FB2021_01, released Feb 18, 2021

Gene: Dmel\m-cup

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General Information
Symbol
Dmel\m-cup
Species
D. melanogaster
Name
mann-cup
Annotation Symbol
CG11896
Feature Type
protein_coding_gene
FlyBase ID
FBgn0038488
Gene Model Status
Current
Stock Availability
4 publicly available
Gene Snapshot
Contributions welcome
Other Summaries
Key Links
Genomic Location
Cytogenetic map
89F1-89F1
Sequence location
3R:17,144,475..17,149,412 [-]
Recombination map

3-60

RefSeq locus
NT_033777 REGION:17144475..17149412
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
GO Summary Ribbons
Gene Ontology (GO) Annotations (3 terms)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in protein ubiquitination
inferred from sequence or structural similarity with HGNC:3649
(FlyBase Curators, 2008--)
involved_in ubiquitin-dependent protein catabolic process
inferred from biological aspect of ancestor with PANTHER:PTN000652632
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of ubiquitin ligase complex
inferred from biological aspect of ancestor with PANTHER:PTN000652632
(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
2
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\m-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 5.48

Sequence Ontology: Class of Gene
gene_with_edited_transcript
(Graveley et al., 2011)
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
m-cup-RA
FBtr0083414
NM_142350
2815
702
m-cup-RB
FBtr0337043
NM_001275731
3789
701
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
m-cup-PA
FBpp0082855
80.2
702
7.98
NP_650607
AAG22155
m-cup-PB
FBpp0307972
80.1
701
7.89
NP_001262660
AGB96040
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

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\m-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
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
(Fisher et al., 2012)
embryonic stage 7 -- 8
organism | faint | ubiquitous
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 9 -- 10
organism | faint | ubiquitous
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 11 -- 12
organism | faint | ubiquitous
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 13 -- 16
organism | faint | ubiquitous
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
spermatogenesis
elongation stage spermatid | distal
(Barreau et al., 2008)
primary spermatocyte

Comment: weak

(Barreau et al., 2008)
Additional Descriptive Data

m-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
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\m-cup in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
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
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 m-cup
Transgenic constructs containing regulatory region of m-cup
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation
Inferred from location
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
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
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\FEM1B
4 of 15
Yes
No
Hsap\FEM1A
3 of 15
No
No
Hsap\FEM1C
3 of 15
No
No
Hsap\ANKRD46
1 of 15
No
Yes
Hsap\LONRF2
1 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (5)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\4931440F15Rik
3 of 15
Yes
No
Mmus\Fem1a
3 of 15
Yes
No
Mmus\Fem1b
3 of 15
Yes
No
Mmus\Fem1c
3 of 15
Yes
No
Mmus\Ankrd46
1 of 15
No
Yes
Rattus norvegicus (Norway rat) (5)
Rnor\Fem1b
4 of 13
Yes
No
Rnor\Fem1a
3 of 13
No
No
Rnor\Fem1c
3 of 13
No
No
Rnor\LOC103690937
2 of 13
No
Yes
Rnor\Ankrd46
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\fem1b
4 of 12
Yes
No
Xtro\fem1c
2 of 12
No
No
Danio rerio (Zebrafish) (5)
Drer\fem1b
4 of 15
Yes
No
Drer\fem1a
2 of 15
No
No
Drer\fem1c
2 of 15
No
No
Drer\LOC110440003
2 of 15
No
Yes
Drer\ankrd46b
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\fem-1
5 of 15
Yes
No
Cele\F40E12.2
1 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (12)
Atha\ACD6
1 of 9
Yes
Yes
Atha\AT1G03670
1 of 9
Yes
Yes
Atha\AT4G03440
1 of 9
Yes
Yes
Atha\AT4G03450
1 of 9
Yes
Yes
Atha\AT4G03460
1 of 9
Yes
No
Atha\AT4G03470
1 of 9
Yes
Yes
Atha\AT4G03480
1 of 9
Yes
No
Atha\AT4G03490
1 of 9
Yes
Yes
Atha\AT4G03500
1 of 9
Yes
No
Atha\AT4G05040
1 of 9
Yes
Yes
Atha\AT4G14390
1 of 9
Yes
Yes
Atha\AT5G54710
1 of 9
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091903RA )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00008271
Drosophila simulans
Dsim\GD20246
Drosophila sechellia
Dsec\GM15380
Drosophila erecta
Dere\GG16786
Drosophila yakuba
Dyak\GE24177
Drosophila ananassae
Dana\GF16889
Drosophila pseudoobscura pseudoobscura
Dpse\GA11266
Drosophila persimilis
Dper\GL23843
Drosophila willistoni
Dwil\GK11460
Drosophila virilis
Dvir\GJ22833
Drosophila mojavensis
Dmoj\GI10371
Drosophila grimshawi
Dgri\GH17503
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150348 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17017862
Glossina morsitans
Tsetse fly
Gmor\GMOY005281
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_05013
Mayetiola destructor
Hessian fly
Mdes\Mdes002633
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL014046
Anopheles darlingi
American malaria mosquito
Adar\ADAC008310
Anopheles gambiae
Malaria mosquito
Agam\AGAP004499
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ012992
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W069T )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA010778
Bombyx mori
Silkmoth
Bmor\BGIBMGA010777
Danaus plexippus
Monarch butterfly
Dple\DPOGS200537-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL008568
Linepithema humile
Argentine ant
Lhum\LH21105
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:001a17
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG006622
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_11225
Tribolium castaneum
Red flour beetle
Tcas\TC010662
Pediculus humanus
Human body louse
Phum\PHUM625280
Pediculus humanus
Human body louse
Phum\PHUM252180
Rhodnius prolixus
Kissing bug
Rpro\RPRC008309
Cimex lectularius
Bed bug
Clec\CLEC000691
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_15902
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0658 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR011917
Ixodes scapularis
Black-legged tick
Isca\ISCW009329
Stegodyphus mimosarum
African social velvet spider
Smim\KFM80845.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur05g07780
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_305705
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G03I9 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Fem1hc
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000006394
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000016010
Gallus gallus
Domestic chicken
Ggal\FEM1A
Gallus gallus
Domestic chicken
Ggal\FEM1C
Gallus gallus
Domestic chicken
Ggal\ENSGALG00000028906
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (2)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
Fem-1
6 of 10
CG6966
5 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?
    FEM1B; fem-1 homolog B
    4 of 15
    613539
        FEM1A; fem-1 homolog A
        3 of 15
        613538
            FEM1C; fem-1 homolog C
            3 of 15
            608767
                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.
                DroID - A comprehensive database of gene and protein interactions.
                InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
                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)
                3R
                Recombination map

                3-60

                Cytogenetic map
                89F1-89F1
                Sequence location
                3R:17,144,475..17,149,412 [-]
                FlyBase Computed Cytological Location
                Cytogenetic map
                Evidence for location
                89F1-89F1
                Limits computationally determined from genome sequence between P{EP}CG5208EP562&P{EP}DadEP3196 and P{PZ}l(3)0788207882
                Experimentally Determined Cytological Location
                Cytogenetic map
                Notes
                References
                Experimentally Determined Recombination Data
                Location

                3-60

                (FlyBase, 2016)

                3-59.2

                (Comeron et al., 2012)
                Left of (cM)
                Right of (cM)
                Notes
                Stocks and Reagents
                Stocks (4)
                Genomic Clones (19)
                 

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

                cDNA Clones (60)
                 

                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
                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
                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: m-cup CG11896

                (Barreau et al., 2008)
                Source for database merge of
                Additional comments

                FlyBase curator comment: the insertion in the "e01527" Exelixis line (PBac{RB}CG12265e01527) was originally assigned to the CG11896 gene in FBrf0179797, resulting in the "CG11896e01527" (FBal0162515) allele. However, FBrf0184340 shows that the insertion is actually within CG12265.

                (Bloomington Drosophila Stock Center, 2004.11.6)
                Other Comments
                Origin and Etymology
                Discoverer
                Etymology

                The gene is named "mann-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 ( 37 )
                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/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
                iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
                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.
                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
                InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
                MIST (protein-protein) - An integrated Molecular Interaction Database
                Synonyms and Secondary IDs (3)
                Reported As
                Symbol Synonym
                CG11896
                (Japanese National Institute of Genetics, 2012.5.21, Keleman et al., 2009.8.5, Perkins et al., 2009, Barreau et al., 2008)
                m-cup
                (Barreau et al., 2008)
                Name Synonyms
                CG11896
                mann-cup
                (Barreau et al., 2008)
                Secondary FlyBase IDs
                  Datasets (0)
                  Study focus (0)
                  Experimental Role
                  Project
                  Project Type
                  Title
                  References (27)