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

    Gene ID: 7307, updated on 9-Jun-2024

    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
    NEW
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    Genomic context

    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

    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 Functions

    What'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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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/TrEMBL
      B5BU08
      Related
      ENSP00000369629.2, ENST00000380276.6
      Conserved Domains (2) summary
      pfam00642
      Location:149175
      zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
      cd12538
      Location:43146
      RRM_U2AF35; RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35)
    2. NM_001025204.2NP_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: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_006758.3NP_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:149175
      zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
      cd12538
      Location:43146
      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_011529743.4XP_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
    2. XM_017028468.3XP_016883957.1  splicing factor U2AF 35 kDa subunit isoform X2

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

      Related
      ENSP00000418705.1, ENST00000459639.5
      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
    4. XM_024452131.2XP_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
    5. XM_024452130.2XP_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

    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_054324837.1XP_054180812.1  splicing factor U2AF 35 kDa subunit isoform X1

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

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

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

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