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U2AF1 U2 small nuclear RNA auxiliary factor 1 [ Homo sapiens (human) ]

Gene ID: 7307, updated on 5-Mar-2024

Summary

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Official Symbol
U2AF1provided by HGNC
Official Full Name
U2 small nuclear RNA auxiliary factor 1provided by HGNC
Primary source
HGNC:HGNC:12453
See related
Ensembl:ENSG00000160201 MIM:191317; AllianceGenome:HGNC:12453
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
RN; FP793; U2AF35; U2AFBP; RNU2AF1
Summary
This gene belongs to the splicing factor SR family of genes. U2 auxiliary factor, comprising 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 small subunit which plays a critical role in both constitutive and enhancer-dependent RNA splicing by directly mediating interactions between the large subunit and proteins bound to the enhancers. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 35.4), colon (RPKM 24.4) and 25 other tissues See more
Orthologs
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Genomic context

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See U2AF1 in Genome Data Viewer
Location:
21q22.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (43092956..43107578, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (41484016..41498649, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (44513066..44527688, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13356 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13357 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13358 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:44395471-44396197 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44401218-44401758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44401759-44402300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44402301-44402840 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:44408954-44409120 Neighboring gene PBX/knotted 1 homeobox 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44412569-44413092 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:44482429-44482929 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44489293-44489916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44489917-44490540 Neighboring gene cystathionine beta-synthase Neighboring gene ReSE screen-validated silencer GRCh37_chr21:44500286-44500457 Neighboring gene Sharpr-MPRA regulatory region 958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44506453-44507245 Neighboring gene uncharacterized LOC101928369 Neighboring gene Sharpr-MPRA regulatory region 15309 Neighboring gene mitochondrial ribosomal protein L51 pseudogene 2 Neighboring gene FOXM1-regulated, gastric cancer associated

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. Clinical and molecular spectrum and prognostic outcomes of U2AF1 mutant clonal hematopoiesis- a prospective mayo clinic cohort study. Pritzl SL, et al. Leuk Res, 2023 Feb. PMID 36586169
  2. Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. Biancon G, et al. Mol Cell, 2022 Mar 17. PMID 35303483, Free PMC Article
  3. Bilineal evolution of a U2AF1-mutated clone associated with acquisition of distinct secondary mutations. Montgomery ND, et al. Blood Adv, 2021 Dec 28. PMID 34581783, Free PMC Article
  4. U2AF1 expression is a novel and independent prognostic indicator of childhood T-lineage acute lymphoblastic leukemia. Zhang P, et al. Int J Lab Hematol, 2021 Aug. PMID 33314767
  5. [Correlation between U2AF1 Gene Mutation Characteristics and Clinical Manifestations and Prognosis in Patients with Myelodysplastic Syndrome]. Zhao WS, et al. Zhongguo Shi Yan Xue Ye Xue Za Zhi, 2020 Dec. PMID 33283729

See all (250) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Global analysis of binding sites of U2AF1 and ZRSR2 reveals RNA elements required for mutually exclusive splicing by the U2- and U12-type spliceosome.
    Title: Global analysis of binding sites of U2AF1 and ZRSR2 reveals RNA elements required for mutually exclusive splicing by the U2- and U12-type spliceosome.
  2. Myelodysplastic neoplasm-associated U2AF1 mutations induce host defense defects by compromising neutrophil chemotaxis.
    Title: Myelodysplastic neoplasm-associated U2AF1 mutations induce host defense defects by compromising neutrophil chemotaxis.
  3. U2AF1 in various neoplastic diseases and relevant targeted therapies for malignant cancers with complex mutations (Review).
    Title: U2AF1 in various neoplastic diseases and relevant targeted therapies for malignant cancers with complex mutations (Review).
  4. Patients with telomere biology disorders show context specific somatic mosaic states with high frequency of U2AF1 variants.
    Title: Patients with telomere biology disorders show context specific somatic mosaic states with high frequency of U2AF1 variants.
  5. U2AF1 pathogenic variants in myeloid neoplasms and precursor states: distribution of co-mutations and prognostic heterogeneity.
    Title: U2AF1 pathogenic variants in myeloid neoplasms and precursor states: distribution of co-mutations and prognostic heterogeneity.
  6. Full-length transcript alterations in human bronchial epithelial cells with U2AF1 S34F mutations.
    Title: Full-length transcript alterations in human bronchial epithelial cells with U2AF1 S34F mutations.
  7. Clinical and molecular spectrum and prognostic outcomes of U2AF1 mutant clonal hematopoiesis- a prospective mayo clinic cohort study.
    Title: Clinical and molecular spectrum and prognostic outcomes of U2AF1 mutant clonal hematopoiesis- a prospective mayo clinic cohort study.
  8. U2AF1 and EZH2 mutations are associated with nonimmune hemolytic anemia in myelodysplastic syndromes.
    Title: U2AF1 and EZH2 mutations are associated with nonimmune hemolytic anemia in myelodysplastic syndromes.
  9. U2AF1 mutation connects DNA damage to the alternative splicing of RAD51 in lung adenocarcinomas.
    Title: U2AF1 mutation connects DNA damage to the alternative splicing of RAD51 in lung adenocarcinomas.
  10. Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies.
    Title: Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies.
Submit: New GeneRIF Correction See all GeneRIFs (94)

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

EBI GWAS Catalog

Description
Genome-wide association study of selenium concentrations.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, U2 small nuclear RNA auxiliary factor 1 (U2AF1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with U2AF1 is increased by RRE 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

Clone Names

  • DKFZp313J1712

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RS domain binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables pre-mRNA 3'-splice site binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA splicing TAS
Traceable Author Statement
more info
 PubMed 
involved_in mRNA processing TAS
Traceable Author Statement
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mRNA splicing, via spliceosome IC
Inferred by Curator
more info
 PubMed 
involved_in mRNA splicing, via spliceosome NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in Cajal body TAS
Traceable Author Statement
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 catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear speck ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
part_of spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
  
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 35 kDa subunit
Names
U2 small nuclear RNA auxillary factor 1
U2 small nuclear ribonucleoprotein auxillary factor, 35-KD subunit
U2 snRNP auxiliary factor small subunit
U2(RNU2) small nuclear RNA auxiliary factor binding protein
splicing factor U2AF 35kDa subunit

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_029455.1 RefSeqGene

    Range
    5001..19623
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_615

mRNA and Protein(s)

  1. NM_001025203.1 → NP_001020374.1  splicing factor U2AF 35 kDa subunit isoform b

    See identical proteins and their annotated locations for NP_001020374.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (b) lacks an in-frame segment of the coding region, compared to variant c. The resulting isoform (b) has a longer N-terminus when compared to isoform c.
    Source sequence(s)
    AF370386, AJ627978, CB110007
    Consensus CDS
    CCDS33574.1
    UniProtKB/TrEMBL
    B5BU08
    Related
    ENSP00000369629.2, ENST00000380276.6
    Conserved Domains (2) summary
    pfam00642
    Location:149 → 175
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    cd12538
    Location:43 → 146
    RRM_U2AF35; RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35)

  2. NM_001025204.2 → NP_001020375.1  splicing factor U2AF 35 kDa subunit isoform c

    See identical proteins and their annotated locations for NP_001020375.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (c) represents the longest transcript, but encodes the shortest isoform (c).
    Source sequence(s)
    AF370386, AJ627978, BC005915, CB110007
    Consensus CDS
    CCDS42948.1
    UniProtKB/Swiss-Prot
    Q01081
    UniProtKB/TrEMBL
    Q7Z780
    Conserved Domains (2) summary
    pfam00642
    Location:76 → 102
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    cl17169
    Location:1 → 73
    RRM_SF; RNA recognition motif (RRM) superfamily

  3. NM_006758.3 → NP_006749.1  splicing factor U2AF 35 kDa subunit isoform a

    See identical proteins and their annotated locations for NP_006749.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (a) lacks an in-frame segment of the coding region, compared to variant c. The resulting isoform (a) has a longer N-terminus when compared to isoform c.
    Source sequence(s)
    AF370386, AJ627978, BC005915, CB110007
    Consensus CDS
    CCDS13694.1
    UniProtKB/Swiss-Prot
    Q01081, Q701P4, Q71RF1
    UniProtKB/TrEMBL
    B5BU08
    Related
    ENSP00000291552.4, ENST00000291552.9
    Conserved Domains (2) summary
    pfam00642
    Location:149 → 175
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    cd12538
    Location:43 → 146
    RRM_U2AF35; RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    43092956..43107578 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011529743.4 → XP_011528045.1  splicing factor U2AF 35 kDa subunit isoform X1

    Conserved Domains (2) summary
    pfam00642
    Location:116 → 142
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    cl17169
    Location:43 → 113
    RRM_SF; RNA recognition motif (RRM) superfamily

  2. XM_017028468.3 → XP_016883957.1  splicing factor U2AF 35 kDa subunit isoform X2

  3. XM_024452129.2 → XP_024307897.1  splicing factor U2AF 35 kDa subunit isoform X3

    Related
    ENSP00000418705.1, ENST00000459639.5
    Conserved Domains (2) summary
    pfam00642
    Location:76 → 102
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    cl17169
    Location:1 → 73
    RRM_SF; RNA recognition motif (RRM) superfamily

  4. XM_024452131.2 → XP_024307899.1  splicing factor U2AF 35 kDa subunit isoform X3

    Conserved Domains (2) summary
    pfam00642
    Location:76 → 102
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    cl17169
    Location:1 → 73
    RRM_SF; RNA recognition motif (RRM) superfamily

  5. XM_024452130.2 → XP_024307898.1  splicing factor U2AF 35 kDa subunit isoform X3

    Conserved Domains (2) summary
    pfam00642
    Location:76 → 102
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    cl17169
    Location:1 → 73
    RRM_SF; RNA recognition motif (RRM) superfamily

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    41484016..41498649 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324837.1 → XP_054180812.1  splicing factor U2AF 35 kDa subunit isoform X1

  2. XM_054324838.1 → XP_054180813.1  splicing factor U2AF 35 kDa subunit isoform X2

  3. XM_054324839.1 → XP_054180814.1  splicing factor U2AF 35 kDa subunit isoform X3

  4. XM_054324840.1 → XP_054180815.1  splicing factor U2AF 35 kDa subunit isoform X3

  5. XM_054324841.1 → XP_054180816.1  splicing factor U2AF 35 kDa subunit isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q01081.3 GenPept UniProtKB/Swiss-Prot:Q01081

Gene LinkOut

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