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WBP4 Gene

protein-coding   GIFtS: 51
GCID: GC13P041635

WW Domain Binding Protein 4

  Search for WBP4
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
WW Domain Binding Protein 41 2     WW Domain-Containing-Binding Protein 42 3
Formin Binding Protein 211 2     Domain-Containing Binding Protein 42
Formin-Binding Protein 212 3     WW Domain-Binding Protein 42
FBP212 3     WW Domain-Containing Binding Protein 42
WBP-42 3     FNBP213

External Ids:    HGNC: 127391   Entrez Gene: 111932   Ensembl: ENSG000001206887   OMIM: 6049815   UniProtKB: O755543   

Export aliases for WBP4 gene to outside databases

Previous GC identifers: GC13P039621 GC13P035622 GC13P040572 GC13P039433 GC13P040533 GC13P022436


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for WBP4 Gene:
This gene encodes WW domain-containing binding protein 4. The WW domain represents a small and compact globular
structure that interacts with proline-rich ligands. This encoded protein is a general spliceosomal protein that
may play a role in cross-intron bridging of U1 and U2 snRNPs in the spliceosomal complex A. (provided by RefSeq,
Jul 2008)

GeneCards Summary for WBP4 Gene:
WBP4 (WW domain binding protein 4) is a protein-coding gene. GO annotations related to this gene include proline-rich region binding and nucleic acid binding.

UniProtKB/Swiss-Prot: WBP4_HUMAN, O75554
Function: Promotes pre-mRNA splicing. A spliceosome-associated protein; may play a role in cross-intron bridging
of U1 and U2 snRNPs in the mammalian A complex

Gene Wiki entry for WBP4 Gene


(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_000013.11  NT_024524.15  NC_018924.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the WBP4 gene promoter:
         STAT1   STAT1beta   Nkx2-5   STAT1alpha   MEF-2A   STAT2   STAT3   Msx-1   aMEF-2   MRF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): WBP4 promoter sequence
   Search Chromatin IP Primers for WBP4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat WBP4


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

Entrez Gene cytogenetic band: 13q14.11   Ensembl cytogenetic band:  13q14.11   HGNC cytogenetic band: 13q13.3

WBP4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
WBP4 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13P041635:  view genomic region     (about GC identifiers)

Start:
41,635,410 bp from pter      End:
41,658,139 bp from pter
Size:
22,730 bases      Orientation:
plus 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: WBP4_HUMAN, O75554 (See protein sequence)
Recommended Name: WW domain-binding protein 4  
Size: 376 amino acids; 42507 Da
Subunit: Associated with U2 snRNPs. Binds splicing factors SNRPB, SNRPC and SF1. Interacts via the WW domains with
the Pro-rich domains of KHDRBS1/SAM68 (By similarity). Interacts via the WW domains with the Pro-rich domains of
WBP11
2 PDB 3D structures from and Proteopedia for WBP4:
2DK1 (3D)        2JXW (3D)    
Secondary accessions: Q32P29

Explore the universe of human proteins at neXtProt for WBP4: NX_O75554

Explore proteomics data for WBP4 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See WBP4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_009118.1  
    ENSEMBL proteins: 
     ENSP00000368801   ENSP00000439301  

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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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    4 InterPro protein domains:
     IPR003604 Znf_U1
     IPR013085 Znf_U1-C
     IPR000690 Znf_C2H2_matrin
     IPR001202 WW_dom

    Graphical View of Domain Structure for InterPro Entry O75554

    ProtoNet protein and cluster: O75554

    1 Blocks protein domain: IPB003604 Zn-finger

    UniProtKB/Swiss-Prot: WBP4_HUMAN, O75554
    Domain: The WW domain recognizes the proline, glycine and methionine-rich (PGM) motif present in the splicing
    factors, as well as the Arg/Gly-rich-flanked Pro-rich domains found in several WW domain-binding proteins (By
    similarity)
    Similarity: Contains 1 matrin-type zinc finger
    Similarity: Contains 2 WW domains


    Find genes that share domains with WBP4           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: WBP4_HUMAN, O75554
    Function: Promotes pre-mRNA splicing. A spliceosome-associated protein; may play a role in cross-intron bridging
    of U1 and U2 snRNPs in the mammalian A complex

         Genatlas biochemistry entry for WBP4:
    WW domain binding protein 4, formin binding 21,general spliceosomal protein binding a third class of
    proline-glycine methionine (PGM) rich motif

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
    GO:0005515protein binding IPI17500595
    GO:0008270zinc ion binding IEA--
    GO:0070064proline-rich region binding IPI19592703
         
    Find genes that share ontologies with WBP4           About GenesLikeMe


    Animal Models:
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    hsa-miR-130a* hsa-miR-23c hsa-miR-374c hsa-miR-23b hsa-miR-655 hsa-miR-369-3p hsa-miR-558 hsa-miR-23a
    SwitchGear 3'UTR luciferase reporter plasmidWBP4 3' UTR sequence
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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
    WBP4_HUMAN, O75554: Nucleus speckle
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    plasma membrane4
    cytosol2

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005681spliceosomal complex IEA--
    GO:0005730NOT nucleolus IDA--
    GO:0005886plasma membrane IDA--
    GO:0016607nuclear speck IDA19592703

    Find genes that share ontologies with WBP4           About GenesLikeMe


    (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 WBP4
    Interactions:

        Search GeneGlobe Interaction Network for WBP4

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for WBP4 (O755542, 3 ENSP000003688014) via UniProtKB, MINT, STRING, and/or I2D (see all 92)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    KHDRBS1Q076662, 3, ENSP000003138294MINT-73037 MINT-56718 MINT-56719 MINT-56723 MINT-56722 I2D: score=4 STRING: ENSP00000313829
    DDX23Q9BUQ82, 3, ENSP000003107234MINT-73032 I2D: score=3 STRING: ENSP00000310723
    DIAPH1O606102, 3, ENSP000003815654MINT-73061 I2D: score=3 STRING: ENSP00000381565
    HLTFQ145272, 3, ENSP000003089444MINT-73028 I2D: score=3 STRING: ENSP00000308944
    PRPF3O433952, 3, ENSP000003153794MINT-73041 I2D: score=3 STRING: ENSP00000315379
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0045292mRNA cis splicing, via spliceosome IDA19592703

    Find genes that share ontologies with WBP4           About GenesLikeMe



    (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 WBP4



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for WBP4 gene: 
    NM_007187.3  

    Unigene Cluster for WBP4:

    WW domain binding protein 4
    Hs.411300  [show with all ESTs]
    Unigene Representative Sequence: AF071185
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000379487(uc001uxt.3 uc010tfd.2) ENST00000542082
    miRNA
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    hsa-miR-130a* hsa-miR-23c hsa-miR-374c hsa-miR-23b hsa-miR-655 hsa-miR-369-3p hsa-miR-558 hsa-miR-23a
    SwitchGear 3'UTR luciferase reporter plasmidWBP4 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat WBP4
      QuantiFast Probe-based Assays in human, mouse, rat WBP4

    Additional mRNA sequence: 

    AF071185.1 AK000979.1 AK001557.1 AK297536.1 AK314525.1 BC104879.1 BC108310.1 

    12 DOTS entries:

    DT.92426388  DT.95200477  DT.451927  DT.91637634  DT.75185738  DT.100009360  DT.100729675  DT.120779043 
    DT.40133310  DT.40219223  DT.40234587  DT.95256657 

    Selected AceView cDNA sequences (see all 160):

    AI668682 BP340945 NM_007187 BE644677 AA433952 CB852317 BU623161 BM462928 
    BQ027684 CR603878 CR624814 BU781855 AI734228 AI198587 BQ014713 CB241394 
    BG697331 AA416964 AA287005 AW237795 CD364365 AW303385 BM456326 BU689600 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for WBP4    About this scheme

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


    ECgene alternative splicing isoforms for WBP4

    (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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    WBP4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TAAGAAAAAA
    WBP4 Expression
    About this image

    WBP4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    WBP4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.411300
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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 animals.

    Orthologs for WBP4 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Wbp41 , 5 WW domain binding protein 41, 5 84(n)1
    79.36(a)1
      14 (42.66 cM)5
    223801  NM_018765.31  NP_061235.21 
     794599375 
    chicken
    (Gallus gallus)
    Aves WBP41 WW domain binding protein 4 (formin binding protein more 65.55(n)
    58.82(a)
      418829  NM_001030824.1  NP_001025995.1 
    lizard
    (Anolis carolinensis)
    Reptilia WBP46
    WW domain binding protein 4
    53(a)
    1 ↔ 1
    3(70669313-70687542)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.14142 Xenopus laevis transcribed sequence with weak similarity more 75.91(n)    BX843730.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wbp41 WW domain binding protein 4 53.78(n)
    48.62(a)
      553723  NM_001020694.1  NP_001018530.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG42911 CG4291 45.8(n)
    35.26(a)
      33264  NM_134707.3  NP_608551.1 


    ENSEMBL Gene Tree for WBP4 (if available)
    TreeFam Gene Tree for WBP4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (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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    Selected SNPs for WBP4 (see all 523)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0363524
    A breast cancer sample4--see VAR_0363522 K R mis40--------
    rs1383789801,2
    --41633771(+) CCCAAC/TAAACA 1 -- us2k10--------
    rs14110421,2
    C,F--41634063(+) GTCGAT/CATACT 1 -- us2k1 tfbs36Minor allele frequency- C:0.02EA NA MN 420
    rs1807474961,2
    --41634084(+) CATCTA/CATCAG 1 -- us2k10--------
    rs14110431,2
    C,F,H--41634168(+) GGCCTT/GTTTTC 1 -- us2k115Minor allele frequency- G:0.03EA NA MN NS 1448
    rs1389899781,2
    C--41634346(+) GGCGCA/GGAAGG 1 -- us2k10--------
    rs1422640491,2
    C--41634372(+) GGGGCC/TTCGTA 1 -- us2k10--------
    rs1855403251,2
    --41634561(+) CCCGGG/TCGTCT 1 -- us2k10--------
    rs1883933721,2
    --41634625(+) CCTCAA/GGGCCC 1 -- us2k10--------
    rs1819354401,2
    --41634855(+) AAAAAA/GAAGAA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for WBP4 (41635410 - 41658139 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for WBP4:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv832587CNV Gain17160897

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing WBP4
    DNA2.0 Custom Variant and Variant Library Synthesis for WBP4

    (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: 604981    OMIM disorders: --


    Find genes that share disorders with WBP4           About GenesLikeMe


    Export disorders for WBP4 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 WBP4 gene, integrated from 10 sources (see all 23):
    (articles sorted by number of sources associating them with WBP4)
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    1. WW domain-mediated interactions reveal a spliceosome-associated protein that binds a third class of proline-rich motif: the proline glycine and methionine-rich motif. (PubMed id 9724750)1, 2, 3 Bedford M.T.... Leder P. (Proc. Natl. Acad. Sci. U.S.A. 1998)
    2. Structure and function of the two tandem WW domains of the pre-mRNA splicing factor FBP21 (formin-binding protein 21). (PubMed id 19592703)1, 2, 9 Huang X.... Shi Y. (J. Biol. Chem. 2009)
    3. The DNA sequence and analysis of human chromosome 13. (PubMed id 15057823)1, 2 Dunham A.... Ross M.T. (Nature 2004)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    5. A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population. (PubMed id 23266558)1 Yamazaki K....Kubo M. (Gastroenterology 2013)
    6. 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)
    7. Multivalent binding of formin-binding protein 21 (FBP21)-tandem-WW domains fosters protein recognition in the pre-spliceosome. (PubMed id 21917930)1 Klippel S....Freund C. (J. Biol. Chem. 2011)
    8. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (Sci. Signal. 2011)
    9. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (Sci. Signal. 2010)
    10. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. (PubMed id 18854154)1 KAPnig R....Chanda S.K. (Cell 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: 11193 HGNC: 12739 AceView: WBP4 Ensembl:ENSG00000120688 euGenes: HUgn11193
    ECgene: WBP4 H-InvDB: WBP4

    (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 WBP4 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    IP news from LifeMap Sciences, Inc.)
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    Patent Information for WBP4 gene:
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    GeneCards and IP:
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