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U2AF2 U2 small nuclear RNA auxiliary factor 2 [ Homo sapiens (human) ]

Gene ID: 11338, updated on 10-Dec-2024

Summary

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Official Symbol
U2AF2provided by HGNC
Official Full Name
U2 small nuclear RNA auxiliary factor 2provided by HGNC
Primary source
HGNC:HGNC:23156
See related
Ensembl:ENSG00000063244 MIM:191318; AllianceGenome:HGNC:23156
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DEVDFB; U2AF65
Summary
U2 auxiliary factor (U2AF), comprised of a large and a small subunit, is a non-snRNP protein required for the binding of U2 snRNP to the pre-mRNA branch site. This gene encodes the U2AF large subunit which contains a sequence-specific RNA-binding region with 3 RNA recognition motifs and an Arg/Ser-rich domain necessary for splicing. The large subunit binds to the polypyrimidine tract of introns early during spliceosome assembly. Multiple transcript variants have been detected for this gene, but the full-length natures of only two have been determined to date. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in spleen (RPKM 33.5), appendix (RPKM 33.2) and 25 other tissues See more
Orthologs
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Genomic context

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See U2AF2 in Genome Data Viewer
Location:
19q13.42
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (55655035..55674716)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (58750963..58771692)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (56166401..56186082)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11051 Neighboring gene Sharpr-MPRA regulatory region 1979 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15102 Neighboring gene zinc finger protein 581 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11053 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:56155949-56156914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11055 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11056 Neighboring gene zinc finger protein 580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15106 Neighboring gene coiled-coil domain containing 106 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11057 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11058 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11061 Neighboring gene Sharpr-MPRA regulatory region 14549 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56192159-56192659 Neighboring gene epsin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56213120-56214004 Neighboring gene vomeronasal 1 receptor 106 pseudogene Neighboring gene NLR family pyrin domain containing 9 Neighboring gene RN7SK pseudogene 109

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Alternative conformations at the RNA-binding surface of the N-terminal U2AF(65) RNA recognition motif. Thickman KR, et al. J Mol Biol, 2007 Feb 23. PMID 17188295, Free PMC Article
  2. Solution structures of the first and second RNA-binding domains of human U2 small nuclear ribonucleoprotein particle auxiliary factor (U2AF(65)). Ito T, et al. EMBO J, 1999 Aug 16. PMID 10449418, Free PMC Article
  3. An extended U2AF(65)-RNA-binding domain recognizes the 3' splice site signal. Agrawal AA, et al. Nat Commun, 2016 Mar 8. PMID 26952537, Free PMC Article
  4. A Broad range of conformations contribute to the solution ensemble of the essential splicing factor U2AF(65). Jenkins JL, et al. Biochemistry, 2012 Jul 3. PMID 22702716, Free PMC Article
  5. In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors. Sutandy FXR, et al. Genome Res, 2018 May. PMID 29643205, Free PMC Article

See all (296) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The U2AF65/circNCAPG/RREB1 feedback loop promotes malignant phenotypes of glioma stem cells through activating the TGF-beta pathway.
    Title: The U2AF65/circNCAPG/RREB1 feedback loop promotes malignant phenotypes of glioma stem cells through activating the TGF-β pathway.
  2. All-Atom Simulations Elucidate the Impact of U2AF2 Cancer-Associated Mutations on Pre-mRNA Recognition.
    Title: All-Atom Simulations Elucidate the Impact of U2AF2 Cancer-Associated Mutations on Pre-mRNA Recognition.
  3. A UHM-ULM interface with unusual structural features contributes to U2AF2 and SF3B1 association for pre-mRNA splicing.
    Title: A UHM-ULM interface with unusual structural features contributes to U2AF2 and SF3B1 association for pre-mRNA splicing.
  4. LncRNA NEAT1 stabilized Wnt3a via U2AF2 and activated Wnt/beta-catenin pathway to alleviate ischemia stroke induced injury.
    Title: LncRNA NEAT1 stabilized Wnt3a via U2AF2 and activated Wnt/β-catenin pathway to alleviate ischemia stroke induced injury.
  5. Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal.
    Title: Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal.
  6. U2 small nuclear RNA auxiliary factor 2, transcriptionally activated by the transcription factor Dp-1/E2F transcription factor 1 complex, enhances the growth and aerobic glycolysis of leiomyosarcoma cells.
    Title: U2 small nuclear RNA auxiliary factor 2, transcriptionally activated by the transcription factor Dp-1/E2F transcription factor 1 complex, enhances the growth and aerobic glycolysis of leiomyosarcoma cells.
  7. Circular RNA FOXP1 Induced by ZNF263 Upregulates U2AF2 Expression to Accelerate Renal Cell Carcinoma Tumorigenesis and Warburg Effect through Sponging miR-423-5p.
    Title: Circular RNA FOXP1 Induced by ZNF263 Upregulates U2AF2 Expression to Accelerate Renal Cell Carcinoma Tumorigenesis and Warburg Effect through Sponging miR-423-5p.
  8. Identification of long non-coding RNAs in advanced prostate cancer associated with androgen receptor splicing factors.
    Title: Identification of long non-coding RNAs in advanced prostate cancer associated with androgen receptor splicing factors.
  9. Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing.
    Title: Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing.
  10. Influenza virus natural sequence heterogeneity in segment 8 affects interactions with cellular RNA-binding proteins and splicing efficiency.
    Title: Influenza virus natural sequence heterogeneity in segment 8 affects interactions with cellular RNA-binding proteins and splicing efficiency.
Submit: New GeneRIF Correction See all GeneRIFs (61)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Developmental delay, dysmorphic facies, and brain anomalies
MedGen: C5882698 OMIM: 620535 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat Expression of HIV-1 Tat upregulates the abundance of U2 small nuclear RNA auxiliary factor 2 (U2AF2) in the nucleoli of Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables C2H2 zinc finger domain binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding HDA PubMed 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables molecular function inhibitor activity EXP
Inferred from Experiment
more info
 PubMed 
enables poly-pyrimidine tract binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables pre-mRNA 3'-splice site binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables pre-mRNA 3'-splice site binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in mRNA processing TAS
Traceable Author Statement
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IC
Inferred by Curator
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splicing, via spliceosome NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of protein ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of protein ubiquitination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of RNA splicing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in spliceosomal complex assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of Prp19 complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2-type prespliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U2-type prespliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2AF complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U2AF complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2AF complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of commitment complex IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nuclear speck IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
part_of spliceosomal complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of spliceosomal complex IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
splicing factor U2AF 65 kDa subunit
Names
U2 (RNU2) small nuclear RNA auxiliary factor 2
U2 auxiliary factor 65 kDa subunit
U2 small nuclear ribonucleoprotein auxiliary factor (65kD)
U2 snRNP auxiliary factor large subunit
hU2AF65

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_032904.1 RefSeqGene

    Range
    5001..25667
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_623

mRNA and Protein(s)

  1. NM_001012478.2 → NP_001012496.1  splicing factor U2AF 65 kDa subunit isoform b

    See identical proteins and their annotated locations for NP_001012496.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AC008735, BC008740, BC030574
    Consensus CDS
    CCDS46197.1
    UniProtKB/TrEMBL
    B5BU25
    Related
    ENSP00000388475.1, ENST00000450554.6
    Conserved Domains (1) summary
    TIGR01642
    Location:63 → 470
    U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

  2. NM_007279.3 → NP_009210.1  splicing factor U2AF 65 kDa subunit isoform a

    See identical proteins and their annotated locations for NP_009210.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC008735, BC008740, BC030574, X64044
    Consensus CDS
    CCDS12933.1
    UniProtKB/Swiss-Prot
    P26368, Q96HC5
    UniProtKB/TrEMBL
    B5BU25
    Related
    ENSP00000307863.3, ENST00000308924.9
    Conserved Domains (1) summary
    TIGR01642
    Location:63 → 474
    U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    55655035..55674716
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011526410.2 → XP_011524712.1  splicing factor U2AF 65 kDa subunit isoform X1

    Conserved Domains (1) summary
    TIGR01642
    Location:1 → 370
    U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

  2. XM_047438120.1 → XP_047294076.1  splicing factor U2AF 65 kDa subunit isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    58750963..58771692
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054319694.1 → XP_054175669.1  splicing factor U2AF 65 kDa subunit isoform X1

  2. XM_054319695.1 → XP_054175670.1  splicing factor U2AF 65 kDa subunit isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P26368.4 GenPept UniProtKB/Swiss-Prot:P26368

Gene LinkOut

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