FlyBase Gene Report: Dmel\c-cup

General Information

Symbol

Dmel\c-cup

Species

D. melanogaster

Name

calcutta cup

Annotation Symbol

CG15623

Feature Type

protein_coding_gene

FlyBase ID

FBgn0031367

Gene Model Status

Current

Stock Availability

3 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

22B3-22B3

Sequence location

2L:1,831,627..1,832,565 [-]

Recombination map

2-3

RefSeq locus

NT_033779 REGION:1831627..1832565

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 (2 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

located_in endomembrane system

inferred from biological aspect of ancestor with PANTHER:PTN000031541

(assigned by GO_Central )

(Gaudet et al., 2011)

located_in membrane

inferred from biological aspect of ancestor with PANTHER:PTN000031541

(assigned by GO_Central )

(Gaudet et al., 2011)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\c-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 model reviewed during 5.47

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

c-cup-RA

FBtr0077894

NM_134779

882

201

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

RefSeq ID

GenBank

c-cup-PA

FBpp0077562

21.9

201

6.78

NP_608623

AAF51335

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

Nucleotide / Polypeptide Records

UniProt

Q9VQ46

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\c-cup using the Feature Mapper tool.

External Data

Crossreferences

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

c-cup_1

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

spermatogenesis

elongation stage spermatid | distal

(Barreau et al., 2008)

primary spermatocyte

Comment: weak

(Barreau et al., 2008)

Additional Descriptive Data

c-cup transcripts are detected at low levels in primary spermatocytes and are barely detected in early elongation spermatids. Robust signals are detected in more elongated spermatids at the distal ends. Transcripts localize in shallow cup-like shapes at the ends of spermatids bundles (called a cup pattern).

(Barreau et al., 2008)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\c-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\c-cup

View exonic expression by tissue for Dmel\c-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

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0031367

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG15623-RA

Flygut - An atlas of the Drosophila adult midgut

FBgn0031367

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 0 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 3 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of c-cup

Transgenic constructs containing regulatory region of c-cup

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene disrupted in

Df(2L)Exel7007

(Ryder, 2004.4.26)

Df(2L)Exel8005

(Ryder, 2004.4.26)

Inferred from location ( 0 )

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

c-cup^GD1623

viable, with Scer\GAL4^Mef2.PR

c-cup^GD1623

viable, with Scer\GAL4^pnr-MD237

c-cup^GD1623

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (5)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\NENF

4 of 15

Yes

2 of 15

2 of 15

1 of 15

1 of 15

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (4)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Nenf

4 of 15

Yes

Mmus\Pgrmc1

2 of 15

Mmus\Pgrmc2

2 of 15

Mmus\Cyb5d2

1 of 15

Rattus norvegicus (Norway rat) (4)

Rnor\Nenf

3 of 13

Yes

Rnor\Cyb5d2

2 of 13

Rnor\Pgrmc2

2 of 13

Rnor\Pgrmc1

1 of 13

Xenopus tropicalis (Western clawed frog) (4)

Xtro\cyb5d2

2 of 12

Yes

Xtro\nenf

2 of 12

Yes

Xtro\pgrmc1

2 of 12

Yes

Xtro\pgrmc2

2 of 12

Yes

Danio rerio (Zebrafish) (4)

Drer\nenf

3 of 15

Yes

Drer\cyb5d2

2 of 15

Drer\pgrmc1

2 of 15

Drer\pgrmc2

2 of 15

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\tag-131

2 of 15

Yes

Cele\vem-1

2 of 15

Yes

Arabidopsis thaliana (thale-cress) (4)

Atha\MAPR2

1 of 9

Yes

Atha\MAPR3

1 of 9

Yes

Atha\MAPR4

1 of 9

Yes

Atha\MSBP1

1 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\DAP1

2 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\dap1

1 of 12

Yes

Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190FON )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA25646

Drosophila persimilis

Dper\GL18465

Drosophila willistoni

Dwil\GK15556

Drosophila virilis

Dvir\GJ17442

Drosophila mojavensis

Dmoj\GI13737

Drosophila grimshawi

Dgri\GH25021

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( None identified )

No non-Drosophilid orthologies identified

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

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (6)

Gene Symbol

Score

Source

Alignment

3 of 10

2 of 10

2 of 10

2 of 10

1 of 10

1 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 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?

NENF; neudesin neurotrophic factor

4 of 15

611874

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

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.

59598

DroID - A comprehensive database of gene and protein interactions.

FBgn0031367

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

33360

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

c-cup

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-3

Cytogenetic map

22B3-22B3

Sequence location

2L:1,831,627..1,832,565 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

22B3-22B3

Limits computationally determined from genome sequence between P{lacW}CG17646^k11021 and P{EP}EP366

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-3

(FlyBase, 2016)

2-3.2

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (3)

Bloomington

61241

y¹ v¹; P{TRiP.HMJ23020}attP40

VDRC

v106603

P{KK105871}VIE-260B

v9282

w¹¹¹⁸; P{GD1623}v9282

Genomic Clones (27)

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

cDNA Clones (4)

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

IP08319

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.

FBgn0031367

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0031367

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

33360

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: c-cup CG15623

(Benson, 2006.3.1)

Source for database merge of

Additional comments

Other Comments

c-cup transcripts accumulate in cup-shaped structures also at the distal tips of elongating spermatids.

(Benson et al., 2006)

Origin and Etymology

Discoverer

Etymology

The gene is named "calcutta-cup", based on the "cup"-like pattern of expression of the transcript in spermatid bundles; the mRNA localises in shallow cup-like shapes at the end of the spermatid bundles.

(Barreau et al., 2008)

Identification

External Crossreferences and Linkouts ( 22 )

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.

33360

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.