed:21937713). Required for correct localization of eIF4E1 in the developing oocyte (PubMed:15465908). Required for translational repression of oskar (osk) mRNA (PubMed:14691132, PubMed:14723848). Also required for the translational repression of nanos (nos) mRNA (PubMed:21081899). Promotes the accumulation of the germ plasm components osk, vas and stau at the posterior pole of the oocyte and is required for germ cell development (PubMed:22454519, PubMed:17277377). Represses orb positive autoregulatory activity which prevents premature activation of orb and ensures its accumulation specifically in the developing oocyte (PubMed:22164257). In 0-1 hour embryos, forms a complex with me31B, cup, tral and pAbp which binds to various mRNAs including maternal mRNAs, and downregulates their expression during the maternal-to-zygotic transition (PubMed:28875934).
(UniProt, Q9VMA3)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
cup: cup (T. Schupbach)
Female-sterile; homozygous females show abnormalities in late oogenesis. Follicle cells do not migrate centripetally between nurse cells and oocyte. They do synthetize a chorion which remains open ended (like a chalice, or cup). Such eggs are usually not laid and remain unfertilized.
Summary (Interactive Fly)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\cup or the JBrowse view of Dmel\cup 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
Comments on Gene Model

gene_with_dicistronic_mRNA ; SO:0000722

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

Gene model reviewed during 5.46

Gene model reviewed during 5.56

Multiphase exon postulated: this gene shares a region of coding sequence with an overlapping gene, but different reading frames are utilized in the overlapping coding region.

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0290322
4002
1117
FBtr0346452
4306
1117
Additional Transcript Data and Comments
Reported size (kB)

4.3, 4.1, 3.8 (northern blot)

Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0288761
125.7
1117
9.27
FBpp0312102
125.7
1117
9.27
Polypeptides with Identical Sequences

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

1117 aa isoforms: cup-PB, cup-PC
Additional Polypeptide Data and Comments
Reported size (kDa)

1312 (aa); 180, 150, 110, 45 (kD observed); 130 (kD predicted)

Comments
External Data
Subunit Structure (UniProtKB)

Component of the osk RNP complex, which is composed of at least exu, yps, aret/bruno, cup, and the mRNA of osk (PubMed:10662770). Interacts with the decapping activators me31B and tral (PubMed:21937713). Component of the nos RNP complex, which is composed of at least smg, cup, tral, me31B, the CCR4-NOT complex members Rga/NOT2 and Caf1, and the mRNA of nos (PubMed:21081899). Interacts with btz (PubMed:14691132, PubMed:14723848). Recruited to the 3'-UTR of nos and osk mRNAs by smg and btz, respectively (PubMed:14685270, PubMed:14691132). Forms a ribonucleoprotein complex (RNP) containing at least me31B, eIF4E1, cup, tral and pAbp; this interaction is required for the translational silencing of maternal mRNAs during the maternal-to-zygotic transition (PubMed:28875934). No interaction was detected with pAbp in 1-5 hour embryos (PubMed:28875934). Interacts with osk and vas (PubMed:22454519). Interacts with Pop2, twin/CCR4, Rga, Not3 and Not1 which are all core components of the CCR4-NOT deadenylase complex; interaction with the complex is required for cup deadenylation activity (PubMed:21937713). Interacts with nos (PubMed:11060247). Interacts with smg (PubMed:14685270). Interacts with eIF4E1; the interaction promotes retention of cup in the cytoplasm (PubMed:14723848, PubMed:14685270, PubMed:15465908, PubMed:21937713). Interacts with orb; the interaction represses the orb positive autoregulatory loop (PubMed:22164257). Interacts with Nup154 (PubMed:17277377).

(UniProt, Q9VMA3)
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\cup using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (24 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from physical interaction with UniProtKB:Q9V463
(assigned by UniProt )
inferred from physical interaction with UniProtKB:Q9VTZ0
(assigned by UniProt )
inferred from direct assay
inferred from direct assay
(assigned by UniProt )
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN001283523
(assigned by GO_Central )
Biological Process (11 terms)
Terms Based on Experimental Evidence (11 terms)
CV Term
Evidence
References
inferred from genetic interaction with UniProtKB:P25724
(assigned by UniProt )
inferred from direct assay
(assigned by UniProt )
inferred from mutant phenotype
inferred from direct assay
inferred from physical interaction with FLYBASE:eIF4E1; FB:FBgn0015218
inferred from mutant phenotype
inferred from genetic interaction with UniProtKB:Q9V463
(assigned by UniProt )
inferred from mutant phenotype
inferred from high throughput mutant phenotype
inferred from high throughput mutant phenotype
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN001283523
(assigned by GO_Central )
Cellular Component (9 terms)
Terms Based on Experimental Evidence (9 terms)
CV Term
Evidence
References
inferred from high throughput direct assay
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
NOT P-body
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN001283523
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN001283523
(assigned by GO_Central )
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
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

cup protein colocalizes with Hsp83 protein in the cytoplasm of germline stem cells in region 1, is nearly absent in the anterior of region 2 (cystoblast cleavage stage), but rises to high levels in the posterior part of region 2, and in the maturing germline cysts of region 3. cup protein is accumulates at the posterior cytoplasm of oocytes up to oogenesis stage 8; around nurse cell nuclei in early egg chambers, and in nurse cell cytoplasm.

cup protein is uniform and abundant in the cytoplasm of all cleavage stage embryos up through stage 9. In the ovary, cup protein is found in the cytoplasm of all germ-line cells. It accumulates preferentially in the future oocyte as early as germarium stage 2a. It continues to be selectively enriched in the oocyte until stage S8. During stage S9, the nurse cells and oocyte contain similar amounts of cup protein and by stage S10, it is localized preferentially in the nurse cells. Within the nurse cells, cup protein accumulates in large aggregates whose location varies as egg chambers develop.

180kD, 110kD and 45kD cup proteins are male-specific and are detected in male testis.

Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from high throughput direct assay
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
NOT P-body
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
Stage
Tissue/Position (including subcellular localization)
Reference
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\cup in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 4-6
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 59 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of cup
Transgenic constructs containing regulatory region of cup
Deletions and Duplications ( 2 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
2 of 15
Yes
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
2 of 15
Yes
No
Rattus norvegicus (Norway rat) (1)
2 of 13
Yes
No
Xenopus tropicalis (Western clawed frog) (0)
No records found.
Danio rerio (Zebrafish) (1)
2 of 15
Yes
No
Caenorhabditis elegans (Nematode, roundworm) (1)
1 of 15
Yes
No
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091901T9 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091501AA )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( None identified )
No non-Dipteran orthologies identified
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( None identified )
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
No non-Arthropod Metazoa orthologies identified
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (1)
2 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 v7.1 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
    esyN Network Diagram
    Show neighbor-neighbor interactions:
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Interactions Browser

    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    RNA-protein
    Physical Interaction
    Assay
    References
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    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
    External Data
    Subunit Structure (UniProtKB)
    Component of the osk RNP complex, which is composed of at least exu, yps, aret/bruno, cup, and the mRNA of osk (PubMed:10662770). Interacts with the decapping activators me31B and tral (PubMed:21937713). Component of the nos RNP complex, which is composed of at least smg, cup, tral, me31B, the CCR4-NOT complex members Rga/NOT2 and Caf1, and the mRNA of nos (PubMed:21081899). Interacts with btz (PubMed:14691132, PubMed:14723848). Recruited to the 3'-UTR of nos and osk mRNAs by smg and btz, respectively (PubMed:14685270, PubMed:14691132). Forms a ribonucleoprotein complex (RNP) containing at least me31B, eIF4E1, cup, tral and pAbp; this interaction is required for the translational silencing of maternal mRNAs during the maternal-to-zygotic transition (PubMed:28875934). No interaction was detected with pAbp in 1-5 hour embryos (PubMed:28875934). Interacts with osk and vas (PubMed:22454519). Interacts with Pop2, twin/CCR4, Rga, Not3 and Not1 which are all core components of the CCR4-NOT deadenylase complex; interaction with the complex is required for cup deadenylation activity (PubMed:21937713). Interacts with nos (PubMed:11060247). Interacts with smg (PubMed:14685270). Interacts with eIF4E1; the interaction promotes retention of cup in the cytoplasm (PubMed:14723848, PubMed:14685270, PubMed:15465908, PubMed:21937713). Interacts with orb; the interaction represses the orb positive autoregulatory loop (PubMed:22164257). Interacts with Nup154 (PubMed:17277377).
    (UniProt, Q9VMA3 )
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2L
    Recombination map

    2-21

    Cytogenetic map
    Sequence location
    2L:6,663,664..6,674,780 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    26F6-26F7
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    27A-27A
    (determined by in situ hybridisation)
    27B-27B
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (12)
    Genomic Clones (19)
    cDNA Clones (89)
     

    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 sequences
    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)
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    Antibody Information
    Laboratory Generated Antibodies
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of

    Source for identity of: cup CG11181

    Source for database merge of
    Additional comments

    One or more of the processed transcripts for this gene contain(s) two non-overlapping open reading frames (ORFs). The non-overlapping ORFs are represented by CG34310 and cup.

    Other Comments

    Cell-free assays indicate that the cup protein represses osk translation by binding to the eIF-4E cap-binding protein and recruiting the aret protein, thus preventing recruitment of the small ribosomal subunit.

    cup functions in smg mediated translation repression.

    cup is a component of the osk RNP complex.

    cup is specifically required to localise btz to the oocyte. cup is required to localise eIF-4E to the posterior of the oocyte.

    cup has been cloned and characterised.

    cup is continuously required for maintenance of nurse cell chromosome structure.

    Mutaions at the cup locus cause defects in midoogenesis.

    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 52 )
    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 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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
    UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
    Other crossreferences
    BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    Flygut - An atlas of the Drosophila adult midgut
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    InterPro - A database of protein families, domains and functional sites
    KEGG Genes - Molecular building blocks of life in the genomic space.
    modMine - A data warehouse for the modENCODE project
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DPiM - Drosophila Protein interaction map
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
    FlyMine - An integrated database for Drosophila genomics
    Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Synonyms and Secondary IDs (8)
    Reported As
    Symbol Synonym
    Secondary FlyBase IDs
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (161)