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Aliases for U2AF1 Gene

Aliases for U2AF1 Gene

  • U2 Small Nuclear RNA Auxiliary Factor 1 2 3 4 5
  • U2(RNU2) Small Nuclear RNA Auxiliary Factor Binding Protein 2 3
  • U2 SnRNP Auxiliary Factor Small Subunit 3 4
  • U2AFBP 3 4
  • U2AF35 3 4
  • U2 Small Nuclear Ribonucleoprotein Auxillary Factor, 35-KD Subunit 3
  • U2(RNU2) Small Nuclear RNA Auxiliary Factor 1 2
  • U2 Small Nuclear RNA Auxillary Factor 1 3
  • Splicing Factor U2AF 35 KDa Subunit 3
  • Splicing Factor U2AF 35kDa Subunit 3
  • U2 Auxiliary Factor 35 KDa Subunit 4
  • RNU2AF1 3
  • FP793 3
  • RN 3

External Ids for U2AF1 Gene

Previous HGNC Symbols for U2AF1 Gene

  • U2AFBP

Previous GeneCards Identifiers for U2AF1 Gene

  • GC21M041060
  • GC21M043407
  • GC21M043386
  • GC21M044513
  • GC21M029931

Summaries for U2AF1 Gene

Entrez Gene Summary for U2AF1 Gene

  • 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]

CIViC summary for U2AF1 Gene

  • U2AF1 is one of several spliceosome complex genes frequently mutated in a variety of hematologic malignancies, particularly de novo myelodysplastic syndromes (MDS), as well as solid tumors such as lung and pancreatic cancers. Two hotspot mutations (S34 and Q157) occur within the two zinc-finger domains of the U2AF1 protein. These mutations have been associated with altered splicing patterns in vitro and in vivo. U2AF1 mutations in MDS have been associated with an increased risk of transformation to secondary acute myeloid leukemia, however, the impact of these mutations on overall survival has been an area of debate.

GeneCards Summary for U2AF1 Gene

U2AF1 (U2 Small Nuclear RNA Auxiliary Factor 1) is a Protein Coding gene. Diseases associated with U2AF1 include Ovarian Mucinous Neoplasm and Retinitis Pigmentosa. Among its related pathways are Formation of HIV elongation complex in the absence of HIV Tat and RNA Polymerase II Transcription Termination. GO annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is U2AF1L5.

UniProtKB/Swiss-Prot for U2AF1 Gene

  • Plays a critical role in both constitutive and enhancer-dependent splicing by mediating protein-protein interactions and protein-RNA interactions required for accurate 3-splice site selection. Recruits U2 snRNP to the branch point. Directly mediates interactions between U2AF2 and proteins bound to the enhancers and thus may function as a bridge between U2AF2 and the enhancer complex to recruit it to the adjacent intron.

Gene Wiki entry for U2AF1 Gene

Additional gene information for U2AF1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for U2AF1 Gene

Genomics for U2AF1 Gene

Regulatory Elements for U2AF1 Gene

Enhancers for U2AF1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH21H043158 1.9 FANTOM5 Ensembl ENCODE dbSUPER 83.8 -55.0 -54969 7 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B YBX1 DMAP1 ZNF302 WDR4 RRP1B U2AF1 ENSG00000233754 PWP2 SIK1 TRAPPC10 HSF2BP CRYAA LINC01678
GH21H042923 1.4 Ensembl ENCODE 101.5 +178.6 178560 11 HDGF PKNOX1 ARNT ARID4B SIN3A ZNF2 ZBTB7B ZNF766 ZNF207 ZNF143 U2AF1 WDR4 RRP1B ENSG00000233754 NDUFV3 SIK1 ENSG00000224100 PKNOX1 FRGCA UBASH3A
GH21H043724 2 FANTOM5 Ensembl ENCODE dbSUPER 58 -625.3 -625313 17 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 MEF2D ZNF610 WDR4 U2AF1 RRP1B PWP2 ENSG00000233754 HSF2BP TRPM2 SIK1 PDXK TRAPPC10
GH21H043174 2 FANTOM5 Ensembl ENCODE dbSUPER 44.5 -69.4 -69397 5 HDGF PKNOX1 FOXA2 ARNT ZFP64 ARID4B DMAP1 ZNF2 SLC30A9 ZNF207 U2AF1 WDR4 ENSG00000233754 RRP1B PWP2 HSF2BP SIK1 LOC101928255 LOC105372821 CRYAA
GH21H043105 1.6 FANTOM5 ENCODE 51.8 -0.8 -760 5 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 WDR4 U2AF1 RRP1B PWP2 ENSG00000233754 PKNOX1 NDUFV3 FRGCA GC21P043111 LOC101928369
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around U2AF1 on UCSC Golden Path with GeneCards custom track

Promoters for U2AF1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000142823 287 2201 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 CBX5

Genomic Location for U2AF1 Gene

Chromosome:
21
Start:
43,092,956 bp from pter
End:
43,107,587 bp from pter
Size:
14,632 bases
Orientation:
Minus strand

Genomic View for U2AF1 Gene

Genes around U2AF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
U2AF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for U2AF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for U2AF1 Gene

Proteins for U2AF1 Gene

  • Protein details for U2AF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q01081-U2AF1_HUMAN
    Recommended name:
    Splicing factor U2AF 35 kDa subunit
    Protein Accession:
    Q01081
    Secondary Accessions:
    • Q701P4
    • Q71RF1

    Protein attributes for U2AF1 Gene

    Size:
    240 amino acids
    Molecular mass:
    27872 Da
    Quaternary structure:
    • Interacts (via RS domain) with PHF5A (via N-terminus) (By similarity). Identified in the spliceosome C complex. Heterodimer with U2AF2. Interacts with ZRANB2.

    Three dimensional structures from OCA and Proteopedia for U2AF1 Gene

    Alternative splice isoforms for U2AF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for U2AF1 Gene

Post-translational modifications for U2AF1 Gene

  • Ubiquitination at posLast=175175
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for U2AF1 Gene

Domains & Families for U2AF1 Gene

Gene Families for U2AF1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Plasma proteins
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

Q01081

UniProtKB/Swiss-Prot:

U2AF1_HUMAN :
  • The C-terminal SR-rich domain is required for interactions with SR proteins and the splicing regulators TRA and TRA2, and the N-terminal domain is required for formation of the U2AF1/U2AF2 heterodimer.
  • Belongs to the splicing factor SR family.
Domain:
  • The C-terminal SR-rich domain is required for interactions with SR proteins and the splicing regulators TRA and TRA2, and the N-terminal domain is required for formation of the U2AF1/U2AF2 heterodimer.
Family:
  • Belongs to the splicing factor SR family.
genes like me logo Genes that share domains with U2AF1: view

Function for U2AF1 Gene

Molecular function for U2AF1 Gene

GENATLAS Biochemistry:
U2 (RNU2) small nuclear RNA auxiliary factor,small subunit,1,35kDa
UniProtKB/Swiss-Prot Function:
Plays a critical role in both constitutive and enhancer-dependent splicing by mediating protein-protein interactions and protein-RNA interactions required for accurate 3-splice site selection. Recruits U2 snRNP to the branch point. Directly mediates interactions between U2AF2 and proteins bound to the enhancers and thus may function as a bridge between U2AF2 and the enhancer complex to recruit it to the adjacent intron.

Phenotypes From GWAS Catalog for U2AF1 Gene

Gene Ontology (GO) - Molecular Function for U2AF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IDA 22658674
GO:0005515 protein binding IPI 11551507
GO:0030628 pre-mRNA 3-splice site binding IBA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with U2AF1: view
genes like me logo Genes that share phenotypes with U2AF1: view

Animal Model Products

CRISPR Products

miRNA for U2AF1 Gene

miRTarBase miRNAs that target U2AF1

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for U2AF1
  • Applied Biological Materials Clones for U2AF1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for U2AF1 Gene

Localization for U2AF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for U2AF1 Gene

Nucleus. Nucleus speckle.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for U2AF1 gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for U2AF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IDA 9731529
GO:0015030 Cajal body TAS 1388271
GO:0016607 nuclear speck ISS --
genes like me logo Genes that share ontologies with U2AF1: view

Pathways & Interactions for U2AF1 Gene

genes like me logo Genes that share pathways with U2AF1: view

Pathways by source for U2AF1 Gene

1 Cell Signaling Technology pathway for U2AF1 Gene
1 BioSystems pathway for U2AF1 Gene

Gene Ontology (GO) - Biological Process for U2AF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006397 mRNA processing TAS 1388271
GO:0006405 RNA export from nucleus TAS --
GO:0006406 mRNA export from nucleus TAS --
genes like me logo Genes that share ontologies with U2AF1: view

No data available for SIGNOR curated interactions for U2AF1 Gene

Drugs & Compounds for U2AF1 Gene

No Compound Related Data Available

Transcripts for U2AF1 Gene

Unigene Clusters for U2AF1 Gene

U2 small nuclear RNA auxiliary factor 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for U2AF1
  • Applied Biological Materials Clones for U2AF1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for U2AF1 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b · 8c ^ 9
SP1: - - -
SP2: -
SP3: - - -
SP4: - - - -
SP5:
SP6: - -

Relevant External Links for U2AF1 Gene

GeneLoc Exon Structure for
U2AF1
ECgene alternative splicing isoforms for
U2AF1

Expression for U2AF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for U2AF1 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for U2AF1 Gene



Protein tissue co-expression partners for U2AF1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of U2AF1 Gene:

U2AF1

SOURCE GeneReport for Unigene cluster for U2AF1 Gene:

Hs.365116

Evidence on tissue expression from TISSUES for U2AF1 Gene

  • Lung(4.4)
  • Spleen(4.4)
  • Nervous system(4.4)
  • Bone marrow(2.9)
  • Blood(2.4)
  • Heart(2)
  • Kidney(2)
genes like me logo Genes that share expression patterns with U2AF1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for U2AF1 Gene

Orthologs for U2AF1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for U2AF1 Gene

Organism Taxonomy Gene Similarity Type Details
mouse
(Mus musculus)
Mammalia U2af1 34
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia U2AF1 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia U2AF1 34
  • 96 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia U2AF1 34
  • 96 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia U2AF1 34
  • 91 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia U2AF1 34
  • 89 (a)
OneToOne
chicken
(Gallus gallus)
Aves U2AF1 34
  • 99 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia U2AF1 34
  • 99 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii u2af1 33 34
  • 79.28 (n)
fruit fly
(Drosophila melanogaster)
Insecta U2af38 35 34
  • 82 (a)
worm
(Caenorhabditis elegans)
Secernentea Y116A8C.35 35
  • 67 (a)
uaf-2 34
  • 51 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons U2AF35B 33
  • 58.38 (n)
rice
(Oryza sativa)
Liliopsida Os05g0564200 33
  • 60.54 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9845 34
  • 80 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4410 33
Species where no ortholog for U2AF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for U2AF1 Gene

ENSEMBL:
Gene Tree for U2AF1 (if available)
TreeFam:
Gene Tree for U2AF1 (if available)

Paralogs for U2AF1 Gene

Paralogs for U2AF1 Gene

(3) SIMAP similar genes for U2AF1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with U2AF1: view

Variants for U2AF1 Gene

Sequence variations from dbSNP and Humsavar for U2AF1 Gene

SNP ID Clin Chr 21 pos Sequence Context AA Info Type
rs1000371308 -- 43,106,997(+) AGATA(A/G)GCGAC intron-variant, upstream-variant-2KB
rs1000811760 -- 43,096,006(+) CATCA(A/G)AAGGG intron-variant
rs1000928499 -- 43,100,981(+) TTACT(A/G)GGCAA intron-variant
rs1001578180 -- 43,107,215(+) CGGCG(C/T)CCCGA intron-variant, upstream-variant-2KB
rs1001639309 -- 43,101,540(+) TTTTT(C/T)CCGCA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for U2AF1 Gene

Variant ID Type Subtype PubMed ID
esv2666871 CNV deletion 23128226
nsv1067412 CNV gain 25217958
nsv459279 CNV loss 19166990
nsv510800 CNV deletion 20534489
nsv587663 CNV loss 21841781

Variation tolerance for U2AF1 Gene

Residual Variation Intolerance Score: 40.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.18; 4.16% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for U2AF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
U2AF1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for U2AF1 Gene

Disorders for U2AF1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for U2AF1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
ovarian mucinous neoplasm
  • malignant ovarian mucinous neoplasm
retinitis pigmentosa
  • retinitis pigmentosa 1
leukemia, acute myeloid
  • leukemia, acute myeloid, somatic
- elite association - COSMIC cancer census association via MalaCards
Search U2AF1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for U2AF1

Genetic Association Database (GAD)
U2AF1
Human Genome Epidemiology (HuGE) Navigator
U2AF1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
U2AF1
genes like me logo Genes that share disorders with U2AF1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for U2AF1 Gene

Publications for U2AF1 Gene

  1. Diversity of vertebrate splicing factor U2AF35: identification of alternatively spliced U2AF1 mRNAS. (PMID: 15096518) Pacheco TR … Carmo-Fonseca M (The Journal of biological chemistry 2004) 3 4 22 60
  2. A novel peptide recognition mode revealed by the X-ray structure of a core U2AF35/U2AF65 heterodimer. (PMID: 11551507) Kielkopf CL … Burley SK (Cell 2001) 3 4 22 60
  3. The gene for human U2 snRNP auxiliary factor small 35-kDa subunit (U2AF1) maps to the progressive myoclonus epilepsy (EPM1) critical region on chromosome 21q22.3. (PMID: 8660980) Lalioti MD … Antonarakis SE (Genomics 1996) 2 3 22 60
  4. The splicing factor U2AF35 mediates critical protein-protein interactions in constitutive and enhancer-dependent splicing. (PMID: 8647433) Zuo P … Maniatis T (Genes & development 1996) 3 4 22 60
  5. Cloning and intracellular localization of the U2 small nuclear ribonucleoprotein auxiliary factor small subunit. (PMID: 1388271) Zhang M … Green MR (Proceedings of the National Academy of Sciences of the United States of America 1992) 3 4 22 60

Products for U2AF1 Gene

  • Addgene plasmids for U2AF1

Sources for U2AF1 Gene

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