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

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: mouse all
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Genomic context

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Paraspeckle-independent co-transcriptional regulation of nuclear microRNA biogenesis by SFPQ.
Title: Paraspeckle-independent co-transcriptional regulation of nuclear microRNA biogenesis by SFPQ.
SFPQ promotes an oncogenic transcriptomic state in melanoma.
Title: SFPQ promotes an oncogenic transcriptomic state in melanoma.
The nucleic acid binding protein SFPQ represses EBV lytic reactivation by promoting histone H1 expression.
Title: The nucleic acid binding protein SFPQ represses EBV lytic reactivation by promoting histone H1 expression.
SARS-CoV-2 nucleocapsid protein promotes TMAO-induced NLRP3 inflammasome activation by SCAP-SREBP signaling pathway.
Title: SARS-CoV-2 nucleocapsid protein promotes TMAO-induced NLRP3 inflammasome activation by SCAP-SREBP signaling pathway.
Splicing factor proline- and glutamine-rich regulates cytotoxic T lymphocytes-mediated cytotoxicity on non-small cell lung cancer by directly binding to PD-L1 3'UTR.
Title: Splicing factor proline- and glutamine-rich regulates cytotoxic T lymphocytes-mediated cytotoxicity on non-small cell lung cancer by directly binding to PD-L1 3'UTR.
SFPQ and Its Isoform as Potential Biomarker for Non-Small-Cell Lung Cancer.
Title: SFPQ and Its Isoform as Potential Biomarker for Non-Small-Cell Lung Cancer.
Familial ALS-associated SFPQ variants promote the formation of SFPQ cytoplasmic aggregates in primary neurons.
Title: Familial ALS-associated SFPQ variants promote the formation of SFPQ cytoplasmic aggregates in primary neurons.
Insight into the Tumor Suppression Mechanism from the Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) Complexed with a 30mer RNA from Murine Virus-like 30S Transcript-1.
Title: Insight into the Tumor Suppression Mechanism from the Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) Complexed with a 30mer RNA from Murine Virus-like 30S Transcript-1.
Molecular Modelling of NONO and SFPQ Dimerization Process and RNA Recognition Mechanism.
Title: Molecular Modelling of NONO and SFPQ Dimerization Process and RNA Recognition Mechanism.
ALS/FTD-causing mutation in cyclin F causes the dysregulation of SFPQ.
Title: ALS/FTD-causing mutation in cyclin F causes the dysregulation of SFPQ.

Submit: New GeneRIF Correction See all GeneRIFs (74)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-74566 (e-PCR)
- UniSTS:4750

RH18090 (e-PCR)
- UniSTS:27581

RH78190 (e-PCR)
- UniSTS:25295

MARC_9965-9966:996688719:1 (e-PCR)
- UniSTS:270035

WI-7518 (e-PCR)
- UniSTS:49631

SHGC-30279 (e-PCR)
- UniSTS:44008

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 more info	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

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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)

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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)

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

NR_136702.2 RNA Sequence

Status: VALIDATED

Source sequence(s)

AL590434
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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

35176380..35193145 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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)
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)
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)
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)
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

NC_060925.1 Alternate T2T-CHM13v2.0

Range

35039049..35055814 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054338165.1 → XP_054194140.1 splicing factor, proline- and glutamine-rich isoform X3
XM_054338163.1 → XP_054194138.1 splicing factor, proline- and glutamine-rich isoform X1

UniProtKB/Swiss-Prot

P23246, P30808, Q5SZ71

UniProtKB/TrEMBL

A0A384N5Z8
XM_054338162.1 → XP_054194137.1 splicing factor, proline- and glutamine-rich isoform X1

UniProtKB/Swiss-Prot

P23246, P30808, Q5SZ71

UniProtKB/TrEMBL

A0A384N5Z8
XM_054338161.1 → XP_054194136.1 splicing factor, proline- and glutamine-rich isoform X1

UniProtKB/Swiss-Prot

P23246, P30808, Q5SZ71

UniProtKB/TrEMBL

A0A384N5Z8
XM_054338164.1 → XP_054194139.1 splicing factor, proline- and glutamine-rich isoform X2