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

Gene ID: 6421, updated on 24-Nov-2020

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
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
Expression
Ubiquitous expression in bone marrow (RPKM 84.2), skin (RPKM 34.9) and 25 other tissues See more
Orthologs

Genomic context

See SFPQ in Genome Data Viewer
Location:
1p34.3
Exon count:
13
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (35176380..35193174, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (35641981..35658766, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene EF-hand calcium binding domain 14 pseudogene 1 Neighboring gene uncharacterized LOC105378644 Neighboring gene zinc finger MYM-type containing 4 Neighboring gene RNA, 7SL, cytoplasmic 503, pseudogene Neighboring gene ribosomal protein L5 pseudogene 4

Genomic regions, transcripts, and products

Expression

  • Project title: 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

Associated conditions

Description Tests
Genome-wide association study identifies a common variant associated with risk of endometrial cancer.
GeneReviews: Not available

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

Homology

Clone Names

  • DKFZp547C228, DKFZp667K0521, DKFZp686K1282

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
E-box binding IEA
Inferred from Electronic Annotation
more info
 
RNA binding HDA PubMed 
chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
histone deacetylase binding IPI
Inferred from Physical Interaction
more info
PubMed 
nucleic acid binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription regulatory region sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
RNA splicing TAS
Traceable Author Statement
more info
PubMed 
activation of innate immune response IDA
Inferred from Direct Assay
more info
PubMed 
alternative mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
alternative mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
double-strand break repair via homologous recombination IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone H3 deacetylation ISS
Inferred from Sequence or Structural Similarity
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
mRNA processing TAS
Traceable Author Statement
more info
PubMed 
mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of circadian rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of sister chromatid cohesion IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of circadian rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
rhythmic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
RNA polymerase II transcription regulator complex ISS
Inferred from Sequence or Structural Similarity
more info
 
chromatin IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
nuclear matrix IDA
Inferred from Direct Assay
more info
PubMed 
nuclear speck IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
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)

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
    UniProtKB/TrEMBL
    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: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    35176380..35193174 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017002053.2XP_016857542.1  splicing factor, proline- and glutamine-rich isoform X1

    UniProtKB/Swiss-Prot
    P23246
    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)
  2. XM_005271113.5XP_005271170.1  splicing factor, proline- and glutamine-rich isoform X1

    See identical proteins and their annotated locations for XP_005271170.1

    UniProtKB/Swiss-Prot
    P23246
    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_005271112.5XP_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
    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_017002054.2XP_016857543.1  splicing factor, proline- and glutamine-rich isoform X1

    UniProtKB/Swiss-Prot
    P23246
    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_005271115.4XP_005271172.1  splicing factor, proline- and glutamine-rich isoform X3

    See identical proteins and their annotated locations for XP_005271172.1

    UniProtKB/Swiss-Prot
    P23246
    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)
  6. XM_011541950.2XP_011540252.1  splicing factor, proline- and glutamine-rich isoform X2

    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)
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