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SFPQ Gene

protein-coding   GIFtS: 64
GCID: GC01M035641

Splicing Factor Proline/Glutamine-Rich

(Previous name: splicing factor proline/glutamine rich (polypyrimidine tract-binding...)
  See SFPQ-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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Aliases
Splicing Factor Proline/Glutamine-Rich1 2     hPOMp1002 3
PSF2 3 5     PTB-Associated-Splicing Factor2 3
Splicing Factor Proline/Glutamine Rich (Polypyrimidine Tract-Binding
Protein-Associated)1 2
     POMP1002
Polypyrimidine Tract Binding Protein Associated1 2     Polypyrimidine Tract-Binding Protein-Associated Splicing Factor2
Polypyrimidine Tract-Binding Protein-Associated-Splicing Factor2 3     PTB-Associated Splicing Factor2
100 KDa DNA-Pairing Protein2 3     Splicing Factor Proline/Glutamine Rich (Polypyrimidine Tract Binding
Protein Associated)2
DNA-Binding P52/P100 Complex, 100 KDa Subunit2 3     Splicing Factor, Proline- And Glutamine-Rich2

External Ids:    HGNC: 107741   Entrez Gene: 64212   Ensembl: ENSG000001165607   OMIM: 6051995   UniProtKB: P232463   

Export aliases for SFPQ gene to outside databases

Previous GC identifers: GC01M035470 GC01M034705 GC01M035068 GC01M035076 GC01M035312 GC01M035421 GC01M033767


(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 SFPQ Gene:
SFPQ (splicing factor proline/glutamine-rich) is a protein-coding gene. Diseases associated with SFPQ include papillary renal cell carcinoma, and renal cell carcinoma, papillary, 1. GO annotations related to this gene include RNA binding and nucleotide binding. An important paralog of this gene is NONO.

UniProtKB/Swiss-Prot: SFPQ_HUMAN, P23246
Function: DNA- and RNA binding protein, involved in several nuclear processes. Essential pre-mRNA splicing factor
required early in spliceosome formation and for splicing catalytic step II, probably as a heteromer with NONO.
Binds to pre-mRNA in spliceosome C complex, and specifically binds to intronic polypyrimidine tracts. Involved in
regulation of signal-induced alternative splicing. During splicing of PTPRC/CD45, a phosphorylated form is
sequestered by THRAP3 from the pre-mRNA in resting T-cells; T-cell activation and subsequent reduced
phosphorylation is proposed to lead to release from THRAP3 allowing binding to pre-mRNA splicing regulatotry
elements which represses exon inclusion. Interacts with U5 snRNA, probably by binding to a purine-rich sequence
located on the 3' side of U5 snRNA stem 1b. May be involved in a pre-mRNA coupled splicing and polyadenylation
process as component of a snRNP-free complex with SNRPA/U1A. The SFPQ-NONO heteromer associated with MATR3 may
play a role in nuclear retention of defective RNAs. SFPQ may be involved in homologous DNA pairing; in vitro,
promotes the invasion of ssDNA between a duplex DNA and produces a D-loop formation. The SFPQ-NONO heteromer may
be involved in DNA unwinding by modulating the function of topoisomerase I/TOP1; in vitro, stimulates
dissociation of TOP1 from DNA after cleavage and enhances its jumping between separate DNA helices. The SFPQ-NONO
heteromer may be involved in DNA nonhomologous end joining (NHEJ) required for double-strand break repair and
V(D)J recombination and may stabilize paired DNA ends; in vitro, the complex strongly stimulates DNA end joining,
binds directly to the DNA substrates and cooperates with the Ku70/G22P1-Ku80/XRCC5 (Ku) dimer to establish a
functional preligation complex. SFPQ is involved in transcriptional regulation. Transcriptional repression is
probably mediated by an interaction of SFPQ with SIN3A and subsequent recruitment of histone deacetylases
(HDACs). The SFPQ-NONO/SF-1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent
transcriptional avtivity. SFPQ isoform Long binds to the DNA binding domains (DBD) of nuclear hormone receptors,
like RXRA and probably THRA, and acts as transcriptional corepressor in absence of hormone ligands. Binds the DNA
sequence 5'-CTGAGTC-3' in the insulin-like growth factor response element (IGFRE) and inhibits IGF-I-stimulated
transcriptional activity

Gene Wiki entry for SFPQ 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 at NCBI GenBank:
NC_000001.10  NT_032977.10  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SFPQ gene promoter:
         SRF   LHX3b/Lhx3b   Sp1   p53   RREB-1   SRF (504 AA)   HNF-3beta   S8   LHX3a/Lhx3a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 4): SFPQ promoter sequence
   Search Chromatin IP Primers for SFPQ

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


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

Entrez Gene cytogenetic band: 1p34.3   Ensembl cytogenetic band:  1p34.3   HGNC cytogenetic band: 1p34.3

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

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M035641:  view genomic region     (about GC identifiers)

Start:
35,641,979 bp from pter      End:
35,658,749 bp from pter
Size:
16,771 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: SFPQ_HUMAN, P23246 (See protein sequence)
Recommended Name: Splicing factor, proline- and glutamine-rich  
Size: 707 amino acids; 76149 Da
Subunit: Monomer and component of the SFPQ-NONO complex, which is probably a heterotetramer of two 52 kDa (NONO)
and two 100 kDa (SFPQ) subunits. SFPQ is a component of spliceosome and U5.4/6 snRNP complexes. Interacts with
SNRPA/U1A. Component of a snRNP-free complex with SNRPA/U1A. Part of complex consisting of SFPQ, NONO and MATR3.
Interacts with polypyrimidine tract-binding protein 1/PTB. Part of a complex consisting of SFPQ, NONO and NR5A1.
Interacts with RXRA, probably THRA, and SIN3A. Interacts with TOP1. Part of a complex consisting of SFPQ, NONO
and TOP1. Interacts with SNRNP70 in apoptotic cells. Interacts with PSPC1. Interacts with RNF43. Interacts with
PITX3 and NR4A2/NURR1. Interacts with PTK6. Interacts with THRAP3; the interaction is dependent on SFPQ
phosphorylation at 'Thr-687' and inhibits binding of SFPQ to a ESS1 exonic splicing silencer element-containing
RNA
Caution: Was originally (PubMed:2480877) thought to be myoblast cell surface antigen 24.1D5 and a possible
membrane-bound protein ectokinase
Secondary accessions: P30808 Q5SZ71
Alternative splicing: 2 isoforms:  P23246-1   P23246-2   

Explore the universe of human proteins at neXtProt for SFPQ: NX_P23246

Explore proteomics data for SFPQ at MOPED

Post-translational modifications: 

  • The N-terminus is blocked1
  • Phosphorylated on multiple serine and threonine residues during apoptosis. In vitro phosphorylated by PKC.
    Phosphorylation stimulates binding to DNA and D-loop formation, but inhibits binding to RNA. Phosphorylation of
    C-terminal tyrosines promotes its cytoplasmic localization, impaired its binding to polypyrimidine RNA and led to
    cell cycle arrest. In resting T-cells is phosphorylated at Thr-687 by GSK3B which is proposed to promote
    association with THRAP and to prevent binding to PTPRC/CD45 pre-mRNA; T-cell activation leads to reduced
    phosphorylation at Thr-6871
  • Arg-7, Arg-9, Arg-19 and Arg-25 are dimethylated, probably to asymmetric dimethylarginine1
  • Ubiquitination2 at Lys279, Lys319, Lys330, Lys338, Lys413
  • Modification sites at PhosphoSitePlus

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

    REFSEQ proteins: NP_005057.1  
    ENSEMBL proteins: 
     ENSP00000425071   ENSP00000424440   ENSP00000349748  

    SFPQ Human Recombinant Protein Products:

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    OriGene Protein Over-expression Lysate for SFPQ
    OriGene Custom MassSpec
    OriGene Custom Protein Services for SFPQ
    GenScript Custom Purified and Recombinant Proteins Services for SFPQ
    Novus Biologicals SFPQ Protein
    Novus Biologicals SFPQ Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for SFPQ

     
    Search eBioscience for Proteins for SFPQ 

     
    antibodies-online proteins for SFPQ (4 products) 

     
    antibodies-online peptides for SFPQ

    SFPQ Antibody Products:

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    Abcam antibodies for SFPQ
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    ThermoFisher Antibody for SFPQ
    antibodies-online antibodies for SFPQ (43 products) 

    SFPQ Assay Products:

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    Browse R&D Systems for biochemical assays
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    Cloud-Clone Corp. ELISAs for SFPQ
    Cloud-Clone Corp. CLIAs for SFPQ
    Search eBioscience for ELISAs for SFPQ 
    antibodies-online kits for SFPQ (4 products) 


    (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

    3 InterPro protein domains:
     IPR012677 Nucleotide-bd_a/b_plait
     IPR012975 NOPS
     IPR000504 RRM_dom

    Graphical View of Domain Structure for InterPro Entry P23246

    ProtoNet protein and cluster: P23246

    2 Blocks protein domains:
    IPB000504 RNA-binding region RNP-1 (RNA recognition motif)
    IPB012975 NOPS


    UniProtKB/Swiss-Prot: SFPQ_HUMAN, P23246
    Similarity: Contains 2 RRM (RNA recognition motif) domains


    Find genes that share domains with SFPQ           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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: SFPQ_HUMAN, P23246
    Function: DNA- and RNA binding protein, involved in several nuclear processes. Essential pre-mRNA splicing factor
    required early in spliceosome formation and for splicing catalytic step II, probably as a heteromer with NONO.
    Binds to pre-mRNA in spliceosome C complex, and specifically binds to intronic polypyrimidine tracts. Involved in
    regulation of signal-induced alternative splicing. During splicing of PTPRC/CD45, a phosphorylated form is
    sequestered by THRAP3 from the pre-mRNA in resting T-cells; T-cell activation and subsequent reduced
    phosphorylation is proposed to lead to release from THRAP3 allowing binding to pre-mRNA splicing regulatotry
    elements which represses exon inclusion. Interacts with U5 snRNA, probably by binding to a purine-rich sequence
    located on the 3' side of U5 snRNA stem 1b. May be involved in a pre-mRNA coupled splicing and polyadenylation
    process as component of a snRNP-free complex with SNRPA/U1A. The SFPQ-NONO heteromer associated with MATR3 may
    play a role in nuclear retention of defective RNAs. SFPQ may be involved in homologous DNA pairing; in vitro,
    promotes the invasion of ssDNA between a duplex DNA and produces a D-loop formation. The SFPQ-NONO heteromer may
    be involved in DNA unwinding by modulating the function of topoisomerase I/TOP1; in vitro, stimulates
    dissociation of TOP1 from DNA after cleavage and enhances its jumping between separate DNA helices. The SFPQ-NONO
    heteromer may be involved in DNA nonhomologous end joining (NHEJ) required for double-strand break repair and
    V(D)J recombination and may stabilize paired DNA ends; in vitro, the complex strongly stimulates DNA end joining,
    binds directly to the DNA substrates and cooperates with the Ku70/G22P1-Ku80/XRCC5 (Ku) dimer to establish a
    functional preligation complex. SFPQ is involved in transcriptional regulation. Transcriptional repression is
    probably mediated by an interaction of SFPQ with SIN3A and subsequent recruitment of histone deacetylases
    (HDACs). The SFPQ-NONO/SF-1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent
    transcriptional avtivity. SFPQ isoform Long binds to the DNA binding domains (DBD) of nuclear hormone receptors,
    like RXRA and probably THRA, and acts as transcriptional corepressor in absence of hormone ligands. Binds the DNA
    sequence 5'-CTGAGTC-3' in the insulin-like growth factor response element (IGFRE) and inhibits IGF-I-stimulated
    transcriptional activity

         Genatlas biochemistry entry for SFPQ:
    splicing factor proline/glutamine rich,widely expressed,interacting with polypyrimidine tract-binding protein
    PTB,essential factor in pre mRNA required early in spliceosome formation

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding IEA--
    GO:0003676nucleic acid binding ----
    GO:0003677DNA binding IEA--
    GO:0003723RNA binding ----
    GO:0005515protein binding IPI10653975
         
    Find genes that share ontologies with SFPQ           About GenesLikeMe


    Phenotypes:
         9 GenomeRNAi human phenotypes for SFPQ:
     Decreased BPV1 E2 protein expr  Decreased NANOG protein expres  Decreased OCT4 protein express  Decreased POU5F1-GFP protein e 
     Decreased viability  Increased G2M DNA content  Increased HPV18 LCR reporter a  Low eccentricity cells 
     Synthetic lethal with Ras 

         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Sfpq):
     behavior/neurological  mortality/aging 

    Find genes that share phenotypes with SFPQ           About GenesLikeMe

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for SFPQ

    miRNA
    Products:
        
    miRTarBase miRNAs that target SFPQ:
    hsa-mir-331-3p (MIRT043279), hsa-mir-615-3p (MIRT040035), hsa-mir-29b-3p (MIRT002310), hsa-mir-92b-3p (MIRT040650), hsa-mir-10a-5p (MIRT047727), hsa-mir-141-3p (MIRT002309), hsa-mir-1229-3p (MIRT036338), hsa-mir-193b-3p (MIRT041361)

    Block miRNA regulation of human, mouse, rat SFPQ using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SFPQ (see all 19):
    hsa-miR-217 hsa-miR-495 hsa-miR-3673 hsa-miR-520d-5p hsa-miR-200a hsa-miR-138-2* hsa-miR-141 hsa-miR-550b
    SwitchGear 3'UTR luciferase reporter plasmidSFPQ 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for SFPQ
    Predesigned siRNA for gene silencing in human, mouse, rat SFPQ

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for SFPQ

    Clone
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    OriGene ORF clones in mouse, rat for SFPQ
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: SFPQ (NM_005066)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SFPQ
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SFPQ
    Addgene plasmids for SFPQ 

    Cell Line
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SFPQ


    (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
    SFPQ_HUMAN, P23246: Nucleus matrix. Cytoplasm. Note=Predominantly in nuclear matrix
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005654nucleoplasm IDA19874820
    GO:0005737cytoplasm IEA--
    GO:0016363nuclear matrix IDA19874820
    GO:0042382paraspeckles IDA19874820

    Find genes that share ontologies with SFPQ           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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    SuperPaths for SFPQ About    
    See pathways by source

    SuperPathContained pathways About
    1mRNA Splicing - Major Pathway
    mRNA processing0.44
    2Development NOTCH1 mediated pathway for NF KB activity modulation
    Transcription Sin3 and NuRD in transcription regulation0.35

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 GeneGo (Thomson Reuters) Pathway for SFPQ
        Transcription Sin3 and NuRD in transcription regulation

    1 BioSystems Pathway for SFPQ
        mRNA processing


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SFPQ
    Interactions:

        GeneGlobe Interaction Network for SFPQ

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

    Selected Interacting proteins for SFPQ (P232461, 2, 3 ENSP000003497484) via UniProtKB, MINT, STRING, and/or I2D (see all 880)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PTK6Q138821, 2, 3, ENSP000002171854EBI-355453,EBI-1383632 MINT-7231528 MINT-7231563 MINT-7231550 MINT-7231537 MINT-7231572 I2D: score=1 STRING: ENSP00000217185
    PTBP1P265991, 2, 3, ENSP000003494284EBI-355453,EBI-350540 MINT-62329 MINT-7945693 MINT-62328 MINT-7947479 I2D: score=5 STRING: ENSP00000349428
    ZMYM2Q9UBW72, 3, ENSP000003723224MINT-62330 MINT-62323 MINT-62320 MINT-62322 I2D: score=3 STRING: ENSP00000372322
    FUSP356372, 3, ENSP000002541084MINT-7945693 MINT-7947479 MINT-62325 I2D: score=2 STRING: ENSP00000254108
    SMN1Q166372, 3, ENSP000003700834MINT-7945693 MINT-7947479 I2D: score=2 STRING: ENSP00000370083
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IMP--
    GO:0000380alternative mRNA splicing, via spliceosome IMP19874820
    GO:0006281DNA repair IEA--
    GO:0006310DNA recombination IEA--
    GO:0006351transcription, DNA-templated IEA--

    Find genes that share ontologies with SFPQ           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 SFPQ

    1 HMDB Compound for SFPQ    About this table
    CompoundSynonyms CAS #PubMed Ids
    Cyclic AMPCyclic AMP (see all 19)60-92-4--

    5 Novoseek inferred chemical compound relationships for SFPQ gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    pyrimidine 49.2 4 15790595 (1), 18689799 (1), 16731528 (1), 9756848 (1)
    steroid 14.1 2 14704271 (1)
    progesterone 11 1 17452459 (1)
    testosterone 0 3 17452459 (3)
    serine 0 1 11956159 (1)



    Find genes that share compounds with SFPQ           About GenesLikeMe



    (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 SFPQ gene: 
    NM_005066.2  

    Unigene Cluster for SFPQ:

    Splicing factor proline/glutamine-rich
    Hs.355934  [show with all ESTs]
    Unigene Representative Sequence: NM_005066
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000471991 ENST00000468598(uc001byq.3 uc001byp.3) ENST00000460428
    ENST00000470472 ENST00000466745 ENST00000466213 ENST00000490668 ENST00000485365
    ENST00000485454 ENST00000357214(uc001bys.3)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SFPQ (see all 19):
    hsa-miR-217 hsa-miR-495 hsa-miR-3673 hsa-miR-520d-5p hsa-miR-200a hsa-miR-138-2* hsa-miR-141 hsa-miR-550b
    SwitchGear 3'UTR luciferase reporter plasmidSFPQ 3' UTR sequence
    Inhib. RNA
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    Clone
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: SFPQ (NM_005066)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SFPQ
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SFPQ
    Addgene plasmids for SFPQ 
    Primer
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    OriGene qPCR primer pairs and template standards for SFPQ
    OriGene qSTAR qPCR primer pairs in human, mouse for SFPQ
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SFPQ
      QuantiTect SYBR Green Assays in human, mouse, rat SFPQ
      QuantiFast Probe-based Assays in human, mouse, rat SFPQ

    Additional mRNA sequence: 

    AK307985.1 BC000546.1 BC004534.2 BC027708.2 BC027717.2 BC051192.1 X16850.1 X70944.1 

    Selected DOTS entries (see all 26):

    DT.75196114  DT.101972073  DT.100653960  DT.102845502  DT.100653959  DT.100661260  DT.95078264  DT.438333 
    DT.92460669  DT.95155156  DT.92068655  DT.75169531  DT.121400134  DT.92460652  DT.91959051  DT.95260170 
    DT.95260223  DT.121400203  DT.121623703  DT.40118300  DT.92460649  DT.92460667  DT.95240902  DT.95260201 

    Selected AceView cDNA sequences (see all 810):

    BQ086278 BQ878840 BM459469 BC027708 AA872895 BM973795 AW261919 CF242793 
    AI377956 CA868489 BM979983 BC004534 BQ686638 BE044027 N47821 AA872902 
    AI291037 BQ691843 BQ917666 AA834544 AI696543 CR609196 BE048392 CB267905 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for SFPQ    About this scheme

    ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12 ^ 13
    SP1:                                                                    -     -                           
    SP2:                                                                    -     -     -                     
    SP3:                                                                                                      
    SP4:                                                                                                      


    ECgene alternative splicing isoforms for SFPQ

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


    SFPQ expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 22) fully expand
     
     Gonad (Reproductive System)
             Primordial Germ Cells Primitive Gonad
     
     Neural Tube (Nervous System)
             Telencephalon
     
     Brain (Nervous System)
             Cerebral Cortex
     
     Bone (Muscoskeletal System)
             Bone Marrow
     
     Intermediate Mesoderm (Gastrulation Derivatives)
             Intermediate Mesoderm
    SFPQ Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SFPQ Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.355934
        Custom PCR Arrays for SFPQ
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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 SFPQ gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sfpq1 , 5 splicing factor proline/glutamine rich (polypyrimidine more1, 5 92.08(n)1
    98.35(a)1
      4 (61.20 cM)5
    715141  NM_023603.31  NP_076092.11 
     1270213245 
    chicken
    (Gallus gallus)
    Aves SFPQ1 splicing factor proline/glutamine-rich 82.46(n)
    94.51(a)
      395803  XM_417784.4  XP_417784.3 
    lizard
    (Anolis carolinensis)
    Reptilia SFPQ6
    splicing factor proline/glutamine-rich
    77(a)
    1 ↔ 1
    GL343558.1(347877-357044)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.18072 Xenopus laevis transcribed sequence with moderate similarity more 83.4(n)    BQ729996.1 
    zebrafish
    (Danio rerio)
    Actinopterygii sfpq1 splicing factor proline/glutamine rich (polypyrimidine more 67.99(n)
    73.36(a)
      406564  NM_213278.1  NP_998443.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta nonA-l6
    nonA6
    no on or off transient A
    30(a)
    28(a)
    many ↔ many
    many ↔ many
    3R(12465927-12468834)
    X(16255566-16265580)
    worm
    (Caenorhabditis elegans)
    Secernentea nono-16
    Protein PSF-1, isoform d
    35(a)
    1 → many
    III(5953525-5958246) WBGene00017778


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SFPQ gene
    NONO2  PSPC12  
    3 SIMAP similar genes for SFPQ using alignment to 6 protein entries:     SFPQ_HUMAN (see all proteins):
    PSPC1    NONO    RBM4B

    Find genes that share paralogs with SFPQ           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for SFPQ
    PGOHUM00000233958


    (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 SFPQ (see all 348)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs716386551,2
    C--35648706(+) CTCTT-/AGAAG 
            
    AGAAC
    1 -- ds50010--------
    rs1146344911,2
    C,F--35648799(+) TATATA/GTAACT 1 -- ds50011Minor allele frequency- G:0.01WA 118
    rs2008313131,2
    --35648825(+) CTAAA-/CCTTTT 1 -- ds50010--------
    rs782945281,2
    C--35648826(+) TAAACC/TTTTTT 1 -- ds50010--------
    rs1499372011,2
    --35648947(+) CCGAGC/TAGCTG 1 -- ds50010--------
    rs1909339721,2
    C--35648994(+) TTTGTA/TTTTTT 1 -- ds50010--------
    rs1823039611,2
    --35649047(+) ACTCCC/TGATCT 1 -- ds50010--------
    rs1854690061,2
    --35649108(+) CCACCA/GCGCCC 1 -- ds50010--------
    rs1450153851,2
    C--35649163(+) ACTACA/GCCCCA 1 -- ds50010--------
    rs1399627571,2
    C--35649203(+) GACTTC/GATGTT 1 -- ut310--------

    HapMap Linkage Disequilibrium report for SFPQ (35641979 - 35658749 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for SFPQ:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv508149CNV Loss20534489
    nsv870757CNV Gain21882294

    Human Gene Mutation Database (HGMD): SFPQ
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SFPQ
    DNA2.0 Custom Variant and Variant Library Synthesis for SFPQ

    (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: 605199    OMIM disorders: --

    UniProtKB/Swiss-Prot: SFPQ_HUMAN, P23246
  • Note=A chromosomal aberration involving SFPQ may be a cause of papillary renal cell carcinoma (PRCC).
    Translocation t(X;1)(p11.2;p34) with TFE3

  • 2 diseases for SFPQ:    
    About MalaCards
    papillary renal cell carcinoma    renal cell carcinoma, papillary, 1


    Find genes that share disorders with SFPQ           About GenesLikeMe

    Genetic Association Database (GAD): SFPQ

    Export disorders for SFPQ 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 SFPQ gene, integrated from 10 sources (see all 166):
    (articles sorted by number of sources associating them with SFPQ)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and characterization of PSF, a novel pre-mRNA splicing factor. (PubMed id 8449401)1, 2, 3, 9 Patton J.G.... Nadal-Ginard B. (Genes Dev. 1993)
    2. The PSF.p54nrb complex is a novel Mnk substrate that binds the mRNA for tumor necrosis factor alpha. (PubMed id 17965020)1, 2, 9 Buxade M.... Proud C.G. (J. Biol. Chem. 2008)
    3. NPM/ALK binds and phosphorylates the RNA/DNA-binding protein PSF in anaplastic large-cell lymphoma. (PubMed id 17537995)1, 2, 9 Galietta A.... Gambacorti-Passerini C. (Blood 2007)
    4. PSF is a novel corepressor that mediates its effect through Sin3A and the DNA binding domain of nuclear hormone receptors. (PubMed id 11259580)1, 2, 9 Mathur M.... Samuels H.H. (Mol. Cell. Biol. 2001)
    5. The snRNP-free U1A (SF-A) complex(es): identification of the largest subunit as PSF, the polypyrimidine-tract binding protein-associated splicing factor. (PubMed id 9848648)1, 2, 9 Lutz C.S.... Alwine J.C. (RNA 1998)
    6. The RNA-splicing factor PSF/p54 controls DNA-topoisomerase I activity by a direct interaction. (PubMed id 9756848)1, 2, 9 Straub T.... Boege F. (J. Biol. Chem. 1998)
    7. Transcriptional activation of human CYP17 in H295R adrenocortical cells depends on complex formation among p54(nrb)/NonO, protein- associated splicing factor, and SF-1, a complex that also participates in repression of transcription. (PubMed id 11897684)1, 2, 9 Sewer M.B....Waterman M.R. (Endocrinology 2002)
    8. Human 100-kDa homologous DNA-pairing protein is the splicing factor PSF and promotes DNA strand invasion. (PubMed id 10931916)1, 2, 9 Akhmedov A.T. and Lopez B.S. (Nucleic Acids Res. 2000)
    9. Proteomic identification of a PSF/p54nrb heterodimer as RNF43 oncoprotein-interacting proteins. (PubMed id 18655028)1, 2, 9 Miyamoto K.... Sugiura T. (Proteomics 2008)
    10. Identification of the polypyrimidine tract binding protein-associated splicing factor.p54(nrb) complex as a candidate DNA double-strand break rejoining factor. (PubMed id 15590677)1, 2, 9 Bladen C.L.... Dynan W.S. (J. Biol. Chem. 2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 6421 HGNC: 10774 AceView: SFPQ Ensembl:ENSG00000116560 euGenes: HUgn6421
    ECgene: SFPQ H-InvDB: SFPQ

    (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 SFPQ Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SFPQ Genetics and Cytogenetics in Oncology and Haematology

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

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



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