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

Summary

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: mouse all
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Genomic context

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_000021.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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).
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed

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
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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-W74700 (e-PCR)
- UniSTS:48228

STS-M96982 (e-PCR)
- UniSTS:74382

RH80644 (e-PCR)
- UniSTS:92322

D11S3537 (e-PCR)
- UniSTS:152776

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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

NG_029455.1 RefSeqGene

Range

5001..19623

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_615

mRNA and Protein(s)

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)
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
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

NC_000021.9 Reference GRCh38.p14 Primary Assembly

Range

43092956..43107578 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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