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PSPC1 paraspeckle component 1 [ Homo sapiens (human) ]

Gene ID: 55269, updated on 3-May-2020

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
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

Genomic context

See PSPC1 in Genome Data Viewer
Location:
13q12.11
Exon count:
16
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (19674752..19783036, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (20248892..20357159, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 350 Neighboring gene M-phase phosphoprotein 8 Neighboring gene RNA, 7SL, cytoplasmic 166, pseudogene Neighboring gene ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 4 pseudogene 1 Neighboring gene zinc finger MYM-type containing 5

Genomic regions, transcripts, and products

Expression

  • 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

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

Homology

Clone Names

  • FLJ10955, FLJ33554, DKFZp566B1447

Gene Ontology Provided by GOA

Function Evidence Code Pubs
E-box binding ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA binding HDA PubMed 
nucleic acid binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
activation of innate immune response IDA
Inferred from Direct Assay
more info
PubMed 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of circadian rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
rhythmic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
fibrillar center IDA
Inferred from Direct Assay
more info
 
nuclear matrix IEA
Inferred from Electronic Annotation
more info
 
nuclear speck IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
paraspeckles IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
paraspeckle component 1
Names
paraspeckle protein 1

NCBI Reference Sequences (RefSeq)

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_029751.2 RefSeqGene

    Range
    5075..85520
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001042414.3NP_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
    Q8WXF1
    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
    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_044998.2 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, AL354808, BP225439, CA425205, DC396174
  3. NR_149052.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL354808, CA425205
  4. NR_149053.1 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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

    Range
    19674752..19783036 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011535139.2XP_011533441.1  paraspeckle component 1 isoform X3

    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)
  2. XM_011535137.2XP_011533439.1  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)
  3. XM_011535138.3XP_011533440.1  paraspeckle component 1 isoform X2

    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_011535142.3XP_011533444.1  paraspeckle component 1 isoform X5

    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_011535141.3XP_011533443.1  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
    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_941617.2 RNA Sequence

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