Sfpq splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated) [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Sfpqprovided by MGI
Official Full Name: splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)provided by MGI
Primary source: MGI:MGI:1918764
See related: Ensembl:ENSMUSG00000028820 AllianceGenome:MGI:1918764
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: PSF; REP1; Gm12940; D4Ertd314e; 1110004P21Rik; 2810416M14Rik; 5730453G22Rik; 9030402K04Rik
Summary: Enables chromatin binding activity and transcription cis-regulatory region binding activity. Involved in several processes, including dendritic transport of messenger ribonucleoprotein complex; histone H3 deacetylation; and negative regulation of circadian rhythm. Acts upstream of or within cellular response to DNA damage stimulus; chromosome organization; and positive regulation of sister chromatid cohesion. Located in paraspeckles. Part of RNA polymerase II transcription regulator complex. Is expressed in several structures, including alimentary system; central nervous system; lung mesenchyme; sensory organ; and testis. Orthologous to human SFPQ (splicing factor proline and glutamine rich). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 54.6), CNS E14 (RPKM 39.2) and 27 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4 D2.2; 4 61.2 cM

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (126914504..126944894)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (127020716..127051101)

Chromosome 4 - NC_000070.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PSF functions as a repressor of hypoxia-induced angiogenesis by promoting mitochondrial function.
Title: PSF functions as a repressor of hypoxia-induced angiogenesis by promoting mitochondrial function.
LncRNA NEAT1 Recruits SFPQ to Regulate MITF Splicing and Control RPE Cell Proliferation.
Title: LncRNA NEAT1 Recruits SFPQ to Regulate MITF Splicing and Control RPE Cell Proliferation.
SFPQ associated with a co-activator for PPARgamma, HELZ2, regulates key nuclear factors for adipocyte differentiation.
Title: SFPQ associated with a co-activator for PPARγ, HELZ2, regulates key nuclear factors for adipocyte differentiation.
Murine Long Noncoding RNA Morrbid Contributes in the Regulation of NRAS Splicing in Hepatocytes In Vitro.
Title: Murine Long Noncoding RNA Morrbid Contributes in the Regulation of NRAS Splicing in Hepatocytes In Vitro.
Expression analysis of Sfpq-regulated genes revealed specific downregulation of developmentally essential neuronal genes longer than 100 kb in Sfpq-disrupted brains; those genes are enriched in associations with neurodegenerative and psychiatric diseases.
Title: Loss of Sfpq Causes Long-Gene Transcriptopathy in the Brain.
SFPQ intron retention and nuclear loss are molecular hallmarks of familial and sporadic of amyotrophic lateral sclerosis.
Title: Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS.
Results indicate that an splicing factor proline-glutamine rich protein (Sfpq)-dependent strategy for controlling miRNA activity takes place in cells, contributing to the complexity of miRNA-dependent gene expression control.
Title: Post-transcriptional gene silencing mediated by microRNAs is controlled by nucleoplasmic Sfpq.
data demonstrate that SFPQ orchestrates spatial gene expression of a newly identified RNA regulon essential for axonal viability.
Title: The RNA-binding protein SFPQ orchestrates an RNA regulon to promote axon viability.
These results are compatible with the idea that SFPQ, plays an important role regulating proliferation and migration during the development of the cerebral cortex.
Title: SFPQ associates to LSD1 and regulates the migration of newborn pyramidal neurons in the developing cerebral cortex.
these results show that PSF can repress the transcriptional activation of VEGF stimulated by IGF-1 via recruitment of the Hakai complex
Title: PTB-associated splicing factor inhibits IGF-1-induced VEGF upregulation in a mouse model of oxygen-induced retinopathy.

Submit: New GeneRIF Correction See all GeneRIFs (20)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (1)
Targeted (3) 1 citation
Endonuclease-mediated (5)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Sfpq (e-PCR), detects polymorphism
- UniSTS:479037

AU021830 (e-PCR)
- UniSTS:207683

AW209050 (e-PCR)
- UniSTS:179069

RH139231 (e-PCR)
- UniSTS:221317

RH136628 (e-PCR)
- UniSTS:210608

RH126927 (e-PCR)
- UniSTS:167386

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables histone deacetylase binding	ISO Inferred from Sequence Orthology more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within DNA repair	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in activation of innate immune response	ISO Inferred from Sequence Orthology more info
involved_in alternative mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in alternative mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chromosome organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in dendritic transport of messenger ribonucleoprotein complex	IDA Inferred from Direct Assay more info	PubMed
involved_in dendritic transport of messenger ribonucleoprotein complex	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within double-strand break repair via homologous recombination	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within immune system process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within innate immune response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of sister chromatid cohesion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within rhythmic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	IDA Inferred from Direct Assay more info	PubMed
part_of chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in dendrite	IMP Inferred from Mutant Phenotype more info	PubMed
located_in dendrite cytoplasm	IMP Inferred from Mutant Phenotype more info	PubMed
located_in nuclear matrix	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in paraspeckles	IDA Inferred from Direct Assay more info	PubMed
located_in paraspeckles	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: splicing factor, proline- and glutamine-rich

Names: DNA-binding p52/p100 complex, 100 kDa subunit; PTB-associated splicing factor; polypyrimidine tract-binding protein-associated-splicing factor

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_023603.3 → NP_076092.1 splicing factor, proline- and glutamine-rich

See identical proteins and their annotated locations for NP_076092.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the functional protein.

Source sequence(s)

AV137948, AW048189, BC089305, CJ067342

Consensus CDS

CCDS18662.1

UniProtKB/Swiss-Prot

A2A7U6, Q8VIJ6, Q9ERW2

UniProtKB/TrEMBL

A0A991ENV6

Related

ENSMUSP00000030623.8, ENSMUST00000030623.8

Conserved Domains (3) summary

cd12948
Location:434 → 530

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:364 → 443

RRM2_p54nrb_like; RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

cd12587
Location:288 → 358

RRM1_PSF; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

RNA

NR_045010.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an exon and includes three alternate 3' exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

BC080848, BM246211, CA319647, CJ067342, CJ304628

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000070.7 Reference GRCm39 C57BL/6J

Range

126914504..126944894

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036164435.1 → XP_036020328.1 splicing factor, proline- and glutamine-rich isoform X2

UniProtKB/TrEMBL

A0A991ENV6

Conserved Domains (4) summary

PRK12704
Location:567 → 675

PRK12704; phosphodiesterase; Provisional

cd12948
Location:523 → 619

NOPS_PSF; NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins

cd12587
Location:377 → 447

RRM1_PSF; RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

cd12590
Location:453 → 532

RRM2_PSF; RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)
XM_036164430.1 → XP_036020323.1 splicing factor, proline- and glutamine-rich isoform X1

UniProtKB/TrEMBL

A0A991ENV6

Conserved Domains (4) summary

PRK12704
Location:567 → 675

PRK12704; phosphodiesterase; Provisional

cd12948
Location:523 → 619

NOPS_PSF; NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins

cd12587
Location:377 → 447

RRM1_PSF; RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

cd12590
Location:453 → 532

RRM2_PSF; RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)
XM_036164431.1 → XP_036020324.1 splicing factor, proline- and glutamine-rich isoform X1

UniProtKB/TrEMBL

A0A991ENV6

Conserved Domains (4) summary

PRK12704
Location:567 → 675

PRK12704; phosphodiesterase; Provisional

cd12948
Location:523 → 619

NOPS_PSF; NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins

cd12587
Location:377 → 447

RRM1_PSF; RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

cd12590
Location:453 → 532

RRM2_PSF; RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)
XM_036164433.1 → XP_036020326.1 splicing factor, proline- and glutamine-rich isoform X2

UniProtKB/TrEMBL

A0A991ENV6

Conserved Domains (4) summary

PRK12704
Location:567 → 675

PRK12704; phosphodiesterase; Provisional

cd12948
Location:523 → 619

NOPS_PSF; NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins

cd12587
Location:377 → 447

RRM1_PSF; RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

cd12590
Location:453 → 532

RRM2_PSF; RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)
XM_036164434.1 → XP_036020327.1 splicing factor, proline- and glutamine-rich isoform X2

UniProtKB/TrEMBL

A0A991ENV6

Conserved Domains (4) summary

PRK12704
Location:567 → 675

PRK12704; phosphodiesterase; Provisional

cd12948
Location:523 → 619

NOPS_PSF; NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins

cd12587
Location:377 → 447

RRM1_PSF; RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

cd12590
Location:453 → 532

RRM2_PSF; RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)
XM_036164429.1 → XP_036020322.1 splicing factor, proline- and glutamine-rich isoform X1

UniProtKB/TrEMBL

A0A991ENV6

Conserved Domains (4) summary

PRK12704
Location:567 → 675

PRK12704; phosphodiesterase; Provisional

cd12948
Location:523 → 619

NOPS_PSF; NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins

cd12587
Location:377 → 447

RRM1_PSF; RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

cd12590
Location:453 → 532

RRM2_PSF; RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)
XM_036164432.1 → XP_036020325.1 splicing factor, proline- and glutamine-rich isoform X1

UniProtKB/TrEMBL

A0A991ENV6

Conserved Domains (4) summary

PRK12704
Location:567 → 675

PRK12704; phosphodiesterase; Provisional

cd12948
Location:523 → 619

NOPS_PSF; NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins

cd12587
Location:377 → 447

RRM1_PSF; RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

cd12590
Location:453 → 532

RRM2_PSF; RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)