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General Information
Symbol
Dmel\U2af50
Species
D. melanogaster
Name
U2 small nuclear riboprotein auxiliary factor 50
Annotation Symbol
CG9998
Feature Type
FlyBase ID
FBgn0005411
Gene Model Status
Stock Availability
Gene Snapshot
U2 small nuclear riboprotein auxiliary factor 50 (U2af50) encodes the large subunit of the heterodimeric complex U2AF. U2AF binds to the intron pyrimidine tract between the branchpoint and the 3' splice site and targets U2 snRNP to the branch site early in spliceosome assembly. [Date last reviewed: 2018-09-13]
Also Known As
dU2AF50, U2AF, l(1)9-21, dU2AF50, l(1)14Cc
Key Links
Genomic Location
Cytogenetic map
Sequence location
X:16,356,696..16,359,039 [-]
Recombination map
1-53
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
Belongs to the splicing factor SR family. (Q24562)
Summaries
Gene Group (FlyBase)
SPLICEOSOME COMPLEX A -
Nuclear pre-mRNA splicing is catalyzed by the spliceosome which assembles in a step-wise manner. Complex A, the pre-spliceosome, is composed of U1 and U2 snRNPs and proteins involved in recognition of the 5' splice site and branch point. (Adapted from PMID:24452469 and PMID:23118483).
U2 SNRNP AUXILIARY FACTOR -
U2AF is a heterodimeric complex that binds to the intron pyrimidine tract between the branchpoint and the 3' splice site and targets U2 snRNP to the branch site early in spliceosome assembly. (Adapted from FBrf0103091).
Protein Function (UniProtKB)
Necessary for the splicing of pre-mRNA. Binds to the polypyrimidine tract of introns early during spliceosome assembly (By similarity).
(UniProt, Q24562)
Summary (Interactive Fly)
splicing factor required for the ATP-dependent association of U2 snRNP with pre-mRNA branchpoints - forms a heterodimer with the small splice factor U2af38 - U2af50 interacts with the intronic 3' polypyrimidine tract - the small subunit functions in recognition of the 3' AG dinucleotide
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
3

Please see the GBrowse view of Dmel\U2af50 or the JBrowse view of Dmel\U2af50 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 5.50
Gene model reviewed during 5.55
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0074234
1527
416
FBtr0307176
1344
427
FBtr0307177
1371
360
FBtr0307178
1473
416
Additional Transcript Data and Comments
Reported size (kB)
1.6 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0074013
46.7
416
7.56
FBpp0298005
48.1
427
7.25
FBpp0298006
39.5
360
4.89
FBpp0298007
46.7
416
7.56
Polypeptides with Identical Sequences

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

416 aa isoforms: U2af50-PA, U2af50-PD
Additional Polypeptide Data and Comments
Reported size (kDa)
416 (aa); 47 (kD predicted)
Comments
External Data
Subunit Structure (UniProtKB)
Forms a heterodimer with the U2AF small subunit.
(UniProt, Q24562)
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\U2af50 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 (18 terms)
Molecular Function (5 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from physical interaction with FLYBASE:U2af38; FB:FBgn0017457
inferred from mutant phenotype
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from sequence or structural similarity
inferred from biological aspect of ancestor with PANTHER:PTN000566979
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000566979
(assigned by GO_Central )
Biological Process (5 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
inferred from high throughput mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred by curator from GO:0071011
inferred from sequence or structural similarity with SGD:S000001557
Cellular Component (8 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from high throughput direct assay
inferred from high throughput direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (6 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000566979
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000566979
(assigned by GO_Central )
inferred by curator from GO:0000381
inferred from sequence or structural similarity with SGD:S000001557
inferred from biological aspect of ancestor with PANTHER:PTN000566979
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000566979
(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
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
U2af50 transcripts are abundant in RNA from 0-12hr embryos and Kc cells and are present throughout development.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from high throughput direct assay
inferred from high throughput 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\U2af50 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
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 8 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 29 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of U2af50
Transgenic constructs containing regulatory region of U2af50
Deletions and Duplications ( 11 )
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) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
15 of 15
Yes
Yes
1 of 15
No
Yes
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 of 15
Yes
Yes
1 of 15
No
Yes
Rattus norvegicus (Norway rat) (2)
10 of 13
Yes
Yes
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (1)
12 of 12
Yes
Yes
Danio rerio (Zebrafish) (3)
13 of 15
Yes
Yes
12 of 15
No
Yes
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (3)
15 of 15
Yes
Yes
2 of 15
No
Yes
1 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (4)
9 of 9
Yes
Yes
9 of 9
Yes
Yes
2 of 9
No
Yes
1 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (2)
2 of 15
Yes
Yes
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (1)
12 of 12
Yes
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190AUA )
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) ( EOG091506TD )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W04FK )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X06QI )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Strigamia maritima
European centipede
Strigamia maritima
European centipede
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Tetranychus urticae
Two-spotted spider mite
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G08BA )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (2)
6 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 ( 2 )
    Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
     
    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
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Subunit Structure (UniProtKB)
    Forms a heterodimer with the U2AF small subunit.
    (UniProt, Q24562 )
    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
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    X
    Recombination map
    1-53
    Cytogenetic map
    Sequence location
    X:16,356,696..16,359,039 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    14B17-14B18
    Limits computationally determined from genome sequence between P{EP}Cyp1EP1073&P{EP}Dsp1EP355 and P{EP}EP1493EP1493
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (9)
    Genomic Clones (17)
     

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

    cDNA Clones (153)
     

    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 database merge of
      Additional comments
      Other Comments
      RNAi screen using dsRNA made from templates generated with primers directed against this gene results in a long metaphase spindle with misaligned chromosomes when assayed in S2 cells. This phenotype can be observed when the screen is performed with or without Cdc27 dsRNA.
      Nuclear export of large intronless mRNA.
      Studies in vivo reveal that the RS domain of U2af50 is completely dispensable: the domain is not required for U2 snRNP recruitment during spliceosome assembly in vivo.
      E.coli copurification assay is used to map the domain on U2af50 that interacts with U2af38 : a 28 amino acid fragment is necessary and sufficient for the interaction. Interaction studies in vivo indicate that the U2af50/U2af38 heterodimer is essential for viability in vivo.
      The presence of one RS domain of U2AF, on either the large subunit (encoded by U2af50) or the small subunit (encoded by U2af38), promotes high-affinity pyrimidine tract RNA binding activity.
      Germline transformation of a wild type copy of U2af50 is capable of rescuing a lethal mutation, establishing that U2af50 is essential for viability.
      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 58 )
      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/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
      KEGG Genes - Molecular building blocks of life in the genomic space.
      KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
      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
      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.
      KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Synonyms and Secondary IDs (17)
      Reported As
      Symbol Synonym
      U2af
      Name Synonyms
      U2 small nuclear riboprotein auxiliary factor 50
      Secondary FlyBase IDs
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (107)