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FUBP3 Gene

protein-coding   GIFtS: 54
GCID: GC09P133454

Far Upstream Element (FUSE) Binding Protein 3


(Previous symbol: FBP3)
  See related diseases
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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Far Upstream Element (FUSE) Binding Protein 31 2
FBP31 2 3 5
FUSE-Binding Protein 32 3
Far Upstream Element-Binding Protein 32

External Ids:    HGNC: 40051   Entrez Gene: 89392   Ensembl: ENSG000001071647   OMIM: 6035365   UniProtKB: Q96I243   
ORGUL members:         

Export aliases for FUBP3 gene to outside databases

Previous GC identifers: GC09P124470 GC09P125001 GC09P126809 GC09P128746 GC09P128730 GC09U900642 GC09P132444 GC09P102941


(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 FUBP3 Gene:
FUBP3 (far upstream element (FUSE) binding protein 3) is a protein-coding gene. Diseases associated with FUBP3 include ataxia, and cerebritis. GO annotations related to this gene include RNA binding. An important paralog of this gene is FUBP1.

UniProtKB/Swiss-Prot: FUBP3_HUMAN, Q96I24
Function: May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression




(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_000009.12  NT_008470.20  NC_018920.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the FUBP3 gene promoter:
         NF-1   NF-1/L   AML1a   p300   Egr-1   Olf-1   MIF-1   AREB6   Cart-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for FUBP3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FUBP3


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

Entrez Gene cytogenetic band: 9q34.11   Ensembl cytogenetic band:  9q34.11   HGNC cytogenetic band: 9q34.11

FUBP3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FUBP3 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P133454:  view genomic region     (about GC identifiers)

Start:
133,454,352 bp from pter      End:
133,513,739 bp from pter
Size:
59,388 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, 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: FUBP3_HUMAN, Q96I24 (See protein sequence)
Recommended Name: Far upstream element-binding protein 3  
Size: 572 amino acids; 61640 Da
Sequence caution: Sequence=AAC50893.1; Type=Frameshift; Positions=18; Sequence=AAH01325.1; Type=Frameshift;
Positions=527;
Secondary accessions: A3KFK8 A3KFL0 Q92946 Q9BVB6
Alternative splicing: 2 isoforms:  Q96I24-1   Q96I24-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for FUBP3: NX_Q96I24

Explore proteomics data for FUBP3 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys15, Lys57, Lys87, Lys186, Lys378
  • Modification sites at PhosphoSitePlus

  • See FUBP3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_003925.1  
    ENSEMBL proteins: 
     ENSP00000318177  

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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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    2 InterPro protein domains:
     IPR004087 KH_dom
     IPR004088 KH_dom_type_1

    Graphical View of Domain Structure for InterPro Entry Q96I24

    ProtoNet protein and cluster: Q96I24

    1 Blocks protein domain: IPB004088 KH

    UniProtKB/Swiss-Prot: FUBP3_HUMAN, Q96I24
    Similarity: Contains 4 KH domains


    FUBP3 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: FUBP3_HUMAN, Q96I24
    Function: May interact with single-stranded DNA from the far-upstream element (FUSE). May activate gene expression

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003723RNA binding ----
    GO:0044822poly(A) RNA binding IDA--
         
    FUBP3 for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for FUBP3
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    miRNA
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    miRTarBase miRNAs that target FUBP3:
    hsa-mir-155-5p (MIRT020823), hsa-mir-128-3p (MIRT045868), hsa-mir-1 (MIRT023861)

    Block miRNA regulation of human, mouse, rat FUBP3 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate FUBP3 (see all 30):
    hsa-miR-498 hsa-miR-188-5p hsa-miR-4328 hsa-miR-429 hsa-miR-128 hsa-miR-3653 hsa-miR-3692 hsa-miR-633
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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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
    FUBP3_HUMAN, Q96I24: Nucleus (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytoskeleton2
    cytosol1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus NAS8940189
    GO:0005737cytoplasm IDA19087307

    FUBP3 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 FUBP3
    Interactions:

        Search GeneGlobe Interaction Network for FUBP3

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

    Selected Interacting proteins for FUBP3 (Q96I243 ENSP000003181774) via UniProtKB, MINT, STRING, and/or I2D (see all 63)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PAX9P557713, ENSP000003552454I2D: score=1 STRING: ENSP00000355245
    SSX1Q163843, ENSP000003661184I2D: score=1 STRING: ENSP00000366118
    XBP1P178613, ENSP000002160374I2D: score=1 STRING: ENSP00000216037
    QKIQ96PU83, ENSP000003549514I2D: score=2 STRING: ENSP00000354951
    GRB2P629933, ENSP000003390074I2D: score=1 STRING: ENSP00000339007
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IDA8940189
    GO:0010628positive regulation of gene expression IDA19087307
    GO:0045893positive regulation of transcription, DNA-templated IDA8940189

    FUBP3 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 FUBP3



    (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 FUBP3 gene: 
    NM_003934.1  

    Unigene Cluster for FUBP3:

    Far upstream element (FUSE) binding protein 3
    Hs.98751  [show with all ESTs]
    Unigene Representative Sequence: NM_003934
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000467100(uc004bzq.1) ENST00000319725(uc004bzr.1) ENST00000465949
    ENST00000487406 ENST00000472006 ENST00000492199
    miRNA
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    Block miRNA regulation of human, mouse, rat FUBP3 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate FUBP3 (see all 30):
    hsa-miR-498 hsa-miR-188-5p hsa-miR-4328 hsa-miR-429 hsa-miR-128 hsa-miR-3653 hsa-miR-3692 hsa-miR-633
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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      QuantiFast Probe-based Assays in human, mouse, rat FUBP3

    Additional mRNA sequence: 

    AK057958.1 AK295155.1 BC001325.1 BC007874.2 BC137338.1 BC137340.1 U69127.1 

    11 DOTS entries:

    DT.112637  DT.106564  DT.97795305  DT.100778504  DT.121166616  DT.121166605  DT.91650046  DT.91703642 
    DT.91748980  DT.91957087  DT.91699635 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for FUBP3 (see all 6)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21
    SP1:                                                                                                                                          
    SP2:        -     -                                                                                                                           
    SP3:        -     -                             -                                                                                             
    SP4:        -     -                                                                                                                           
    SP5:                                            -     -                                                                                       


    ECgene alternative splicing isoforms for FUBP3

    (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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    FUBP3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGGTTTTTAA
    FUBP3 Expression
    About this image


    FUBP3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Brain (Nervous System)    fully expand to see all 2 entries
             Cerebral Cortex
     
     Eye (Sensory Organs)
             Lens
     
     Neural Tube (Nervous System)
             Telencephalon
    FUBP3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    FUBP3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.98751

    UniProtKB/Swiss-Prot: FUBP3_HUMAN, Q96I24
    Tissue specificity: Detected in a number of cell lines

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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 FUBP3 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Fubp31 , 5 far upstream element (FUSE) binding protein 31, 5 88.83(n)1
    93.47(a)1
      2 (21.84 cM)5
    3202671  NM_001033389.31  NP_001028561.21 
     315726515 
    chicken
    (Gallus gallus)
    Aves FUBP31 far upstream element (FUSE) binding protein 3 84.26(n)
    90.02(a)
      417184  NM_001006199.1  NP_001006199.1 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia fubp31 far upstream element (FUSE) binding protein 3 78.41(n)
    85.14(a)
      100038226  NM_001097365.1  NP_001090834.1 
    zebrafish
    (Danio rerio)
    Actinopterygii fubp31 far upstream element (FUSE) binding protein 3 71.01(n)
    73.74(a)
      493616  NM_001007776.1  NP_001007777.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Psi1 P-element somatic inhibitor 48.12(n)
    41.06(a)
      36889  NM_057775.4  NP_477123.1 
    worm
    (Caenorhabditis elegans)
    Secernentea C12D8.1b3
    CELE_C12D8.11
    RNA binding protein3
    CELE_C12D8.11
    36(a)
    (best of 6)3
    47.92(n)1
    42.24(a)1
      V(10238862-10240838)3
    1794231  NM_073232.41  NP_505633.11 


    ENSEMBL Gene Tree for FUBP3 (if available)
    TreeFam Gene Tree for FUBP3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for FUBP3 gene
    FUBP12  KHSRP2  
    4 SIMAP similar genes for FUBP3 using alignment to 1 protein entry:     FUBP3_HUMAN:
    FUBP1    KHSRP    NOVA1    PCBP2

    FUBP3 for paralogs           About GeneDecksing



    (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 FUBP3 (see all 1298)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1381064891,2
    --133457240(+) AGATCA/GTAATA 1 -- int10--------
    rs1495194421,2
    --133457248(+) ATACTC/TTCAGT 1 -- int10--------
    rs117925801,2
    C,F,H--133457277(+) AACCTG/ACAGTT 1 -- int110Minor allele frequency- A:0.03NA EA NS 884
    rs1842994311,2
    --133457354(+) CCTCCA/GTGTAT 1 -- int10--------
    rs584773981,2
    C,F--133457546(+) TAGAAA/GTGTGA 1 -- int15Minor allele frequency- G:0.05WA CSA 125
    rs1151190371,2
    C,F--133457570(+) CAGTGG/ACTCAT 1 -- int11Minor allele frequency- A:0.04WA 118
    rs1998179991,2
    C--133457593(+) AGCAC-/TTTGGGA 1 -- int10--------
    rs755647501,2
    C,F--133457690(+) AAAAAT/ATAGCT 1 -- int12Minor allele frequency- A:0.05NA EA 240
    rs1441201921,2
    --133457705(+) GTGGTG/TGCCCA 1 -- int10--------
    rs1486947451,2
    --133457763(+) GAGCAC/TGGAGA 1 -- int10--------

    HapMap Linkage Disequilibrium report for FUBP3 (133454352 - 133513739 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for FUBP3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv831735CNV Loss17160897
    nsv825122CNV Gain20364138
    esv1002669CNV Gain20482838
    nsv831734CNV Gain17160897
    nsv825121CNV Gain20364138

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing FUBP3
    DNA2.0 Custom Variant and Variant Library Synthesis for FUBP3

    (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: 603536    OMIM disorders: --

    3 diseases for FUBP3:    
    About MalaCards
    ataxia    cerebritis    prostatitis


    FUBP3 for disorders           About GeneDecksing

    Genetic Association Database (GAD): FUBP3
    Human Genome Epidemiology (HuGE) Navigator: FUBP3 (1 document)

    Export disorders for FUBP3 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 FUBP3 gene, integrated from 10 sources (see all 41):
    (articles sorted by number of sources associating them with FUBP3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The far upstream element-binding proteins comprise an ancient family of single-strand DNA-binding transactivators. (PubMed id 8940189)1, 2, 3 Davis-Smyth T.... Levens D. (J. Biol. Chem. 1996)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    3. Hundreds of variants clustered in genomic loci and biological pathways affect human height. (PubMed id 20881960)1, 4 Lango Allen H....Hirschhorn J.N. (Nature 2010)
    4. Identification of ten loci associated with height highlights new biological pathways in human growth. (PubMed id 18391950)1, 4 Lettre G.... Hirschhorn J.N. (Nat. Genet. 2008)
    5. 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)
    6. The FUSE binding proteins FBP1 and FBP3 are potential c-myc regulators in renal, but not in prostate and bladder cancer. (PubMed id 19087307)1, 9 Weber A....Kristiansen G. (BMC Cancer 2008)
    7. Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. (PubMed id 23563607)1 Berndt S.I....Ingelsson E. (Nat. Genet. 2013)
    8. Development and application of a DNA microarray-based yeast two-hybrid system. (PubMed id 23275563)1 Suter B....Wanker E.E. (Nucleic Acids Res. 2013)
    9. Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions. (PubMed id 24255178)1 Couzens A.L....Gingras A.C. (Sci Signal 2013)
    10. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)

    (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: 8939 HGNC: 4005 Ensembl:ENSG00000107164 euGenes: HUgn8939 ECgene: FUBP3
    H-InvDB: FUBP3

    (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 FUBP3 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 FUBP3 gene:
    Search GeneIP for patents involving FUBP3

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



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