FlyBase Gene Report: Dmel\cup

General Information

Symbol

Dmel\cup

Species

D. melanogaster

Name

cup

Annotation Symbol

CG11181

Feature Type

protein_coding_gene

FlyBase ID

FBgn0000392

Gene Model Status

Current

Stock Availability

13 publicly available

Gene Summary

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 down-regulates their expression during the maternal-to-zygotic transition (PubMed:28875934). (UniProt, Q9VMA3)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
UniProtKB
Red Book
Interactive Fly

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

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

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Other Genome Views

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

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (27 terms)

Molecular Function (5 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

enables eukaryotic initiation factor 4E binding

inferred from direct assay

(Igreja et al., 2014)

enables protein binding

inferred from physical interaction with UniProtKB:Q9V463

(assigned by UniProt )

(Grimaldi et al., 2007)

inferred from physical interaction with UniProtKB:Q9VTZ0

(assigned by UniProt )

(Wilhelm et al., 2005)

enables RNA binding

inferred from direct assay

(Chekulaeva et al., 2006)

enables translation regulator activity

inferred from direct assay

(assigned by UniProt )

(Nakamura et al., 2004)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables mRNA binding

inferred from biological aspect of ancestor with PANTHER:PTN001283523

(assigned by GO_Central )

(Gaudet et al., 2011)

Biological Process (13 terms)

Terms Based on Experimental Evidence (13 terms)

CV Term

Evidence

References

involved_in dorsal/ventral pattern formation

inferred from mutant phenotype

(Clouse et al., 2008)

involved_in female meiotic nuclear division

inferred from genetic interaction with UniProtKB:P25724

(assigned by UniProt )

(Verrotti and Wharton, 2000)

involved_in intracellular mRNA localization

inferred from mutant phenotype

(Clouse et al., 2008)

involved_in meiotic chromosome segregation

inferred from direct assay

(assigned by UniProt )

(Keyes and Spradling, 1997)

involved_in negative regulation of eukaryotic translation initiation factor 4F complex assembly

inferred from direct assay

(Igreja et al., 2014)

involved_in negative regulation of oskar mRNA translation

inferred from mutant phenotype

(Wilhelm et al., 2003)

inferred from direct assay

(Chekulaeva et al., 2006)

involved_in negative regulation of translational initiation

inferred from direct assay

(Igreja et al., 2014)

involved_in negative regulation of translation

inferred from mutant phenotype

(Clouse et al., 2008)

inferred from physical interaction with FLYBASE:eIF4E1; FB:FBgn0015218

(Nelson et al., 2004)

involved_in oocyte growth in germarium-derived egg chamber

inferred from genetic interaction with UniProtKB:Q9V463

(assigned by UniProt )

(Grimaldi et al., 2007)

involved_in oogenesis

inferred from high throughput mutant phenotype

(Schupbach and Wieschaus, 1991)

inferred from mutant phenotype

(Clouse et al., 2008)

involved_in ovarian follicle cell migration

inferred from high throughput mutant phenotype

(Schupbach and Wieschaus, 1991)

involved_in regulation of pole plasm oskar mRNA localization

inferred from mutant phenotype

(Lasko, 2003, Wilhelm et al., 2003)

involved_in regulation of synaptic assembly at neuromuscular junction

inferred from mutant phenotype

(Menon et al., 2015)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in negative regulation of translation

inferred from biological aspect of ancestor with PANTHER:PTN001283523

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (9 terms)

Terms Based on Experimental Evidence (9 terms)

CV Term

Evidence

References

located_in cytoplasm

inferred from direct assay

(Kamenska et al., 2014, Pisa et al., 2009)

located_in cytosol

inferred from high throughput direct assay

(Lye et al., 2014)

colocalizes_with endoplasmic reticulum exit site

inferred from direct assay

(assigned by UniProt )

(Wilhelm et al., 2005)

part_of messenger ribonucleoprotein complex

inferred from direct assay

(assigned by UniProt )

(Barbee et al., 2006, Wilhelm et al., 2005)

located_in neuromuscular junction

inferred from direct assay

(Menon et al., 2015)

located_in neuronal ribonucleoprotein granule

inferred from direct assay

(assigned by UniProt )

(Barbee et al., 2006)

located_in nucleus

inferred from direct assay

(Kamenska et al., 2014)

located_in P-body

inferred from direct assay

(assigned by UniProt )

(Wilhelm et al., 2005)

inferred from direct assay

(Cauchi et al., 2010)

located_in terminal bouton

inferred from direct assay

(Menon et al., 2015)

NOT located_in P-body

inferred from direct assay

(Kamenska et al., 2014)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in cytoplasm

inferred from biological aspect of ancestor with PANTHER:PTN001283523

(assigned by GO_Central )

(Gaudet et al., 2011)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN001283523

(assigned by GO_Central )

(Gaudet et al., 2011)

Gene Group (FlyBase)

Protein Family (UniProt)

Belongs to the 4E-T/EIF4E-T family. (Q9VMA3)

Protein Signatures (InterPro)

Eukaryotic translation initiation factor 4E binding protein

Summaries

Protein Function (UniProtKB)

(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)

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see 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

Structure New Section

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q9VMA3)

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

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

gene_with_dicistronic_mRNA

(FlyBase Genome Annotators, 2012)

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

cup-RB

FBtr0290322

NM_078769

4002

1117

cup-RC

FBtr0346452

NM_001298758

4306

1117

Additional Transcript Data and Comments

Reported size (kB)

4.3, 4.1, 3.8 (northern blot)

(Keyes and Spradling, 1997)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

cup-PB

FBpp0288761

125.7

1117

9.27

NP_523493

AAF52418

cup-PC

FBpp0312102

125.7

1117

9.27

NP_001285687

AHN54202

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)

(Keyes and Spradling, 1997)

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 (via YXXXXLphi motifs) with eIF4E1; the interaction promotes retention of cup in the cytoplasm (PubMed:14723848, PubMed:14685270, PubMed:15465908, PubMed:21937713, PubMed:22832024). Interacts with orb; the interaction represses the orb positive autoregulatory loop (PubMed:22164257). Interacts with Nup154 (PubMed:17277377).

(UniProt, Q9VMA3)

Domain

The YXXXXLphi motifs mediate interaction with eIF4E1.

(UniProt, Q9VMA3)

Crossreferences

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

Eukaryotic translation initiation factor 4E binding protein

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\cup using the Feature Mapper tool.

External Data

Crossreferences

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

cup_1
cup_2

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 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism

Comment: rapidly degraded

(Fisher et al., 2012)

primordial germ cell

(Fisher et al., 2012)

embryonic stage 7 -- 8

primordial germ cell

(Fisher et al., 2012)

embryonic stage 9 -- 10

germline cell

(Fisher et al., 2012)

embryonic stage 11 -- 12

germline cell

(Fisher et al., 2012)

embryonic stage 13 -- 16

germline cell

(Fisher et al., 2012)

gonad

(Fisher et al., 2012)

adult stage | female & oogenesis

germarium

(Keyes and Spradling, 1997)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 9

organism

(Keyes and Spradling, 1997)

adult stage | male

(Keyes and Spradling, 1997)

oogenesis & adult stage | female

ovary

(Keyes and Spradling, 1997)

adult stage & oogenesis

germline stem cell

(Keyes and Spradling, 1997)

germarium region 2a

(Keyes and Spradling, 1997)

germarium region 1

(Keyes and Spradling, 1997)

germarium region 3

(Keyes and Spradling, 1997)

cystoblast

(Keyes and Spradling, 1997)

germarium region 2b

(Keyes and Spradling, 1997)

oogenesis stage S1 -- S8

(Keyes and Spradling, 1997)

oogenesis stage S10 -- S14

(Keyes and Spradling, 1997)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

cleavage stage

organism

(Keyes and Spradling, 1997)

adult stage | female

germarium region 1

(Pisa et al., 2009)

germarium region 2b

(Pisa et al., 2009)

germarium region 3

(Pisa et al., 2009)

female germline stem cell

(Pisa et al., 2009)

adult stage & oogenesis

nurse cell

(Keyes and Spradling, 1997)

oocyte

(Keyes and Spradling, 1997)

oogenesis

nurse cell

(Pisa et al., 2009)

oogenesis stage S1 -- S8

oocyte

(Pisa et al., 2009)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | female

ovary

(Pisa et al., 2009)

adult stage

adult head

• membrane

(Aradska et al., 2015)

western blot

Stage

Tissue/Position (including subcellular localization)

Reference

spermatogenesis & adult stage

testis

(Keyes and Spradling, 1997)

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.

(Pisa et al., 2009)

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.

(Keyes and Spradling, 1997)

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

(Keyes and Spradling, 1997)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in cytoplasm

inferred from direct assay

(Kamenska et al., 2014, Pisa et al., 2009)

located_in cytosol

inferred from high throughput direct assay

(Lye et al., 2014)

colocalizes_with endoplasmic reticulum exit site

inferred from direct assay

(assigned by UniProt )

(Wilhelm et al., 2005)

part_of messenger ribonucleoprotein complex

inferred from direct assay

(assigned by UniProt )

(Barbee et al., 2006, Wilhelm et al., 2005)

located_in neuromuscular junction

inferred from direct assay

(Menon et al., 2015)

located_in neuronal ribonucleoprotein granule

inferred from direct assay

(assigned by UniProt )

(Barbee et al., 2006)

located_in nucleus

inferred from direct assay

(Kamenska et al., 2014)

located_in P-body

inferred from direct assay

(assigned by UniProt )

(Wilhelm et al., 2005)

inferred from direct assay

(Cauchi et al., 2010)

located_in terminal bouton

inferred from direct assay

(Menon et al., 2015)

NOT located_in P-body

inferred from direct assay

(Kamenska et al., 2014)

Expression Deduced from Reporters

Reporter: PBac{681.P.FSVS-1}cup^CPTI001409

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult brain cell body rind

(Knowles-Barley, 2011.8.24)

adult brain

Comment: low expression throughout adult brain

(Knowles-Barley, 2011.8.24)

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

View exonic expression by developmental stage for Dmel\cup

View exonic expression by tissue for Dmel\cup

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

FBgn0000392

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

33934/tissue=All

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

FBgn0000392

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0000392

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

FBgn0000392

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

CG11181

Flygut - An atlas of the Drosophila adult midgut

FBgn0000392

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\cup

Stages(s) 4-6
Stages(s) 9-10
Stages(s) 11-12
Stages(s) 13-16

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

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

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene disrupted in

Df(2L)BSC187

(Christensen and Cook, 2006.12.5)

Df(2L)BSC188

(Christensen and Cook, 2006.8.29)

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

cup^GD7226

viable, with Scer\GAL4^Mef2.PR

cup^GD7226

viable, with Scer\GAL4^pnr-MD237

cup^GD7226

Sterility

Allele

female sterile

female sterile | partially | recessive

cup²¹

female sterile | recessive

Other Phenotypes

Allele

abnormal mitotic cell cycle | oogenesis stage S5

cup²¹

abnormal neuroanatomy | semidominant | third instar larval stage

cup^Δ212

abnormal neuroanatomy | third instar larval stage, with Scer\GAL4^elav-C155

cup^GL00327

abnormal neuroanatomy | third instar larval stage (with cup⁸)

cup^Δ212

abnormal neuroanatomy | third instar larval stage (with cup²⁰)

cup^Δ212

abnormal neuroanatomy | third instar larval stage (with cup^Δ212)

abnormal neuroanatomy | third instar larval stage (with Df(2L)BSC7)

abnormal neurophysiology | third instar larval stage (with cup²⁰)

cup^Δ212

abnormal neurophysiology | third instar larval stage (with cup^Δ212)

cup²⁰

abnormal neurophysiology | third instar larval stage (with Df(2L)BSC7)

Phenotype manifest in

Allele

cleavage nucleus

cup²¹

dorsal appendage

cup¹

egg | maternal effect

cup^Δ212

egg chamber

egg chorion

cup⁰¹³⁵⁵

embryonic/larval neuromuscular junction | third instar larval stage (with cup²⁰)

cup^Δ212

embryonic/larval neuromuscular junction | third instar larval stage (with cup^Δ212)

cup²⁰

embryonic/larval neuromuscular junction | third instar larval stage (with Df(2L)BSC7)

karyosome

cup¹

NMJ bouton | increased number | third instar larval stage

cup^Δ212

NMJ bouton | increased number | third instar larval stage, with Scer\GAL4^elav-C155

cup^GL00327

NMJ bouton | increased number | third instar larval stage (with cup⁸)

cup^Δ212

NMJ bouton | increased number | third instar larval stage (with cup²⁰)

cup^Δ212

NMJ bouton | increased number | third instar larval stage (with cup^Δ212)

NMJ bouton | increased number | third instar larval stage (with Df(2L)BSC7)

nurse cell & chromatin

nurse cell | oogenesis stage S5

cup²¹

ovary

cup²¹

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\EIF4ENIF1

3 of 15

Yes

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Eif4enif1

3 of 15

Yes

Rattus norvegicus (Norway rat) (1)

Rnor\Eif4enif1

3 of 13

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\eif4enif1

2 of 12

Yes

Danio rerio (Zebrafish) (1)

Drer\eif4enif1

2 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\ifet-1

1 of 15

Yes

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.

Other Organism Orthologs (via OrthoDB)

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (1)

Gene Symbol

Score

Source

Alignment

3 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 ( 1 )

Allele

Disease

Interaction

References

cup^NIG.11181R

exacerbates frontotemporal dementia and/or amyotrophic lateral sclerosis-1

modeled by Zzzz\poly-PR^PO-36.UAS

(Park et al., 2021)

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?

EIF4ENIF1; eukaryotic translation initiation factor 4E nuclear import factor 1

3 of 15

607445

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

View in Interactions Browser

Please see the Physical Interaction reports below for full details

RNA-protein

Physical Interaction

Assay

References

cup - Su(var)205

clip, reverse transcription pcr

(Casale et al., 2019)

cup - nos

pull down, autoradiography, two hybrid, Identification by mass spectrometry, western blot

(Götze et al., 2017, Jeske et al., 2011, Kadyrova et al., 2007, Sonoda and Wharton, 2001, Verrotti and Wharton, 2000)

cup - orb

anti bait coimmunoprecipitation, quantitative reverse transcription pcr, western blot

(Ote and Yamamoto, 2018, Wong and Schedl, 2011)

protein-protein

Physical Interaction

Assay

References

cup - BicC

anti tag coimmunoprecipitation, western blot

(Kugler et al., 2009)

cup - Gp93

anti tag coimmunoprecipitation, anti tag western blot

(Pisa et al., 2009)

cup - Hrb27C

anti tag coimmunoprecipitation, Identification by mass spectrometry, anti tag western blot, anti bait coimmunoprecipitation, western blot

(Bansal et al., 2020, Clouse et al., 2008)

cup - Not1

anti tag coimmunoprecipitation, anti tag western blot

(Igreja and Izaurralde, 2011)

cup - Not3

anti tag coimmunoprecipitation, anti tag western blot

(Igreja and Izaurralde, 2011)

cup - Pop2

anti tag coimmunoprecipitation, anti tag western blot

(Igreja and Izaurralde, 2011)

cup - Pur-α

anti tag coimmunoprecipitation, peptide massfingerprinting, western blot

(Aumiller et al., 2012)

cup - RanBPM

anti tag coimmunoprecipitation, Identification by mass spectrometry, anti bait coimmunoprecipitation, western blot

(Zavortink et al., 2020)

cup - Rga

anti tag coimmunoprecipitation, anti tag western blot

(Igreja and Izaurralde, 2011)

cup - bru1

two hybrid, pull down, anti tag western blot, anti bait coimmunoprecipitation, western blot

(Kim et al., 2015, Nakamura et al., 2004)

cup - cnn

anti bait coimmunoprecipitation, peptide massfingerprinting

(Habermann et al., 2012)

cup - exu

anti tag coimmunoprecipitation, western blot

(Wilhelm et al., 2003)

cup - glo

anti tag coimmunoprecipitation, anti tag western blot, Identification by mass spectrometry

(Bansal et al., 2020)

cup - me31B

anti tag coimmunoprecipitation, western blot, anti bait coimmunoprecipitation, peptide massfingerprinting

(Wang et al., 2017, Igreja and Izaurralde, 2011, Kugler et al., 2009, Nakamura et al., 2004)

cup - mira

two hybrid, pull down, western blot

(Piccioni et al., 2009)

cup - nos

pull down, autoradiography, two hybrid, Identification by mass spectrometry, western blot

(Götze et al., 2017, Jeske et al., 2011, Kadyrova et al., 2007, Sonoda and Wharton, 2001, Verrotti and Wharton, 2000)

cup - orb

anti bait coimmunoprecipitation, quantitative reverse transcription pcr, western blot

(Ote and Yamamoto, 2018, Wong and Schedl, 2011)

cup - osk

two hybrid, anti tag coimmunoprecipitation, Identification by mass spectrometry, anti bait coimmunoprecipitation, western blot

(Tanaka et al., 2021, Ottone et al., 2012)

cup - pAbp

anti bait coimmunoprecipitation, western blot, Identification by mass spectrometry

(Wang et al., 2017, Clouse et al., 2008)

cup - pum

three hybrid

(Sonoda and Wharton, 2001)

cup - smg

pull down, autoradiography, peptide massfingerprinting, anti bait coimmunoprecipitation, western blot

(Nelson et al., 2004)

cup - sqd

anti tag coimmunoprecipitation, western blot, anti bait coimmunoprecipitation, peptide massfingerprinting

(Clouse et al., 2008)

cup - sstn

anti tag coimmunoprecipitation, peptide massfingerprinting

(Liu et al., 2015)

cup - stau

anti bait coimmunoprecipitation, western blot, pull down

(Piccioni et al., 2009)

cup - stumps

two hybrid

(Battersby et al., 2003)

cup - tral

anti tag coimmunoprecipitation, anti tag western blot, anti bait coimmunoprecipitation, Identification by mass spectrometry, western blot

(Igreja and Izaurralde, 2011, Tritschler et al., 2008, Wilhelm et al., 2005)

cup - twin

anti tag coimmunoprecipitation, anti tag western blot

(Igreja and Izaurralde, 2011)

cup - vas

anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, anti tag western blot, Identification by mass spectrometry

(Bansal et al., 2020, Ottone et al., 2012)

cup - yps

anti bait coimmunoprecipitation, western blot

(Wilhelm et al., 2005, Wilhelm et al., 2003)

Summary of Genetic Interactions

esyN Network Diagram

esyN Network Key:

Suppression

Enhancement

View in Interactions Browser

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

cup

enhanceable

Dad

(Menon et al., 2015)

cup

enhanceable

eIF4E1

(Zappavigna et al., 2004)

cup

enhanceable

EndoA

(Menon et al., 2015)

cup

enhanceable

Hsp83

(Pisa et al., 2009)

cup

enhanceable

mira

(Piccioni et al., 2009)

cup

suppressible

otu

(Keyes and Spradling, 1997)

cup

enhanceable

otu

(Keyes and Spradling, 1997)

cup

suppressible

spoon

(Neuman-Silberberg, 2007)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

eIF4E1

enhanceable

cup

(Menon et al., 2015)

nos

suppressible

cup

(Verrotti and Wharton, 2000)

otu

enhanceable

cup

(Keyes and Spradling, 1997)

Rbp9

suppressible

cup

(Keyes and Spradling, 1997)

External Data

Subunit Structure (UniProtKB)

(UniProt, Q9VMA3 )

Linkouts

BioGRID - A database of protein and genetic interactions.

60088

DroID - A comprehensive database of gene and protein interactions.

FBgn0000392

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)

Recombination map

2-21

Cytogenetic map

26F6-26F7

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

27B-27B

(Keyes, 1997.5.20)

27A-27A

(determined by in situ hybridisation)

(Spradling et al., 1999)

27B-27B

(determined by in situ hybridisation)

(Keyes and Spradling, 1997)

Experimentally Determined Recombination Data

Location

2-21

(FlyBase, 2016)

2-21.5

(Comeron et al., 2012)

2-23

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (13)

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

Bloomington

26732

y¹ v¹; P{TRiP.JF02274}attP2

12218

P{PZ}cup⁰¹³⁵⁵ cn¹/CyO; ry⁵⁰⁶

29718

y¹; cup¹⁵ cn¹ bw¹/CyO

29719

y¹; cup²¹ cn¹ bw¹/CyO

14399

y¹ w^67c23; P{SUPor-P}cup^KG01851

14339

y¹ w^67c23; P{SUPor-P}Galt^KG00049 cup^KG00049

4978

cup¹ cn¹ bw¹ speck¹/CyO, l(2)DTS513¹

35406

y¹ sc^* v¹ sev²¹; P{TRiP.GL00327}attP2/TM3, Sb¹

Kyoto

122049

w¹¹¹⁸; P{EP}cup^EP2349

115161

w¹¹¹⁸; PBac{681.P.FSVS-1}cup^CPTI001409

107980

cup¹ cn¹ bw¹ speck¹/CyO, l(2)DTS513¹

VDRC

v18179

w¹¹¹⁸; P{GD7226}v18179

More stocks available...

Genomic Clones (19)

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

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 sequenced

BDGP DGC clones

Other clones

DPiM_LD47924

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.

FBgn0000392

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0000392

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

33934

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Nakamura et al., 2004, Nelson et al., 2004, Keyes and Spradling, 1997)

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: cup CG11181

(Wortman, 1999.11)

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.

(FlyBase Genome Annotators, 2012)

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.

(Chekulaeva et al., 2006)

cup functions in smg mediated translation repression.

(Nelson et al., 2004)

cup is a component of the osk RNP complex.

(Wilhelm et al., 2003)

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

(Wilhelm et al., 2003)

cup has been cloned and characterised.

(Keyes and Spradling, 1997)

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

(Keyes and Spradling, 1995)

Mutaions at the cup locus cause defects in midoogenesis.

(Schupbach and Wieschaus, 1991)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 55 )

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.

33934

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.

Q9VMA3

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q9VMA3

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

X2J9P9

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.

Q9VMA3

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0000392

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

FBgn0000392

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

33934/tissue=All

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

FBgn0000392

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

cup_1
cup_2

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0000392

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

FBgn0000392

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

CG11181

Flygut - An atlas of the Drosophila adult midgut

FBgn0000392

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

33934

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

Eukaryotic translation initiation factor 4E binding protein

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

Dmel_CG11181

MARRVEL_MODEL - MARRVEL (model organism gene)

33934

modMine - A data warehouse for the modENCODE project

FBgn0000392

Linkouts

BioGRID - A database of protein and genetic interactions.

60088

DroID - A comprehensive database of gene and protein interactions.

FBgn0000392

DRSC - Results frm RNAi screens

FBgn0000392

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0000392

FlyMine - An integrated database for Drosophila genomics

FBgn0000392

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

MIST (genetic) - An integrated Molecular Interaction Database

MIST (protein-protein) - An integrated Molecular Interaction Database

Synonyms and Secondary IDs (8)

Reported As

Symbol Synonym

CG11181

(Na et al., 2016, Kamenska et al., 2014, Ni et al., 2011.7.19, Müller et al., 2010, Perkins et al., 2009.3.31, Pisa et al., 2009, Hughes et al., 2008, Woo et al., 2006, Battersby et al., 2003, Giannakou and Dow, 2001)

CUP

(Igreja et al., 2014, Tritschler et al., 2008, Semotok et al., 2005)

Cup

(Park et al., 2021, Tanaka et al., 2021, Bansal et al., 2020, Lasko, 2020, Sankaranarayanan and Weil, 2020, Warsaba et al., 2020, Zavortink et al., 2020, Specchia et al., 2019, Ote and Yamamoto, 2018, Specchia et al., 2017, Wang et al., 2017, Kim et al., 2015, Kamenska et al., 2014, Temme et al., 2014, Barckmann and Simonelig, 2013, Vlasova-St Louis et al., 2013, Aumiller et al., 2012, Azzam et al., 2012, Gonsalvez and Long, 2012, Jansen and Niessing, 2012, Ottone et al., 2012, Vazquez-Pianzola and Suter, 2012, Cauchi et al., 2010, Liu, 2010, Iwasaki et al., 2009, Kugler et al., 2009, Lee et al., 2009, Navarro et al., 2009, Nie et al., 2009, Hughes et al., 2008, Kadyrova et al., 2007, Ottone et al., 2007, Wong et al., 2007, Chekulaeva et al., 2006, Cox and Spradling, 2006, Valencia-Sanchez et al., 2006, Berg, 2005, Nelson et al., 2004, Sonoda and Wharton, 2001)

DmCup

(Kamenska et al., 2014)

cup

(Casale et al., 2021, Kim et al., 2021, Hinnant et al., 2020, McCambridge et al., 2020, Schüpbach, 2019, Whittle and Extavour, 2019, Flora et al., 2018, Gene Disruption Project members, 2018-, Broyer et al., 2017, Davidson et al., 2016, Na et al., 2016, Liu et al., 2015, Menon et al., 2015, Peter et al., 2015, FlyBase Genome Annotators, 2012, Habermann et al., 2012, Japanese National Institute of Genetics, 2012.5.21, Baxley et al., 2011, Jeske et al., 2011, Baig et al., 2010, Kushner et al., 2010, Müller et al., 2010, Tastan et al., 2010, Temme et al., 2010, Piccioni et al., 2009, Pisa et al., 2009, Snee and Macdonald, 2009, Clouse et al., 2008, Barnes et al., 2007, Galasso et al., 2007, Grimaldi et al., 2007, Neuman-Silberberg, 2007, Tadros et al., 2007, Christensen and Cook, 2006.8.29, Christensen and Cook, 2006.12.5, Kozak, 2006, McCaffrey et al., 2006, Sugimura and Lilly, 2006, Walser et al., 2006, Woo et al., 2006, Wilhelm et al., 2005, Nakamura et al., 2004, Gigliotti et al., 2000)

fs(1)cup

(Dobens and Raftery, 2000, Keyes and Spradling, 1995)

fs(2)cup

(Zappavigna et al., 2004, Deng and Lin, 2001, Dobens and Raftery, 2000, Deng and Bownes, 1998, Keyes and Spradling, 1997, Keyes and Spradling, 1997, Keyes and Spradling, 1996)

i239

(Battersby et al., 2003)

Name Synonyms

CUP

(Gouw et al., 2009)

Cup

(Costa et al., 2013, Buckingham and Liu, 2011, Fan et al., 2011)

cup

(Schüpbach, 2019, Baig et al., 2010, Kushner et al., 2010, Barnes et al., 2007)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

References (176)

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

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