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    PSPC1 paraspeckle component 1 [ Homo sapiens (human) ]

    Gene ID: 55269, updated on 10-Dec-2024

    Summary

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    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

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    See PSPC1 in Genome Data Viewer
    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_000013.11Genomic Context describing neighboring genes Neighboring gene transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 Neighboring gene uncharacterized LOC124903271 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5137 Neighboring gene mitochondrial ribosomal protein S31 pseudogene 2 Neighboring gene TPTE2 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:20161162-20161342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7405 Neighboring gene GOLM2 pseudogene 1 Neighboring gene estrogen-related receptor alpha pseudogene 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr13:20173929-20174918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7406 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:20219053-20219554 Neighboring gene M-phase phosphoprotein 8 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:20316454-20317223 Neighboring gene RNA, 7SL, cytoplasmic 166, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:20340248-20340748 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:20343088-20343647 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:20392071-20392598 Neighboring gene ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 4 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5140 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:20437895-20438623 Neighboring gene zinc finger MYM-type containing 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Paraspeckles. Fox AH, et al. Cold Spring Harb Perspect Biol, 2010 Jul. PMID 20573717, Free PMC Article
    2. PSPC1 Binds to HCV IRES and Prevents Ribosomal Protein S5 Binding, Inhibiting Viral RNA Translation. Tripathi SK, et al. Viruses, 2024 May 7. PMID 38793620, Free PMC Article
    3. Paraspeckle protein 1 (PSPC1) is involved in the cisplatin induced DNA damage response--role in G1/S checkpoint. Gao X, et al. PLoS One, 2014. PMID 24819514, Free PMC Article
    4. Obstructive sleep apnoea is related to melanoma aggressiveness through paraspeckle protein-1 upregulation. Cubillos-Zapata C, et al. Eur Respir J, 2023 Feb. PMID 36265878
    5. Depletion of Paraspeckle Protein 1 Enhances Methyl Methanesulfonate-Induced Apoptosis through Mitotic Catastrophe. Gao X, et al. PLoS One, 2016. PMID 26785254, Free PMC Article

    See all (182) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. Elevated PSPC1 and KDM5C expression indicates poor prognosis in prostate cancer.
      Title: Elevated PSPC1 and KDM5C expression indicates poor prognosis in prostate cancer.
    3. 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.
    4. 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.
    5. 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.
    6. PSPC1 Potentiates IGF1R Expression to Augment Cell Adhesion and Motility.
      Title: PSPC1 Potentiates IGF1R Expression to Augment Cell Adhesion and Motility.
    7. 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.
    8. 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.
    9. 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.
    10. 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

    Homology

    Clone Names

    • FLJ10955, FLJ33554, DKFZp566B1447

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA 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 membraneless organelle assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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

    1. NG_029751.3 RefSeqGene

      Range
      5000..85445
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. 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)

    2. 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)

    3. 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)

    4. 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

    1. 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

    2. 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

    3. NR_149052.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL354808, CA425205

    4. NR_149053.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL354808, CA425205

    5. 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

    1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      19671205..19782945 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047430435.1 → XP_047286391.1  paraspeckle component 1 isoform X2

    2. 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)

    3. 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)

    4. 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

    5. 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)

    RNA

    1. XR_007063689.1 RNA Sequence

    2. XR_007063688.1 RNA Sequence

    3. XR_941617.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      18867270..18979203 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054374665.1 → XP_054230640.1  paraspeckle component 1 isoform X2

    2. XM_054374664.1 → XP_054230639.1  paraspeckle component 1 isoform X2

    3. XM_054374663.1 → XP_054230638.1  paraspeckle component 1 isoform X1

    4. XM_054374667.1 → XP_054230642.1  paraspeckle component 1 isoform X4

    5. XM_054374666.1 → XP_054230641.1  paraspeckle component 1 isoform X3

    RNA

    1. XR_008488772.1 RNA Sequence

    2. XR_008488771.1 RNA Sequence

    3. XR_008488770.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WXF1.1 GenPept UniProtKB/Swiss-Prot:Q8WXF1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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