Format

Send to:

Choose Destination

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

Gene ID: 7307, updated on 3-Jan-2019

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
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

Genomic context

See U2AF1 in Genome Data Viewer
Location:
21q22.3
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 21 NC_000021.9 (43092956..43108291, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (44513066..44527716, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene PBX/knotted 1 homeobox 1 Neighboring gene cystathionine-beta-synthase Neighboring gene uncharacterized LOC101928369 Neighboring gene mitochondrial ribosomal protein L51 pseudogene 2 Neighboring gene FOXM1-regulated, gastric cancer associated

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

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 BioSystems

  • Cleavage of Growing Transcript in the Termination Region, organism-specific biosystem (from REACTOME)
    Cleavage of Growing Transcript in the Termination Region, organism-specific biosystemThis section includes the cleavage of both polyadenylated and non-polyadenylated transcripts. In the former case polyadenylation has to precede transcript cleavage, while in the latter case there is ...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • RNA Polymerase II Transcription, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription, organism-specific biosystem
    RNA Polymerase II Transcription
  • RNA Polymerase II Transcription Termination, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription Termination, organism-specific biosystemThe detailed annotation of this section will be completed in the next release.
  • Shigellosis, organism-specific biosystem (from KEGG)
    Shigellosis, organism-specific biosystemShigellosis, or bacillary dysentery, is an intestinal infection caused by Shigella, a genus of enterobacteria. Shigella are potential food-borne pathogens that are capable of colonizing the intestina...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Transport of Mature Transcript to Cytoplasm, organism-specific biosystem (from REACTOME)
    Transport of Mature Transcript to Cytoplasm, organism-specific biosystemTransport of mRNA through the Nuclear Pore Complex (NPC) is a dynamic process involving distinct machinery and receptor subsets. The separation of the two compartments and the regulation of this tran...
  • Transport of Mature mRNA derived from an Intron-Containing Transcript, organism-specific biosystem (from REACTOME)
    Transport of Mature mRNA derived from an Intron-Containing Transcript, organism-specific biosystemTransport of mRNA from the nucleus to the cytoplasm, where it is translated into protein, is highly selective and closely coupled to correct RNA processing. This coupling is achieved by the nuclear p...
  • mRNA 3'-end processing, organism-specific biosystem (from REACTOME)
    mRNA 3'-end processing, organism-specific biosystemThe 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3'-end processing consists of two steps: (i) the mRNA is first ...
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp313J1712

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
RS domain binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
pre-mRNA 3'-splice site binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA export from nucleus TAS
Traceable Author Statement
more info
 
RNA splicing TAS
Traceable Author Statement
more info
PubMed 
mRNA 3'-end processing TAS
Traceable Author Statement
more info
 
mRNA export from nucleus TAS
Traceable Author Statement
more info
 
mRNA processing TAS
Traceable Author Statement
more info
PubMed 
mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA splicing, via spliceosome IC
Inferred by Curator
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
Cajal body TAS
Traceable Author Statement
more info
PubMed 
U2AF IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U2AF IDA
Inferred from Direct Assay
more info
PubMed 
catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
nuclear speck ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spliceosomal complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

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_001025203.1NP_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/Swiss-Prot
    Q01081
    Related
    ENSP00000369629.2, ENST00000380276.6
    Conserved Domains (2) summary
    cd12538
    Location:43146
    RRM_U2AF35; RNA recognition motif in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35)
    pfam00642
    Location:149175
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
  2. NM_001025204.1NP_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
    Related
    ENSP00000381205.1, ENST00000398137.5
    Conserved Domains (2) summary
    pfam00642
    Location:76102
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    cl17169
    Location:173
    RRM_SF; RNA recognition motif (RRM) superfamily
  3. NM_006758.2NP_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
    P0DN76, Q01081
    UniProtKB/TrEMBL
    Q7Z780
    Related
    ENSP00000291552.4, ENST00000291552.8
    Conserved Domains (2) summary
    cd12538
    Location:43146
    RRM_U2AF35; RNA recognition motif in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35)
    pfam00642
    Location:149175
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p12 Primary Assembly

    Range
    43092956..43108291 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (2) summary
    pfam00642
    Location:76102
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    cl17169
    Location:173
    RRM_SF; RNA recognition motif (RRM) superfamily
  2. XM_024452131.1XP_024307899.1  splicing factor U2AF 35 kDa subunit isoform X3

    Conserved Domains (2) summary
    pfam00642
    Location:76102
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    cl17169
    Location:173
    RRM_SF; RNA recognition motif (RRM) superfamily
  3. XM_024452130.1XP_024307898.1  splicing factor U2AF 35 kDa subunit isoform X3

    Conserved Domains (2) summary
    pfam00642
    Location:76102
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    cl17169
    Location:173
    RRM_SF; RNA recognition motif (RRM) superfamily
  4. XM_011529743.3XP_011528045.1  splicing factor U2AF 35 kDa subunit isoform X1

    Conserved Domains (2) summary
    pfam00642
    Location:116142
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    cl17169
    Location:43113
    RRM_SF; RNA recognition motif (RRM) superfamily
  5. XM_017028468.2XP_016883957.1  splicing factor U2AF 35 kDa subunit isoform X2

Support Center