FB2026_02 , released June 18, 2026
FB2026_02 , released June 18, 2026
Gene: Dmel\U2af38
Open Close
General Information
Symbol
Dmel\U2af38
Species
D. melanogaster
Name
U2 small nuclear riboprotein auxiliary factor 38
Annotation Symbol
CG3582
Feature Type
protein_coding_gene
FlyBase ID
FBgn0017457
Gene Model Status
Current
Stock Availability
12 publicly available
Gene Summary
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] (FlyBase Gene Snapshot)
All Summaries
Also Known As

U2AF, dU2AF38, dU2AF38

Key Links
Genomic Location
Cytogenetic map
21B7-21B8
Sequence location
Recombination map
2-0.5
RefSeq locus
NT_033779 REGION:292959..294681
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
Gene Ontology (GO) Annotations (13 terms)
Molecular Function (6 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables poly-pyrimidine tract binding
inferred from direct assay
(Rudner et al., 1998)
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
enables metal ion binding
inferred from electronic annotation with InterPro:IPR000571
(InterPro Project Members, 2004-)
enables mRNA binding
inferred from sequence or structural similarity
(Lasko, 2000)
enables nucleic acid binding
inferred from electronic annotation with InterPro:IPR003954, InterPro:IPR035979
(InterPro Project Members, 2004-)
enables pre-mRNA 3'-splice site binding
inferred from biological aspect of ancestor with PANTHER:PTN000289700
(GO Reference Genome Project, 2011-)
enables RNA binding
inferred from electronic annotation with InterPro:IPR000504, InterPro:IPR009145
(InterPro Project Members, 2004-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
involved_in mRNA splicing, via spliceosome
inferred from mutant phenotype
(Rudner et al., 1998)
involved_in regulation of alternative mRNA splicing, via spliceosome
inferred from mutant phenotype
(Katzenberger et al., 2009)
inferred from high throughput mutant phenotype
(Park et al., 2004)
involved_in RNA splicing
inferred from mutant phenotype
(Taliaferro et al., 2011)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in mRNA splicing, via spliceosome
inferred by curator from GO:0071011
(Herold et al., 2009)
inferred from biological aspect of ancestor with PANTHER:PTN000289700
(GO Reference Genome Project, 2011-)
inferred from electronic annotation with InterPro:IPR009145
(InterPro Project Members, 2004-)
Cellular Component (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
part_of precatalytic spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
part_of U2AF complex
inferred from direct assay
(Rudner et al., 1998)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
located_in nucleus
inferred by curator from GO:0000381
(Park et al., 2004)
part_of spliceosomal complex
inferred from biological aspect of ancestor with PANTHER:PTN000289700
(GO Reference Genome Project, 2011-)
part_of U2AF complex
inferred from electronic annotation with InterPro:IPR009145
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN000289700
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the splicing factor SR family. (Q94535)
Protein Signatures (InterPro)
Summaries
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]
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 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
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q94535)

If you don't see a structure in the viewer, 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.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Gene model reviewed during 5.44

Gene model reviewed during 5.46

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
U2af38-RA
FBtr0078133
NM_057860
1261
264
U2af38-RB
FBtr0333408
NM_001272885
1655
264
Additional Transcript Data and Comments
Reported size (kB)

1.3 (northern blot)

(Rudner et al., 1996)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
U2af38-PA
FBpp0077792
29.9
264
9.06
Q94535
NP_477208
AAF51512
U2af38-PB
FBpp0305600
29.9
264
9.06
Q94535
NP_001259814
AGB92351
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)

(Rudner et al., 1996)
Comments
External Data
Subunit Structure (UniProtKB)

Associates with a 65 kDa protein.

(UniProt, Q94535)
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\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
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

2.02

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 | ubiquitous
(Fisher et al., 2012)
embryonic stage 9 -- 10
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 11 -- 12
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 13 -- 16
embryonic brain
(Fisher et al., 2012)
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage | female
(Rudner et al., 1996)
adult stage | male
(Rudner et al., 1996)
Additional Descriptive Data

U2af38 transcripts are detected in RNA from adult flies. Levels are reduced in mutants.

(Rudner et al., 1996)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of precatalytic spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
part_of U2AF complex
inferred from direct assay
(Rudner et al., 1998)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\U2af38 in JBrowse
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
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
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 ( 3 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 17 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of U2af38
Transgenic constructs containing regulatory region of U2af38
Aberrations (Deficiencies and Duplications) ( 8 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (7)
Hsap\U2AF1
13 of 14
Yes
Yes
1  
Hsap\U2AF1L5
13 of 14
Yes
Yes
Hsap\U2AF1L4
12 of 14
No
Yes
Hsap\ZRSR2
3 of 14
No
No
1  
Hsap\HTATSF1
1 of 14
No
No
Hsap\SRP19
1 of 14
No
No
1  
Hsap\ZRSR2P1
1 of 14
No
No
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (6)
Rnor\U2af1
14 of 14
Yes
Yes
Rnor\U2af1l4
11 of 14
No
Yes
Rnor\Zrsr1
3 of 14
No
No
Rnor\Zrsr2
3 of 14
No
No
Rnor\Htatsf1
1 of 14
No
No
Rnor\Pabpc1l
1 of 14
No
No
Mus musculus (laboratory mouse) (6)
Mmus\U2af1
14 of 14
Yes
Yes
Mmus\U2af1l4
11 of 14
No
Yes
Mmus\Zrsr1
3 of 14
No
No
Mmus\Zrsr2
3 of 14
No
No
Mmus\Htatsf1
1 of 14
No
No
Mmus\Pabpc1l
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (2)
Xtro\u2af1
6 of 13
Yes
Yes
Xtro\zrsr2
2 of 13
No
No
Danio rerio (Zebrafish) (6)
Drer\u2af1
12 of 14
Yes
Yes
Drer\zrsr2
4 of 14
No
No
Drer\rbm14a
1 of 14
No
No
Drer\rbm39a
1 of 14
No
No
Drer\rbm39b
1 of 14
No
No
Drer\uhmk1
1 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\uaf-2
14 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (3)
Agam\AgaP_AGAP002956
12 of 12
Yes
Yes
Agam\AgaP_AGAP010194
3 of 12
No
No
Agam\AgaP_AGAP008433
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (4)
Atha\ATU2AF35A
12 of 13
Yes
Yes
Atha\U2AF35B
12 of 13
Yes
Yes
Atha\AT1G10320
3 of 13
No
No
Atha\AT3G44785
3 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\SPAP8A3.06
12 of 12
Yes
Yes
Spom\rsd1
1 of 12
No
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:U2af38. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (2)
CG3294
5 of 13
Spf45
1 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
    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
    U2af38HMS04505
    exacerbates  cancer
    modeled by RbfHMS03004
    (Parkhitko et al., 2021)
    Disease Associations of Human Orthologs (via DIOPT v9.1 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?
    U2AF1; U2 small nuclear RNA auxiliary factor 1
    13 of 14
    191317
         
        Hsap\U2AF1L5
        13 of 14
            U2AF1L4; U2 small nuclear RNA auxiliary factor 1 like 4
            12 of 14
            601080
                ZRSR2; zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2
                3 of 14
                300028
                   
                  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
                  Summary of Genetic Interactions
                  Interaction Browsers
                  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.
                  MIST (protein-protein) - An integrated Molecular Interaction Database
                  Pathways
                  Signaling Pathways (FlyBase)
                  Metabolic Pathways
                  FlyBase
                  External Links
                  External Data
                  Linkouts
                  KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
                  Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                  Class of Gene
                  Genomic Location and Detailed Mapping Data
                  Chromosome (arm)
                  2L
                  Recombination map
                  2-0.5
                  Cytogenetic map
                  21B7-21B8
                  Sequence location
                  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
                  (Rudner, 1996.8.15, BDGP Project Members, 1994-1999)
                  21B7-21B8
                  (determined by in situ hybridisation)
                  (Spradling et al., 1999, Rudner et al., 1996)
                  Experimentally Determined Recombination Data
                  Location

                  2-0.5

                  (FlyBase, 2016)

                  2-0.0

                  (Comeron et al., 2012)

                  2-

                  (Rudner, 1996.8.15)
                  Left of (cM)
                  Right of (cM)
                  Notes
                  Stocks and Reagents
                  Stocks (12)
                  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 JBrowse 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
                    Antibody Information
                    Laboratory Generated Antibodies
                     
                    Commercially Available Antibodies
                     
                    Cell Line Information
                    Publicly Available Cell Lines
                     
                      Other Stable Cell Lines
                       
                        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.

                        (Goshima et al., 2007)

                        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.

                        (Rudner et al., 1998)

                        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.

                        (Rudner et al., 1998)

                        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.

                        (Rudner et al., 1998)

                        A U2af38 cDNA has been cloned and sequenced.

                        (Rudner et al., 1996)
                        Relationship to Other Genes
                        Source for database merge of
                        Additional comments
                        Nomenclature History
                        Source for database identify of

                        Source for identity of: U2af38 CG3582

                        (Guan, 1999.11)
                        Nomenclature comments
                        Etymology
                        Synonyms and Secondary IDs (12)
                        Datasets (0)
                        Study focus (0)
                        Experimental Role
                        Project
                        Project Type
                        Title
                        Study result (0)
                        Result
                        Result Type
                        Title
                        External Crossreferences and Linkouts ( 52 )
                        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/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.
                        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
                        AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
                        BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
                        DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
                        EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
                        FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
                        FlyMine - An integrated database for Drosophila genomics
                        InterPro - A database of protein families, domains and functional sites
                        KEGG Genes - Molecular building blocks of life in the genomic space.
                        MARRVEL_MODEL - MARRVEL (model organism gene)
                        Linkouts
                        BioGRID - A database of protein and genetic interactions.
                        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
                        DroID - A comprehensive database of gene and protein interactions.
                        DRSC - Results frm RNAi screens
                        Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
                        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
                        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
                        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
                        Flygut - An atlas of the Drosophila adult midgut
                        FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
                        iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
                        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
                        MIST (protein-protein) - An integrated Molecular Interaction Database
                        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                        References (90)