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U2AF1L4 Gene

protein-coding   GIFtS: 47
GCID: GC19M036233

U2 Small Nuclear RNA Auxiliary Factor 1-Like 4

(Previous names: U2(RNU2) small nuclear RNA auxiliary factor 1-like 3, U2...)
(Previous symbol: U2AF1L3)
  Search for U2AF1L4
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
U2 Small Nuclear RNA Auxiliary Factor 1-Like 41 2     U2 Small Nuclear RNA Auxiliary Factor 1-Like Protein 42 3
U2AF1L31 2 3     U2(RNU2) Small Nuclear RNA Auxiliary Factor 1-Like Protein 32 3
U2 Small Nuclear RNA Auxiliary Factor 1-Like 31 2     U2AF1-Like Protein 32 3
U2(RNU2) Small Nuclear RNA Auxiliary Factor 1-Like 31 2     U2AF1RS32 5
U2AF1-RS32 3     U2AF1L3V12
U2 Auxiliary Factor 262 3     U2af262
U2 Small Nuclear RNA Auxiliary Factor 1-Like Protein 32 3     Splicing Factor U2AF 26 KDa Subunit2

External Ids:    HGNC: 230201   Entrez Gene: 1997462   Ensembl: ENSG000001612657   OMIM: 6010805   UniProtKB: Q8WU683   

Export aliases for U2AF1L4 gene to outside databases

Previous GC identifers: GC00U914419 GC19M040926 GC19M032738


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for U2AF1L4 Gene:
U2AF1L4 (U2 small nuclear RNA auxiliary factor 1-like 4) is a protein-coding gene. GO annotations related to this gene include RNA binding and nucleotide binding. An important paralog of this gene is ENSG00000267120.

UniProtKB/Swiss-Prot: U2AF4_HUMAN, Q8WU68
Function: RNA-binding protein that function as a pre-mRNA splicing factor. 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. Acts by enhancing the binding of U2AF2 to weak
pyrimidine tracts. Also participates in the regulation of alternative pre-mRNA splicing. Activates exon 5
skipping of PTPRC during T-cell activation; an event reversed by GFI1. Binds to RNA at the AG dinucleotide at the
3'-splice site (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000019.10  NC_018930.2  NT_011109.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the U2AF1L4 gene promoter:
         NF-1/L   NF-1   p53   c-Ets-1   CREB   POU2F1   POU2F1a   deltaCREB   COMP1   ZIC2/Zic2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidU2AF1L4 promoter sequence
   Search Chromatin IP Primers for U2AF1L4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat U2AF1L4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.12   Ensembl cytogenetic band:  19q13.12   HGNC cytogenetic band: 19q13.13

U2AF1L4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
U2AF1L4 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M036233:  view genomic region     (about GC identifiers)

Start:
36,233,365 bp from pter      End:
36,236,346 bp from pter
Size:
2,982 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: U2AF4_HUMAN, Q8WU68 (See protein sequence)
Recommended Name: Splicing factor U2AF 26 kDa subunit  
Size: 220 amino acids; 25744 Da
Subunit: Interacts with GFI1 and U2AF2 (By similarity)
Secondary accessions: A6NKI8 Q56UU3
Alternative splicing: 3 isoforms:  Q8WU68-1   Q8WU68-2   Q8WU68-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for U2AF1L4: NX_Q8WU68

Explore proteomics data for U2AF1L4 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys13
  • Modification sites at PhosphoSitePlus

  • See U2AF1L4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001035515.1  NP_659424.2  

    ENSEMBL proteins: 
     ENSP00000465242   ENSP00000475046   ENSP00000471804   ENSP00000474493   ENSP00000465170  
     ENSP00000473940   ENSP00000368258   ENSP00000292879   ENSP00000469891   ENSP00000467441  
     ENSP00000397645  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    RBM: RNA binding motif (RRM) containing

    5 InterPro protein domains:
     IPR000571 Znf_CCCH
     IPR012677 Nucleotide-bd_a/b_plait
     IPR003954 RRM_dom_euk
     IPR000504 RRM_dom
     IPR009145 U2_small

    Graphical View of Domain Structure for InterPro Entry Q8WU68

    ProtoNet protein and cluster: Q8WU68

    2 Blocks protein domains:
    IPB000504 RNA-binding region RNP-1 (RNA recognition motif)
    IPB000571 Zn-finger


    UniProtKB/Swiss-Prot: U2AF4_HUMAN, Q8WU68
    Domain: The second zinc finger in necessary for interaction with GFI1 and for alternative pre-mRNA splicing events
    (By similarity)
    Similarity: Belongs to the splicing factor SR family
    Similarity: Contains 2 C3H1-type zinc fingers
    Similarity: Contains 1 RRM (RNA recognition motif) domain


    U2AF1L4 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: U2AF4_HUMAN, Q8WU68
    Function: RNA-binding protein that function as a pre-mRNA splicing factor. 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. Acts by enhancing the binding of U2AF2 to weak
    pyrimidine tracts. Also participates in the regulation of alternative pre-mRNA splicing. Activates exon 5
    skipping of PTPRC during T-cell activation; an event reversed by GFI1. Binds to RNA at the AG dinucleotide at the
    3'-splice site (By similarity)

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding IEA--
    GO:0003676nucleic acid binding ----
    GO:0003723RNA binding IEA--
    GO:0046872metal ion binding IEA--
         
    U2AF1L4 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for U2AF1L4:
     Increased cell number in G1, s 

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    U2AF4_HUMAN, Q8WU68: Nucleus (By similarity). Nucleus speckle (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    extracellular2
    cytosol1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ----
    GO:0005681spliceosomal complex IEA--
    GO:0016607nuclear speck IEA--

    U2AF1L4 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for U2AF1L4
    Interactions:

        Search GeneGlobe Interaction Network for U2AF1L4

    STRING Interaction Network Preview (showing 5 interactants - click image to see more details)

    5 Interacting proteins for U2AF1L4 (Q8WU683 ENSP000002928794) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GIGYF2Q6Y7W63, ENSP000003871704I2D: score=1 STRING: ENSP00000387170
    GFI1ENSP000002947024STRING: ENSP00000294702
    HTATSF1ENSP000002183644STRING: ENSP00000218364
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    SRSF3ENSP000003628204STRING: ENSP00000362820
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006397mRNA processing IEA--
    GO:0008380RNA splicing IEA--

    U2AF1L4 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for U2AF1L4 (U2AF4)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for U2AF1L4 gene (2 alternative transcripts): 
    NM_001040425.2  NM_144987.3  

    Unigene Cluster for U2AF1L4:

    U2 small nuclear RNA auxiliary factor 1-like 4
    Hs.351558  [show with all ESTs]
    Unigene Representative Sequence: BC049208
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 21):
    ENST00000591057 ENST00000591084 ENST00000590135 ENST00000585554 ENST00000591855
    ENST00000594792 ENST00000600296 ENST00000587987 ENST00000589429 ENST00000588980
    ENST00000378975(uc002obe.3) ENST00000592913 ENST00000292879(uc002obf.3)
    ENST00000588892 ENST00000586476 ENST00000601236 ENST00000585771 ENST00000587886

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    Additional mRNA sequence: 

    AK092844.1 AK303983.1 AY461582.1 AY569437.3 BC010865.1 BC021186.1 BC049208.1 BC062474.1 

    24 DOTS entries:

    DT.101984198  DT.100789061  DT.101984199  DT.213499  DT.121488876  DT.121488788  DT.213497  DT.100700046 
    DT.100789057  DT.99936823  DT.100699338  DT.95161758  DT.91660602  DT.100789056  DT.121488888  DT.121488838 
    DT.121488905  DT.422019  DT.100037322  DT.100789054  DT.100789055  DT.100789060  DT.121488843  DT.95188629 

    Selected AceView cDNA sequences (see all 175):

    AI311085 AW978267 BU608847 BC010865 BC031329 AX775837 BU735432 BM695629 
    BX337984 AI925610 CA748721 AX775839 BU542243 AW672936 BF445882 AI597639 
    AI205252 BQ882427 AI498787 AK026226 BI838452 BC049208 CD367166 CD742768 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for U2AF1L4 (see all 15)    About this scheme

    ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c ^ 8a · 8b · 8c · 8d ^ 9 ^ 10 ^ 11a · 11b ·
    SP1:                                -                 -     -     -     -     -                             -                       -     -     -               
    SP2:                                -     -           -     -     -     -     -                             -                       -     -     -     -         
    SP3:                                -                                                                       -                       -     -     -               
    SP4:                                -                 -     -     -     -     -                                                     -     -     -               
    SP5:                                -     -           -                                                     -                                                   

    ExUns: 11c · 11d · 11e
    SP1:                  
    SP2:                  
    SP3:                  
    SP4:                  
    SP5:                  


    ECgene alternative splicing isoforms for U2AF1L4

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    U2AF1L4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGACCTTCT
    U2AF1L4 Expression
    About this image

    U2AF1L4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    U2AF1L4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.351558

    UniProtKB/Swiss-Prot: U2AF4_HUMAN, Q8WU68
    Tissue specificity: Isoform 2 is widely expressed. Isoform 3 is highly expressed in heart, brain and lung, lower
    expressed in thymus and much lower expressed in peripheral blood leukocytes

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for U2AF1L4 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia U2af1l45 U2 small nuclear RNA auxiliary factor 1-like 4   --   7 (18.61 cM) 30563301 
    fruit fly
    (Drosophila melanogaster)
    Insecta U2af386
    U2 small nuclear riboprotein auxiliary factor 38
    33(a)
    1 → many
    2L(292959-294681)
    worm
    (Caenorhabditis elegans)
    Secernentea uaf-26
    Protein UAF-2 (uaf-2) mRNA, complete cds
    27(a)
    1 → many
    IV(17116763-17118760) WBGene00006698
    rice
    (Oryza sativa)
    Liliopsida Os.120752 Oryza sativa hypothetical protein mRNA, partial cds 76.81(n)    NM_191929.1 


    ENSEMBL Gene Tree for U2AF1L4 (if available)
    TreeFam Gene Tree for U2AF1L4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for U2AF1L4 gene
    ENSG000002671202  ZRSR22  U2AF12  ZRSR12  
    3 SIMAP similar genes for U2AF1L4 using alignment to 9 protein entries:     U2AF4_HUMAN (see all proteins):
    DKFZp313J1712    U2AF1    ZRSR2

    U2AF1L4 for paralogs           About GeneDecksing


    2 Pseudogenes.org Pseudogenes for U2AF1L4
    PGOHUM00000250411 PGOHUM00000251204


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for U2AF1L4:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv3853n71CNV Loss21882294
    dgv3852n71CNV Loss21882294
    nsv515536CNV Loss19592680

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 601080    OMIM disorders: --


    U2AF1L4 for disorders           About GeneDecksing


    Export disorders for U2AF1L4 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for U2AF1L4 gene, integrated from 10 sources (see all 18):
    (articles sorted by number of sources associating them with U2AF1L4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Characterization of U2AF(6), a splicing factor related to U2AF(35). (PubMed id 11739736)1, 3 Shepard J....Graveley B.R. (Mol. Cell. Biol. 2002)
    2. Isolation and mapping of human homologues of an imprinted mouse gene U2af1-rs1. (PubMed id 8586425)1, 3 Kitagawa K.... Mukai T. (Genomics 1995)
    3. Human PSENEN and U2AF1L4 genes are concertedly regulated by a genuine bidirectional promoter. (PubMed id 23246698)1 Didych D.A....Sverdlov E.D. (Gene 2013)
    4. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    5. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
    6. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    7. Functional dissection of an enhancer-like element located within the second intron of the human U2AF1L4 gene. (PubMed id 22022969)1 Didych D.A....Sverdlov E.D. (Biochemistry Mosc. 2011)
    8. Conserved beta-hairpin recognition by the GYF domains of Smy2 and GIGYF2 in mRNA surveillance and vesicular transport complexes. (PubMed id 20696395)1 Ash M.R....Freund C. (Structure 2010)
    9. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (EMBO J. 2009)
    10. Differential isoform expression and interaction with the P32 regulatory protein controls the subcellular localization of the splicing factor U2AF26. (PubMed id 18460468)1 Heyd F....MAPrAPy T. (J. Biol. Chem. 2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 199746 HGNC: 23020 AceView: FLJ22573andU2AF1L3 Ensembl:ENSG00000161265 euGenes: HUgn199746
    ECgene: U2AF1L4 H-InvDB: U2AF1L4

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for U2AF1L4 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for U2AF1L4 gene:
    Search GeneIP for patents involving U2AF1L4

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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