FlyBase Gene Report: Dmel\U2af50

General Information

Symbol

Dmel\U2af50

Species

D. melanogaster

Name

U2 small nuclear riboprotein auxiliary factor 50

Annotation Symbol

CG9998

Feature Type

protein_coding_gene

FlyBase ID

FBgn0005411

Gene Model Status

Current

Stock Availability

8 publicly available

Gene Summary

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] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

dU2AF⁵⁰, U2AF, l(1)9-21, dU2AF50, l(1)14Cc

Key Links

Genomic Location

Cytogenetic map

14B17-14B18

Sequence location

X:16,356,696..16,359,039 [-]

Recombination map

1-53

RefSeq locus

NC_004354 REGION:16356696..16359039

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (21 terms)

Molecular Function (6 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

enables poly-pyrimidine tract binding

inferred from direct assay

(Rudner et al., 1998)

enables protein binding

inferred from physical interaction with FLYBASE:U2af38; FB:FBgn0017457

(Taliaferro et al., 2011)

enables RNA binding

inferred from mutant phenotype

(Taliaferro et al., 2011)

Terms Based on Predictions or Assertions (5 terms)

CV Term

Evidence

References

enables mRNA binding

inferred from sequence or structural similarity

(Lasko, 2000)

enables nucleic acid binding

inferred from electronic annotation with InterPro:IPR035979

(InterPro Project Members, 2004-)

enables poly-pyrimidine tract binding

inferred from biological aspect of ancestor with PANTHER:PTN000566979

(GO Reference Genome Project, 2011-)

enables pre-mRNA 3'-splice site binding

inferred from biological aspect of ancestor with PANTHER:PTN000566979

(GO Reference Genome Project, 2011-)

enables RNA binding

inferred from electronic annotation with InterPro:IPR000504, InterPro:IPR006529

(InterPro Project Members, 2004-)

Biological Process (7 terms)

Terms Based on Experimental Evidence (5 terms)

CV Term

Evidence

References

involved_in mRNA splicing, via spliceosome

inferred from mutant phenotype

(Rudner et al., 1998)

involved_in nuclear export

inferred from mutant phenotype

(Blanchette et al., 2004)

involved_in positive regulation of RNA export from nucleus

inferred from mutant phenotype

(Tsoi et al., 2011)

involved_in regulation of alternative mRNA splicing, via spliceosome

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 (3 terms)

CV Term

Evidence

References

involved_in mRNA processing

inferred from electronic annotation with InterPro:IPR006529

(InterPro Project Members, 2004-)

involved_in mRNA splicing, via spliceosome

inferred by curator from GO:0071011

(Herold et al., 2009)

inferred from sequence or structural similarity with SGD:S000001557

(Mount and Salz, 2000)

involved_in spliceosomal complex assembly

inferred from biological aspect of ancestor with PANTHER:PTN000566979

(GO Reference Genome Project, 2011-)

Cellular Component (8 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

located_in nucleoplasm

inferred from high throughput direct assay

(Lye et al., 2014)

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 (6 terms)

CV Term

Evidence

References

part_of commitment complex

inferred from biological aspect of ancestor with PANTHER:PTN000566979

(GO Reference Genome Project, 2011-)

is_active_in nuclear speck

inferred from biological aspect of ancestor with PANTHER:PTN000566979

(GO Reference Genome Project, 2011-)

located_in nucleus

inferred from electronic annotation with InterPro:IPR006529

(InterPro Project Members, 2004-)

inferred by curator from GO:0000381

(Park et al., 2004)

part_of spliceosomal complex

inferred from sequence or structural similarity with SGD:S000001557

(Mount and Salz, 2000)

part_of U2-type prespliceosome

inferred from biological aspect of ancestor with PANTHER:PTN000566979

(GO Reference Genome Project, 2011-)

part_of U2AF complex

inferred from biological aspect of ancestor with PANTHER:PTN000566979

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

SPLICEOSOME COMPLEX A

U2 SNRNP AUXILIARY FACTOR

Protein Family (UniProt)

Belongs to the splicing factor SR family. (Q24562)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

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

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see 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

Structure

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q24562)

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 5.50

Gene model reviewed during 5.55

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

U2af50-RA

FBtr0074234

NM_057543

1527

416

U2af50-RB

FBtr0307176

NM_001258779

1344

427

U2af50-RC

FBtr0307177

NM_001258780

1371

360

U2af50-RD

FBtr0307178

NM_001258781

1473

416

Additional Transcript Data and Comments

Reported size (kB)

1.6 (northern blot)

(Kanaar et al., 1993)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

U2af50-PA

FBpp0074013

46.7

416

7.56

FBpp0298005

48.1

427

7.25

FBpp0298006

39.5

360

4.89

FBpp0298007

46.7

416

7.56

Q24562

NP_001245710

AFH07423

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)

(Kanaar et al., 1993)

Comments

External Data

Subunit Structure (UniProtKB)

Forms a heterodimer with the U2AF small subunit.

(UniProt, Q24562)

Crossreferences

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

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

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).

2.51

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 | ubiquitous

(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

organism | ubiquitous

(Fisher et al., 2012)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage -- adult stage

(Kanaar et al., 1993)

Additional Descriptive Data

U2af50 transcripts are abundant in RNA from 0-12hr embryos and Kc cells and are present throughout development.

(Kanaar et al., 1993)

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

located_in nucleoplasm

inferred from high throughput direct assay

(Lye et al., 2014)

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

Reporter: PBac{681.P.FSVS-1}U2af50^CPTI002092

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult brain cell body rind

(Knowles-Barley, 2011.8.24)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\U2af50 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\U2af50

View exonic expression by tissue for Dmel\U2af50

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

FBgn0005411

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

32602/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0005411

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0005411

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0005411

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG9998

Flygut - An atlas of the Drosophila adult midgut

FBgn0005411

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

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

Aberrations (Deficiencies and Duplications) ( 11 )

Inferred from experimentation ( 11 )

Gene disrupted in

Df(1)4b18

(Stanewsky et al., 1993)

Df(1)6b4

(Stanewsky et al., 1993)

Df(1)l32

(Banga et al., 1995, Lindsley, 1993)

Df(1)r75c

(Jones and Rubin, 1990)

Df(1)XR26

(Rudner et al., 1998, Stanewsky et al., 1993)

Gene duplicated in

Dp(1;2)r⁺75c

(Banga et al., 1995, Schalet, 1986)

Dp(1;4)80f18c

(Banga et al., 1995)

Dp(1;4)81l8g

(Banga et al., 1995)

Dp(1;4)81l12h

(Banga et al., 1995)

Gene not disrupted in

Df(1)r-D1

(Banga et al., 1995, Lindsley, 1993, Schalet, 1986)

T(1;4)9e2-10

(Stanewsky et al., 1993)

Inferred from location ( 16 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

U2af50^GD13809

lethal, with Scer\GAL4^elav.PU

lethal, with Scer\GAL4^insc-Mz1407

U2af50^GD13809

lethal, with Scer\GAL4^nub-AC-62

U2af50^HMC03810

lethal | female limited, with Scer\GAL4^dome-PG14

U2af50^HMC03810

lethal | heat sensitive

U2af50^XR15

lethal | recessive

lethal - all die before end of larval stage | recessive

lethal - all die before end of P-stage, with Scer\GAL4^elav.PU

U2af50^JF02693

lethal - all die before end of pupal stage, with Scer\GAL4^pnr-MD237

U2af50^GD13809

lethal - all die during P-stage, with Scer\GAL4^Mef2.PR

U2af50^GD13809

lethal - all die during pupal stage, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

U2af50^GD13809

viable, with Scer\GAL4^tin.CΔ4

U2af50^GD13809

viable, with Scer\GAL4^Toll-6-D42

U2af50^JF02693

Sterility

Allele

female sterile, with Scer\GAL4^VP16.otu

U2af50^HMC03810

Other Phenotypes

Allele

abnormal behavior | adult stage, with Scer\GAL4^ey-OK107

U2af50^JF02693

abnormal heat stress response | adult stage, with Scer\GAL4^Toll-6-D42

U2af50^JF02693

abnormal neuroanatomy | larval stage, with Scer\GAL4^insc-Mz1407

U2af50^GD13809

abnormal neuroanatomy | larval stage, with Scer\GAL4^ppk.PG

U2af50^JF02693

abnormal starvation stress response | larval stage | somatic clone, with Scer\GAL4^Act.PU

U2af50^JF02693

decreased occurrence of cell division | larval stage, with Scer\GAL4^elav.PU

U2af50^JF02693

decreased size | larval stage, with Scer\GAL4^elav.PU

U2af50^JF02693

decreased size | larval stage, with Scer\GAL4^ey-OK107

U2af50^JF02693

paralytic | adult stage, with Scer\GAL4^Toll-6-D42

U2af50^JF02693

short lived, with Scer\GAL4^elav.PU

U2af50^JF02693

some die during larval stage | recessive

some die during pupal stage, with Scer\GAL4^pnr-MD237

U2af50^GD13809

visible, with Scer\GAL4^Bx-MS1096

U2af50^GD13809

wild-type

Phenotype manifest in

Allele

autophagosome | larval stage | somatic clone | conditional, with Scer\GAL4^Act.PU

U2af50^JF02693

dendrite | larval stage, with Scer\GAL4^ppk.PG

U2af50^JF02693

embryonic/larval fat body | larval stage | somatic clone | conditional, with Scer\GAL4^Act.PU

U2af50^JF02693

embryonic/larval sensory neuron | larval stage, with Scer\GAL4^ppk.PG

U2af50^JF02693

ganglion mother cell | larval stage, with Scer\GAL4^insc-Mz1407

U2af50^GD13809

larval brain | larval stage, with Scer\GAL4^elav.PU

U2af50^JF02693

larval neuroblast | larval stage, with Scer\GAL4^insc-Mz1407

U2af50^GD13809

lobe system of larval mushroom body | larval stage, with Scer\GAL4^elav.PU

U2af50^JF02693

medial lobe of larval mushroom body, with Scer\GAL4^ey-OK107

U2af50^JF02693

wing, with Scer\GAL4^Bx-MS1096

U2af50^GD13809

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (55)

Hsap\U2AF2

14 of 14

Yes

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Hsap\UNC79

1 of 14

Hsap\ZCRB1

1 of 14

Yes

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (31)

Rnor\U2af2

14 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Mus musculus (laboratory mouse) (32)

Mmus\U2af2

13 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (28)

Xtro\u2af2

7 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Danio rerio (Zebrafish) (35)

Drer\u2af2a

14 of 14

Yes

Drer\u2af2b

14 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (26)

Cele\uaf-1

13 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Cele\Y82E9BR.19

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (31)

Agam\AgaP_AGAP002908

11 of 12

Yes

2 of 12

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Yes

Agam\AgaP_AGAP013440

1 of 12

Arabidopsis thaliana (thale-cress) (95)

Atha\AT1G60900

12 of 13

Yes

Atha\ATU2AF65A

12 of 13

Yes

Atha\AT1G60830

4 of 13

Yes

Atha\AT2G33435

3 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Atha\LIF2

1 of 13

Atha\ML4

1 of 13

Yes

Atha\ML5

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (12)

Scer\MUD2

3 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Scer\PAB1

1 of 13

Scer\PUB1

1 of 13

Scer\SNP1

1 of 13

Schizosaccharomyces pombe (Fission yeast) (15)

Spom\prp2

12 of 12

Yes

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:U2af50. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (39)

LS2

11 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

dom

1 of 13

elav

1 of 13

fne

1 of 13

hfp

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

msi

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Spx

1 of 13

Srrm234

1 of 13

ssx

1 of 13

Syp

1 of 13

TBPH

1 of 13

trv

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

developmental delay, dysmorphic facies, and brain anomalies

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 3 )

Allele

Disease

Evidence

References

U2af50^GD13809

model of developmental delay, dysmorphic facies, and brain anomalies

CEC

(Li et al., 2024)

U2af50^HMC03810

model of developmental delay, dysmorphic facies, and brain anomalies

CEC

(Li et al., 2024)

U2af50^JF02693

model of developmental delay, dysmorphic facies, and brain anomalies

CEC

(Li et al., 2024)

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

U2AF2; U2 small nuclear RNA auxiliary factor 2

model of developmental delay, dysmorphic facies, and brain anomalies

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 5 )

Allele

Disease

Interaction

References

U2af50^XR15

exacerbates neurodegenerative disease

modeled by Hsap\ATXN3^{tr.Q78.UAS.Tag:HA}

(Tsoi et al., 2011)

U2af50^KK102790

ameliorates C9orf72 frontotemporal dementia and/or amyotrophic lateral sclerosis

modeled by Zzzz\poly-GR^50.UAS.EGFP

(Lee et al., 2016)

U2af50^HMC03810

exacerbates cancer

modeled by Rbf^HMS03004

(Parkhitko et al., 2021)

U2af50^JF02693

model of syndromic intellectual disability

is ameliorated by Iswi^{UAS.RR.Tag:FLAG,Tag:HA}

(Li et al., 2024)

is ameliorated by RpS19a^UAS.ORF

(Li et al., 2024)

U2af50^RNAi.UAS.cUa

exacerbates neurodegenerative disease

modeled by Hsap\ATXN3^{tr.Q78.UAS.Tag:HA}

(Tsoi et al., 2011)

modeled by Zzzz\CAG^{100.UAS.DsRed2}

(Tsoi et al., 2011)

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?

U2AF2; U2 small nuclear RNA auxiliary factor 2

14 of 14

U2 SMALL NUCLEAR RNA AUXILIARY FACTOR 2; U2AF2

DEVELOPMENTAL DELAY, DYSMORPHIC FACIES, AND BRAIN ANOMALIES; DEVDFB

developmental delay, dysmorphic facies, and brain anomalies

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.

Dmel gene

Ortholog showing functional complementation

Supporting References

U2af50

Hsap\U2AF2

(Li et al., 2024)

Interactions

Summary of Physical Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

U2af50 - Hexo2

anti tag coimmunoprecipitation, western blot

(White-Grindley et al., 2014)

U2af50 - Polr2A

anti bait coimmunoprecipitation, western blot

(Minocha et al., 2018)

U2af50 - Prp19

anti bait coimmunoprecipitation, western blot

(Minocha et al., 2018)

U2af50 - SF1

pull down, autoradiography

(Mazroui et al., 1999)

U2af50 - Sxl

anti bait coimmunoprecipitation, western blot

(Penn et al., 2008)

U2af50 - U2af38

anti tag coimmunoprecipitation, western blot, pull down, molecular weight estimation by staining

(Taliaferro et al., 2011, Rudner et al., 1998, Rudner et al., 1998)

U2af50 - U5-40k

anti bait coimmunoprecipitation, western blot

(Penn et al., 2008)

U2af50 - Upf1

anti tag coimmunoprecipitation, anti tag western blot

(Stoiber et al., 2015)

U2af50 - eIF4E1

anti bait coimmunoprecipitation, western blot

(Graham et al., 2011)

U2af50 - fand

anti bait coimmunoprecipitation, western blot

(Minocha et al., 2018)

U2af50 - fl(2)d

anti bait coimmunoprecipitation, western blot

(Penn et al., 2008)

U2af50 - orb2

anti tag coimmunoprecipitation, Identification by mass spectrometry

(White-Grindley et al., 2014)

RNA-protein

Physical Interaction

Assay

References

U2af50 - mle

nucleic acid uv cross-linking assay, autoradiography, anti bait coimmunoprecipitation

(Kennedy et al., 1998)

Summary of Genetic Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

suppressible

(Li et al., 2024)

suppressible

(Li et al., 2024)

suppressible

(Li et al., 2024)

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.

58942

DroID - A comprehensive database of gene and protein interactions.

FBgn0005411

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

32602

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.

Spliceosome

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-53

Cytogenetic map

14B17-14B18

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}Cyp1^EP1073&P{EP}Dsp1^EP355 and P{EP}EP1493^EP1493

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

14C1-14C2

(Kanaar, 1993.12.6)

Experimentally Determined Recombination Data

Location

1-53

(FlyBase, 2016)

1-54.5

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (8)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

27542

y¹ v¹; P{TRiP.JF02693}attP2

14619

y¹ w^67c23 P{Mae-UAS.6.11}U2af50^GG01531

55153

y¹ sc^* v¹ sev²¹; P{TRiP.HMC03810}attP40

Kyoto

115265

w¹¹¹⁸ PBac{681.P.FSVS-1}U2af50^CPTI002092

NIG-Fly

HMJ23059

y¹ v¹; P{TRiP.HMJ23059}attP40/CyO

VDRC

v107723

P{KK102790}VIE-260B

v24176

w¹¹¹⁸; P{GD13809}v24176

v318726

PBac{fTRG01022.sfGFP-TVPTBF}VK00002

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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

LD03714

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.

FBgn0005411

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0005411

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Minocha et al., 2018)

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)

Nuclear export of large intronless mRNA.

(Blanchette et al., 2004)

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.

(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)

Germline transformation of a wild type copy of U2af50 is capable of rescuing a lethal mutation, establishing that U2af50 is essential for viability.

(Kanaar et al., 1993)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (17)

Reported As

Symbol Synonym

9-21

(Jones and Rubin, 1990)

CG9998

(National Institute of Genetics Fly Stocks, 2023-, Bilousov et al., 2014, Taliaferro et al., 2011, Tsoi et al., 2011, Ni et al., 2010.12.1, Herold et al., 2009, Keleman et al., 2009.8.5, Pan and Zhang, 2009, Perkins et al., 2009, Goshima et al., 2007, Olson et al., 2007, McIntyre et al., 2006, Mount and Salz, 2000)

DU2AF50

(Page-McCaw et al., 1999)

DmU2AF⁵⁰

(Mazroui et al., 1999)

U2AF

(Nagengast and Salz, 2004, Nagengast et al., 2004, Graveley, 2002, Maniatis and Tasic, 2002, Smith and Valcarcel, 2000, Kennedy et al., 1998, Rudner et al., 1998)

U2AF 50

(Graham et al., 2011)

U2AF-50

(Boucher et al., 2001)

U2AF50

(Berry et al., 2022, Minocha et al., 2018, Tang et al., 2018, Moschall et al., 2017, Tsoi et al., 2011, Penn et al., 2008, Park et al., 2004, Kanaar, 1993.12.6)

U2af

(Rio, 2002)

dU2AF50

(Tsoi et al., 2011, Olson et al., 2007, Graveley and Celotto, 2003, Tacke and Manley, 1999)

dU2AF⁵⁰

(Taliaferro et al., 2011, Hieronymus and Silver, 2004, Dauwalder and Mattox, 1998, Rudner et al., 1998, Rudner et al., 1998, Kennedy and Berget, 1997, Kanaar et al., 1993)

dUTAf⁵⁰

(Blanchette et al., 2004)

l(1)14Ca

(Banga, 1996.5.2, Banga et al., 1995)

l(1)14Cc

(Lindsley, 1993, Stanewsky et al., 1993)

l(1)9-21

(Banga, 1996.5.2, Banga et al., 1995, Lindsley, 1993, Stanewsky et al., 1993)

Name Synonyms

U2 small nuclear riboprotein auxiliary factor 50

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 57 )

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.

32602

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.

Q24562

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q24562

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.

Q24562

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0005411

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

32602/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0005411

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0005411

FlyMine - An integrated database for Drosophila genomics

FBgn0005411

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG9998

MARRVEL_MODEL - MARRVEL (model organism gene)

32602

Linkouts

BioGRID - A database of protein and genetic interactions.

58942

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0005411

DroID - A comprehensive database of gene and protein interactions.

FBgn0005411

DRSC - Results frm RNAi screens

FBgn0005411

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0005411

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0005411

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG9998

Flygut - An atlas of the Drosophila adult midgut

FBgn0005411

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0005411

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC005736

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Spliceosome

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

32602

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

References (120)

The following external sites may use different assemblies or annotations than FlyBase.

2.51

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