PSPC1 paraspeckle component 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PSPC1provided by HGNC
Official Full Name: paraspeckle component 1provided by HGNC
Primary source: HGNC:HGNC:20320
See related: Ensembl:ENSG00000121390 MIM:612408; AllianceGenome:HGNC:20320
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PSP1
Summary: This gene encodes a nucleolar protein that localizes to punctate subnuclear structures that occur close to splicing speckles, known as paraspeckles. These paraspeckles are composed of RNA-protein structures that include a non-coding RNA, NEAT1/Men epsilon/beta, and the Drosophila Behavior Human Splicing family of proteins, which include the product of this gene and the P54NRB/NONO and PSF/SFPQ proteins. Paraspeckles may function in the control of gene expression via an RNA nuclear retention mechanism. The protein encoded by this gene is found in paraspeckles in transcriptionally active cells, but it localizes to unique cap structures at the nucleolar periphery when RNA polymerase II transcription is inhibited, or during telophase. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene, which is also located on chromosome 13, has been identified. [provided by RefSeq, Aug 2011]
Expression: Ubiquitous expression in testis (RPKM 5.7), bone marrow (RPKM 5.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q12.11

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (19671205..19782945, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (18867270..18979203, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (20248892..20357085, complement)

Chromosome 13 - NC_000013.11 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?

PSPC1 Binds to HCV IRES and Prevents Ribosomal Protein S5 Binding, Inhibiting Viral RNA Translation.
Title: PSPC1 Binds to HCV IRES and Prevents Ribosomal Protein S5 Binding, Inhibiting Viral RNA Translation.
Elevated PSPC1 and KDM5C expression indicates poor prognosis in prostate cancer.
Title: Elevated PSPC1 and KDM5C expression indicates poor prognosis in prostate cancer.
Obstructive sleep apnoea is related to melanoma aggressiveness through paraspeckle protein-1 upregulation.
Title: Obstructive sleep apnoea is related to melanoma aggressiveness through paraspeckle protein-1 upregulation.
PSPC1 is a potential prognostic marker for hormone-dependent breast cancer patients and modulates RNA processing of ESR1 and SCFD2.
Title: PSPC1 is a potential prognostic marker for hormone-dependent breast cancer patients and modulates RNA processing of ESR1 and SCFD2.
Nuclear receptor 4A1 (NR4A1) antagonists target paraspeckle component 1 (PSPC1) in cancer cells.
Title: Nuclear receptor 4A1 (NR4A1) antagonists target paraspeckle component 1 (PSPC1) in cancer cells.
PSPC1 Potentiates IGF1R Expression to Augment Cell Adhesion and Motility.
Title: PSPC1 Potentiates IGF1R Expression to Augment Cell Adhesion and Motility.
Paraspeckle components NONO and PSPC1 are not mislocalized from motor neuron nuclei in sporadic ALS.
Title: Paraspeckle components NONO and PSPC1 are not mislocalized from motor neuron nuclei in sporadic ALS.
PSPC1, a nuclear substrate of PTK6, sequesters PTK6 in the nucleus and loses its metastasis driving capability in hepatocellular carcinoma. Conversely, PSPC1 upregulation or PSPC1-Y523F mutation promotes epithelial-mesenchymal transition, stemness, and metastasis via cytoplasmic translocation of active PTK6 and nuclear translocation of beta-catenin, which interacts with PSPC1 to augment Wnt3a autocrine signaling.
Title: PSPC1-interchanged interactions with PTK6 and β-catenin synergize oncogenic subcellular translocations and tumor progression.
This study determined that Hepatitis Delta Virus replication induces the delocalization of PSP1 to cytoplasmic foci containing PABP and increases NEAT1 level causing an enlargement of NEAT1 foci.
Title: The Hepatitis Delta Virus accumulation requires paraspeckle components and affects NEAT1 level and PSP1 localization.
PSPC1 and TET2 contribute to ERVL and ERVL-associated gene regulation by both transcriptional repression via histone deacetylases and post-transcriptional destabilization of RNAs through 5hmC modification.
Title: RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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
Rev	rev	HIV-1 Rev interacting protein, paraspeckle protein 1 (PSPC1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with PSPC1 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

D13S183E (e-PCR)
- UniSTS:87626

STS-M78307 (e-PCR)
- UniSTS:4954

SHGC-110875 (e-PCR)
- UniSTS:168061

D20S530E (e-PCR)
- UniSTS:5523

RH99234 (e-PCR)
- UniSTS:84641

RH102397 (e-PCR)
- UniSTS:96731

G64217 (e-PCR)
- UniSTS:167648

D13S972 (e-PCR)
- UniSTS:152307

SHGC-58322 (e-PCR)
- UniSTS:63987

D13S977 (e-PCR)
- UniSTS:152311

RH94086 (e-PCR)
- UniSTS:91389

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in activation of innate immune response	IDA Inferred from Direct Assay more info	PubMed
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in non-membrane-bounded organelle assembly	IDA Inferred from Direct Assay 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
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in fibrillar center	IDA Inferred from Direct Assay more info
located_in nuclear matrix	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in paraspeckles	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: paraspeckle component 1

Names: paraspeckle protein 1

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.

Genomic

NG_029751.3 RefSeqGene

Range

5000..85445

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001042414.4 → NP_001035879.1 paraspeckle component 1 isoform 1

See identical proteins and their annotated locations for NP_001035879.1

Status: REVIEWED

Description

Transcript Variant: This variant (1, also known as PSP1-alpha) encodes isoform 1.

Source sequence(s)

AK301554, AL354808, BM981042, DC396174

Consensus CDS

CCDS41870.1

UniProtKB/Swiss-Prot

Q5JTQ3, Q8NCZ9, Q8WXE8, Q8WXF1, Q9NV36

UniProtKB/TrEMBL

B4DWI8

Related

ENSP00000481916.1, ENST00000619300.4

Conserved Domains (3) summary

cd12949
Location:227 → 320

NOPS_PSPC1; NOPS domain, including C-terminal coiled-coil region, in paraspeckle protein component 1 (PSPC1) and similar proteins

cd12586
Location:81 → 151

RRM1_PSP1; RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

cd12589
Location:157 → 236

RRM2_PSP1; RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)
NM_001354908.2 → NP_001341837.1 paraspeckle component 1 isoform 2

Status: REVIEWED

Source sequence(s)

AL354808, CA425205

Conserved Domains (3) summary

cd12946
Location:227 → 319

NOPS_p54nrb_PSF_PSPC1; NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSPC1 family proteins

cd12586
Location:81 → 151

RRM1_PSP1; RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

cd12589
Location:157 → 236

RRM2_PSP1; RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)
NM_001354909.2 → NP_001341838.1 paraspeckle component 1 isoform 1

Status: REVIEWED

Source sequence(s)

AL354808

Consensus CDS

CCDS41870.1

UniProtKB/Swiss-Prot

Q5JTQ3, Q8NCZ9, Q8WXE8, Q8WXF1, Q9NV36

UniProtKB/TrEMBL

B4DWI8

Related

ENSP00000343966.4, ENST00000338910.9

Conserved Domains (3) summary

cd12949
Location:227 → 320

NOPS_PSPC1; NOPS domain, including C-terminal coiled-coil region, in paraspeckle protein component 1 (PSPC1) and similar proteins

cd12586
Location:81 → 151

RRM1_PSP1; RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

cd12589
Location:157 → 236

RRM2_PSP1; RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)
NM_001363660.2 → NP_001350589.1 paraspeckle component 1 isoform 3

Status: REVIEWED

Source sequence(s)

AL354808

Consensus CDS

CCDS86343.1

Related

ENSP00000435921.1, ENST00000492741.5

Conserved Domains (3) summary

cd12946
Location:227 → 319

NOPS_p54nrb_PSF_PSPC1; NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSPC1 family proteins

cd12589
Location:157 → 236

RRM2_PSP1; RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

cl17169
Location:81 → 151

RRM_SF; RNA recognition motif (RRM) superfamily

RNA

NR_003272.4 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2, also known as PSP1-beta) contains an alternate exon structure at its 3' end, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

BC014184, BP225439, CA425205, DC396174
NR_044998.3 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate exon structure at its 3' end, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK001817, BP225439, CA425205, DC396174
NR_149052.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL354808, CA425205
NR_149053.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL354808, CA425205
NR_156729.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL354808

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_000013.11 Reference GRCh38.p14 Primary Assembly

Range

19671205..19782945 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047430435.1 → XP_047286391.1 paraspeckle component 1 isoform X2
XM_011535139.3 → XP_011533441.1 paraspeckle component 1 isoform X2

See identical proteins and their annotated locations for XP_011533441.1

Conserved Domains (3) summary

cd12946
Location:227 → 319

NOPS_p54nrb_PSF_PSPC1; NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSPC1 family proteins

cd12586
Location:81 → 151

RRM1_PSP1; RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

cd12589
Location:157 → 236

RRM2_PSP1; RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)
XM_011535138.4 → XP_011533440.1 paraspeckle component 1 isoform X1

Conserved Domains (3) summary

cd12946
Location:227 → 319

NOPS_p54nrb_PSF_PSPC1; NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSPC1 family proteins

cd12586
Location:81 → 151

RRM1_PSP1; RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

cd12589
Location:157 → 236

RRM2_PSP1; RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)
XM_011535142.4 → XP_011533444.1 paraspeckle component 1 isoform X4

Conserved Domains (3) summary

cd12946
Location:227 → 319

NOPS_p54nrb_PSF_PSPC1; NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSPC1 family proteins

cd12589
Location:157 → 236

RRM2_PSP1; RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

cl17169
Location:81 → 151

RRM_SF; RNA recognition motif (RRM) superfamily
XM_011535141.4 → XP_011533443.1 paraspeckle component 1 isoform X3

Conserved Domains (3) summary

cd12946
Location:227 → 319

NOPS_p54nrb_PSF_PSPC1; NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSPC1 family proteins

cd12586
Location:81 → 151

RRM1_PSP1; RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

cd12589
Location:157 → 236

RRM2_PSP1; RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)