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    PSPC1 paraspeckle component 1 [ Homo sapiens (human) ]

    Gene ID: 55269, updated on 28-Oct-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    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

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 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

    Preferred Names
    paraspeckle component 1
    Names
    paraspeckle protein 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001042414.4NP_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:227320
      NOPS_PSPC1; NOPS domain, including C-terminal coiled-coil region, in paraspeckle protein component 1 (PSPC1) and similar proteins
      cd12586
      Location:81151
      RRM1_PSP1; RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)
      cd12589
      Location:157236
      RRM2_PSP1; RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)
    2. NM_001354908.2NP_001341837.1  paraspeckle component 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL354808, CA425205
      Conserved Domains (3) summary
      cd12946
      Location:227319
      NOPS_p54nrb_PSF_PSPC1; NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSPC1 family proteins
      cd12586
      Location:81151
      RRM1_PSP1; RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)
      cd12589
      Location:157236
      RRM2_PSP1; RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)
    3. NM_001354909.2NP_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:227320
      NOPS_PSPC1; NOPS domain, including C-terminal coiled-coil region, in paraspeckle protein component 1 (PSPC1) and similar proteins
      cd12586
      Location:81151
      RRM1_PSP1; RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)
      cd12589
      Location:157236
      RRM2_PSP1; RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)
    4. NM_001363660.2NP_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:227319
      NOPS_p54nrb_PSF_PSPC1; NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSPC1 family proteins
      cd12589
      Location:157236
      RRM2_PSP1; RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)
      cl17169
      Location:81151
      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_047430435.1XP_047286391.1  paraspeckle component 1 isoform X2

    2. XM_011535139.3XP_011533441.1  paraspeckle component 1 isoform X2

      See identical proteins and their annotated locations for XP_011533441.1

      Conserved Domains (3) summary
      cd12946
      Location:227319
      NOPS_p54nrb_PSF_PSPC1; NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSPC1 family proteins
      cd12586
      Location:81151
      RRM1_PSP1; RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)
      cd12589
      Location:157236
      RRM2_PSP1; RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)
    3. XM_011535138.4XP_011533440.1  paraspeckle component 1 isoform X1

      Conserved Domains (3) summary
      cd12946
      Location:227319
      NOPS_p54nrb_PSF_PSPC1; NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSPC1 family proteins
      cd12586
      Location:81151
      RRM1_PSP1; RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)
      cd12589
      Location:157236
      RRM2_PSP1; RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)
    4. XM_011535142.4XP_011533444.1  paraspeckle component 1 isoform X4

      Conserved Domains (3) summary
      cd12946
      Location:227319
      NOPS_p54nrb_PSF_PSPC1; NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSPC1 family proteins
      cd12589
      Location:157236
      RRM2_PSP1; RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)
      cl17169
      Location:81151
      RRM_SF; RNA recognition motif (RRM) superfamily
    5. XM_011535141.4XP_011533443.1  paraspeckle component 1 isoform X3

      Conserved Domains (3) summary
      cd12946
      Location:227319
      NOPS_p54nrb_PSF_PSPC1; NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSPC1 family proteins
      cd12586
      Location:81151
      RRM1_PSP1; RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)
      cd12589
      Location:157236
      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_054374665.1XP_054230640.1  paraspeckle component 1 isoform X2

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

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

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

    5. XM_054374666.1XP_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