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General Information
Symbol
Dmel\U2af38
Species
D. melanogaster
Name
U2 small nuclear riboprotein auxiliary factor 38
Annotation Symbol
CG3582
Feature Type
FlyBase ID
FBgn0017457
Gene Model Status
Stock Availability
Gene Snapshot
U2 small nuclear riboprotein auxiliary factor 38 (U2af38) encodes the small subunit of the pre-mRNA splicing factor complex U2AF. This heterodimeric complex binds to the intron pyrimidine tract and targets the product of snf to the branch site early in spliceosome assembly. The U2af38 product binds to the AG dinucleotide at the 3' splice site. [Date last reviewed: 2018-09-20]
Also Known As
U2AF, dU2AF38, dU2AF38
Key Links
Genomic Location
Cytogenetic map
Sequence location
2L:292,959..294,681 [-]
Recombination map
2-0.5
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. (Q94535)
Molecular Function (GO)
[Detailed GO annotations]
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, Q94535)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\U2af38 or the JBrowse view of Dmel\U2af38 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 5.44
Gene model reviewed during 5.46
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0078133
1261
264
FBtr0333408
1655
264
Additional Transcript Data and Comments
Reported size (kB)
1.3 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0077792
29.9
264
9.06
FBpp0305600
29.9
264
9.06
Polypeptides with Identical Sequences

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

264 aa isoforms: U2af38-PA, U2af38-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
264 (aa); 30 (kD predicted)
Comments
External Data
Subunit Structure (UniProtKB)
Associates with a 65 kDa protein.
(UniProt, Q94535)
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\U2af38 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 (11 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR000571
(assigned by InterPro )
inferred from sequence or structural similarity
inferred from biological aspect of ancestor with PANTHER:PTN000289700
(assigned by GO_Central )
Biological Process (3 terms)
Terms Based on Experimental Evidence (3 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 biological aspect of ancestor with PANTHER:PTN000289700
(assigned by GO_Central )
Cellular Component (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from high throughput direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred by curator from GO:0000381
inferred from biological aspect of ancestor with PANTHER:PTN000289700
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000289700
(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
U2af38 transcripts are detected in RNA from adult flies. Levels are reduced in mutants.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from high throughput direct assay
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\U2af38 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 ( 3 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 16 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of U2af38
Transgenic constructs containing regulatory region of U2af38
Deletions and Duplications ( 8 )
Phenotypes
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (4)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
10 of 15
Yes
Yes
10 of 15
Yes
Yes
9 of 15
Yes
No
 
2 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (4)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
15 of 15
Yes
Yes
8 of 15
No
Yes
2 of 15
No
No
1 of 15
No
No
Rattus norvegicus (Norway rat) (4)
10 of 13
Yes
Yes
7 of 13
No
Yes
2 of 13
No
No
2 of 13
No
No
Xenopus tropicalis (Western clawed frog) (1)
8 of 12
Yes
Yes
Danio rerio (Zebrafish) (2)
9 of 15
Yes
Yes
2 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (1)
13 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (4)
8 of 9
Yes
Yes
8 of 9
Yes
Yes
1 of 9
No
No
1 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (1)
12 of 12
Yes
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190FOW )
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) ( EOG09150B3S )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
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) ( EOG090W0CSE )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0CPW )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
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
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0CUI )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (1)
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
    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
    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)
    Associates with a 65 kDa protein.
    (UniProt, Q94535 )
    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)
    2L
    Recombination map
    2-0.5
    Cytogenetic map
    Sequence location
    2L:292,959..294,681 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    21B7-21B8
    Limits computationally determined from genome sequence between P{lacW}spenk06805&P{lacW}l(2)k13604k13604 and P{lacW}U2af38k14504
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    21B7-21B8
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (10)
    Genomic Clones (15)
     

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

    cDNA Clones (90)
     

    Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequences
    BDGP DGC clones
    Other clones
      Drosophila Genomics Resource Center cDNA clones

      For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

      cDNA Clones, End Sequenced (ESTs)
      RNAi and Array Information
      Linkouts
      DRSC - Results frm RNAi screens
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      Antibody Information
      Laboratory Generated Antibodies
       
      Commercially Available Antibodies
       
      Other Information
      Relationship to Other Genes
      Source for database identify of
      Source for identity of: U2af38 CG3582
      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.
      Studies in vivo reveal that the RS domain of U2af38 is completely dispensable: the domain is not necessary for constitutive splicing in vitro. The RS domain is also not required for enhancer-dependent splicing of dsx in vitro.
      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.
      A U2af38 cDNA has been cloned and sequenced.
      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.
      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
      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
      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
      ApoDroso - Functional genomic database for photoreceptor development, survival and function
      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
      FlyMine - An integrated database for Drosophila genomics
      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 (12)
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (80)