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    SFPQ splicing factor proline and glutamine rich [ Homo sapiens (human) ]

    Gene ID: 6421, updated on 3-Nov-2024

    Summary

    Official Symbol
    SFPQprovided by HGNC
    Official Full Name
    splicing factor proline and glutamine richprovided by HGNC
    Primary source
    HGNC:HGNC:10774
    See related
    Ensembl:ENSG00000116560 MIM:605199; AllianceGenome:HGNC:10774
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PSF; POMP100; PPP1R140
    Summary
    Enables DNA binding activity; histone deacetylase binding activity; and protein homodimerization activity. Involved in several processes, including alternative mRNA splicing, via spliceosome; positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway; and regulation of transcription by RNA polymerase II. Acts upstream of or within double-strand break repair via homologous recombination. Located in chromatin; nuclear matrix; and paraspeckles. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 84.2), skin (RPKM 34.9) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SFPQ in Genome Data Viewer
    Location:
    1p34.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (35176380..35193145, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (35039049..35055814, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (35641981..35658746, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr1:35594172-35594351 Neighboring gene EF-hand calcium binding domain 14 pseudogene 1 Neighboring gene uncharacterized LOC105378644 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 637 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:35658451-35659243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 725 Neighboring gene Sharpr-MPRA regulatory region 666 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:35676251-35676918 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:35681555-35682151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 726 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 727 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 639 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:35738409-35738909 Neighboring gene zinc finger MYM-type containing 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:35766904-35767102 Neighboring gene RNA, 7SL, cytoplasmic 503, pseudogene Neighboring gene small nucleolar RNA SNORA62/SNORA6 family

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies a common variant associated with risk of endometrial cancer.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify splicing factor proline/glutamine-rich (SFPQ), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify splicing factor proline/glutamine-rich (SFPQ), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify splicing factor proline/glutamine-rich (SFPQ), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify splicing factor proline/glutamine-rich (SFPQ), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Rev rev Association of PSF with MATR3 is involved in nuclear retention of unspliced HIV-1 RNA and Rev activity PubMed
    rev HIV-1 Rev interacting protein, splicing factor proline/glutamine-rich (SFPQ), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with SFPQ is increased by RRE PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • DKFZp547C228, DKFZp667K0521, DKFZp686K1282

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables histone deacetylase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription cis-regulatory region binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in RNA splicing TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in activation of innate immune response IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in alternative mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in alternative mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in chromatin remodeling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within double-strand break repair via homologous recombination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mRNA processing TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of circadian rhythm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of circadian rhythm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in rhythmic process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in nuclear matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in paraspeckles IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    splicing factor, proline- and glutamine-rich
    Names
    100 kDa DNA-pairing protein
    DNA-binding p52/p100 complex, 100 kDa subunit
    PTB-associated splicing factor
    epididymis secretory sperm binding protein
    polypyrimidine tract binding protein associated
    polypyrimidine tract-binding protein-associated splicing factor
    protein phosphatase 1, regulatory subunit 140
    splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
    splicing factor proline/glutamine-rich

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_005066.3NP_005057.1  splicing factor, proline- and glutamine-rich

      See identical proteins and their annotated locations for NP_005057.1

      Status: VALIDATED

      Source sequence(s)
      AL590434, BC051192, X70944
      Consensus CDS
      CCDS388.1
      UniProtKB/Swiss-Prot
      P23246, P30808, Q5SZ71
      UniProtKB/TrEMBL
      A0A384N5Z8, Q86VG2
      Related
      ENSP00000349748.5, ENST00000357214.6
      Conserved Domains (4) summary
      PTZ00121
      Location:499599
      PTZ00121; MAEBL; Provisional
      cd12948
      Location:442538
      NOPS_PSF; NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins
      cd12333
      Location:372451
      RRM2_p54nrb_like; RNA recognition motif 2 in the p54nrb/PSF/PSP1 family
      cd12587
      Location:296366
      RRM1_PSF; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

    RNA

    1. NR_136702.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL590434
    2. NR_136703.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL590434

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      35176380..35193145 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005271115.5XP_005271172.1  splicing factor, proline- and glutamine-rich isoform X3

      See identical proteins and their annotated locations for XP_005271172.1

      UniProtKB/TrEMBL
      A0A8Q3WMA7
      Conserved Domains (4) summary
      PRK12704
      Location:486594
      PRK12704; phosphodiesterase; Provisional
      cd12948
      Location:442538
      NOPS_PSF; NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins
      cd12333
      Location:372451
      RRM2_p54nrb_like; RNA recognition motif 2 in the p54nrb/PSF/PSP1 family
      cd12587
      Location:296366
      RRM1_PSF; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)
    2. XM_005271112.6XP_005271169.1  splicing factor, proline- and glutamine-rich isoform X1

      See identical proteins and their annotated locations for XP_005271169.1

      UniProtKB/Swiss-Prot
      P23246, P30808, Q5SZ71
      UniProtKB/TrEMBL
      A0A384N5Z8, Q86VG2
      Conserved Domains (4) summary
      PTZ00121
      Location:499599
      PTZ00121; MAEBL; Provisional
      cd12948
      Location:442538
      NOPS_PSF; NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins
      cd12333
      Location:372451
      RRM2_p54nrb_like; RNA recognition motif 2 in the p54nrb/PSF/PSP1 family
      cd12587
      Location:296366
      RRM1_PSF; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)
    3. XM_017002054.3XP_016857543.1  splicing factor, proline- and glutamine-rich isoform X1

      UniProtKB/Swiss-Prot
      P23246, P30808, Q5SZ71
      UniProtKB/TrEMBL
      A0A384N5Z8, Q86VG2
      Conserved Domains (4) summary
      PTZ00121
      Location:499599
      PTZ00121; MAEBL; Provisional
      cd12948
      Location:442538
      NOPS_PSF; NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins
      cd12333
      Location:372451
      RRM2_p54nrb_like; RNA recognition motif 2 in the p54nrb/PSF/PSP1 family
      cd12587
      Location:296366
      RRM1_PSF; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)
    4. XM_017002053.3XP_016857542.1  splicing factor, proline- and glutamine-rich isoform X1

      UniProtKB/Swiss-Prot
      P23246, P30808, Q5SZ71
      UniProtKB/TrEMBL
      A0A384N5Z8, Q86VG2
      Conserved Domains (4) summary
      PTZ00121
      Location:499599
      PTZ00121; MAEBL; Provisional
      cd12948
      Location:442538
      NOPS_PSF; NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins
      cd12333
      Location:372451
      RRM2_p54nrb_like; RNA recognition motif 2 in the p54nrb/PSF/PSP1 family
      cd12587
      Location:296366
      RRM1_PSF; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)
    5. XM_011541950.3XP_011540252.1  splicing factor, proline- and glutamine-rich isoform X2

      UniProtKB/TrEMBL
      A0A8Q3WMA7
      Conserved Domains (3) summary
      cd12948
      Location:442538
      NOPS_PSF; NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins
      cd12333
      Location:372451
      RRM2_p54nrb_like; RNA recognition motif 2 in the p54nrb/PSF/PSP1 family
      cd12587
      Location:296366
      RRM1_PSF; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      35039049..35055814 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338165.1XP_054194140.1  splicing factor, proline- and glutamine-rich isoform X3

    2. XM_054338163.1XP_054194138.1  splicing factor, proline- and glutamine-rich isoform X1

      UniProtKB/Swiss-Prot
      P23246, P30808, Q5SZ71
      UniProtKB/TrEMBL
      A0A384N5Z8
    3. XM_054338162.1XP_054194137.1  splicing factor, proline- and glutamine-rich isoform X1

      UniProtKB/Swiss-Prot
      P23246, P30808, Q5SZ71
      UniProtKB/TrEMBL
      A0A384N5Z8
    4. XM_054338161.1XP_054194136.1  splicing factor, proline- and glutamine-rich isoform X1

      UniProtKB/Swiss-Prot
      P23246, P30808, Q5SZ71
      UniProtKB/TrEMBL
      A0A384N5Z8
    5. XM_054338164.1XP_054194139.1  splicing factor, proline- and glutamine-rich isoform X2