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

    Gene ID: 6421, updated on 10-Dec-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, Dec 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 84.2), skin (RPKM 34.9) and 25 other tissues See more
    Orthologs
    NEW
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    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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    BioGRID CRISPR Screen Phenotypes (808 hits/1291 screens)

    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

    General gene information

    Clone Names

    • DKFZp547C228, DKFZp667K0521, DKFZp686K1282

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding PubMed 
    enables RNA binding PubMed 
    enables RNA binding  
    enables chromatin binding  
    enables histone deacetylase binding PubMed 
    enables protein binding PubMed 
    enables protein homodimerization activity PubMed 
    enables transcription cis-regulatory region binding  
    Process Evidence Code Pubs
    involved_in RNA splicing PubMed 
    involved_in activation of innate immune response PubMed 
    involved_in alternative mRNA splicing, via spliceosome  
    involved_in alternative mRNA splicing, via spliceosome PubMed 
    involved_in chromatin remodeling  
    acts_upstream_of_or_within double-strand break repair via homologous recombination PubMed 
    involved_in innate immune response  
    involved_in mRNA processing PubMed 
    involved_in negative regulation of DNA-templated transcription  
    involved_in negative regulation of circadian rhythm  
    involved_in negative regulation of transcription by RNA polymerase II PubMed 
    involved_in negative regulation of transcription by RNA polymerase II PubMed 
    involved_in negative regulation of transcription by RNA polymerase II PubMed 
    involved_in positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway PubMed 
    involved_in positive regulation of transcription by RNA polymerase II PubMed 
    involved_in regulation of DNA-templated transcription  
    involved_in regulation of circadian rhythm  
    involved_in rhythmic process  
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex  
    located_in chromatin PubMed 
    located_in cytosol  
    located_in nuclear matrix PubMed 
    located_in nuclear speck  
    located_in nucleoplasm PubMed 
    located_in nucleoplasm  
    is_active_in nucleus  
    located_in nucleus PubMed 
    located_in paraspeckles 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_005066.3 → NP_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:499 → 599
      PTZ00121; MAEBL; Provisional
      cd12948
      Location:442 → 538
      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:372 → 451
      RRM2_p54nrb_like; RNA recognition motif 2 in the p54nrb/PSF/PSP1 family
      cd12587
      Location:296 → 366
      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_005271115.5 → XP_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:486 → 594
      PRK12704; phosphodiesterase; Provisional
      cd12948
      Location:442 → 538
      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:372 → 451
      RRM2_p54nrb_like; RNA recognition motif 2 in the p54nrb/PSF/PSP1 family
      cd12587
      Location:296 → 366
      RRM1_PSF; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)
    2. XM_005271112.6 → XP_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:499 → 599
      PTZ00121; MAEBL; Provisional
      cd12948
      Location:442 → 538
      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:372 → 451
      RRM2_p54nrb_like; RNA recognition motif 2 in the p54nrb/PSF/PSP1 family
      cd12587
      Location:296 → 366
      RRM1_PSF; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)
    3. XM_017002054.3 → XP_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:499 → 599
      PTZ00121; MAEBL; Provisional
      cd12948
      Location:442 → 538
      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:372 → 451
      RRM2_p54nrb_like; RNA recognition motif 2 in the p54nrb/PSF/PSP1 family
      cd12587
      Location:296 → 366
      RRM1_PSF; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)
    4. XM_017002053.3 → XP_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:499 → 599
      PTZ00121; MAEBL; Provisional
      cd12948
      Location:442 → 538
      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:372 → 451
      RRM2_p54nrb_like; RNA recognition motif 2 in the p54nrb/PSF/PSP1 family
      cd12587
      Location:296 → 366
      RRM1_PSF; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)
    5. XM_011541950.3 → XP_011540252.1  splicing factor, proline- and glutamine-rich isoform X2

      UniProtKB/TrEMBL
      A0A8Q3WMA7
      Conserved Domains (3) summary
      cd12948
      Location:442 → 538
      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:372 → 451
      RRM2_p54nrb_like; RNA recognition motif 2 in the p54nrb/PSF/PSP1 family
      cd12587
      Location:296 → 366
      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_054338165.1 → XP_054194140.1  splicing factor, proline- and glutamine-rich isoform X3

      UniProtKB/TrEMBL
      A0A8Q3WMA7
    2. XM_054338163.1 → XP_054194138.1  splicing factor, proline- and glutamine-rich isoform X1

      UniProtKB/Swiss-Prot
      P23246, P30808, Q5SZ71
      UniProtKB/TrEMBL
      A0A384N5Z8, Q86VG2
    3. XM_054338162.1 → XP_054194137.1  splicing factor, proline- and glutamine-rich isoform X1

      UniProtKB/Swiss-Prot
      P23246, P30808, Q5SZ71
      UniProtKB/TrEMBL
      A0A384N5Z8, Q86VG2
    4. XM_054338161.1 → XP_054194136.1  splicing factor, proline- and glutamine-rich isoform X1

      UniProtKB/Swiss-Prot
      P23246, P30808, Q5SZ71
      UniProtKB/TrEMBL
      A0A384N5Z8, Q86VG2
    5. XM_054338164.1 → XP_054194139.1  splicing factor, proline- and glutamine-rich isoform X2

      UniProtKB/TrEMBL
      A0A8Q3WMA7
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