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PCNP PEST proteolytic signal containing nuclear protein [ Homo sapiens (human) ]

Gene ID: 57092, updated on 3-Nov-2024

Summary

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Official Symbol
PCNPprovided by HGNC
Official Full Name
PEST proteolytic signal containing nuclear proteinprovided by HGNC
Primary source
HGNC:HGNC:30023
See related
Ensembl:ENSG00000081154 MIM:615210; AllianceGenome:HGNC:30023
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Involved in proteasome-mediated ubiquitin-dependent protein catabolic process and protein ubiquitination. Located in nuclear body. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in ovary (RPKM 78.0), thyroid (RPKM 65.5) and 25 other tissues See more
Orthologs
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Genomic context

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See PCNP in Genome Data Viewer
Location:
3q12.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (101574094..101594465)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (104286707..104307080)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (101292938..101313309)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ARB2 family member B, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr3.3097 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:101274853-101275465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20166 Neighboring gene tRNA methyltransferase 10C, mitochondrial RNase P subunit Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:101292235-101293180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20171 Neighboring gene ribosomal protein S18 pseudogene 5 Neighboring gene ribosomal protein L32 pseudogene 7 Neighboring gene RNA, U6 small nuclear 1256, pseudogene

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 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. PCNP promotes ovarian cancer progression by accelerating β-catenin nuclear accumulation and triggering EMT transition. Dong P, et al. J Cell Mol Med, 2020 Jul. PMID 32548978, Free PMC Article
  2. PEST-containing nuclear protein mediates the proliferation, migration, and invasion of human neuroblastoma cells through MAPK and PI3K/AKT/mTOR signaling pathways. Wu DD, et al. BMC Cancer, 2018 May 2. PMID 29716528, Free PMC Article
  3. PCNP is a novel regulator of proliferation, migration, and invasion in human thyroid cancer. Chen YG, et al. Int J Biol Sci, 2022. PMID 35813472, Free PMC Article
  4. TIPE2 and PCNP expression abnormalities in peripheral blood mononuclear cells associated with disease activity in rheumatoid arthritis: a meta-analysis. Han ZP, et al. Eur Rev Med Pharmacol Sci, 2021 Feb. PMID 33629294
  5. NIRF, a novel RING finger protein, is involved in cell-cycle regulation. Mori T, et al. Biochem Biophys Res Commun, 2002 Aug 23. PMID 12176013

See all (79) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PCNP is a novel regulator of proliferation, migration, and invasion in human thyroid cancer.
    Title: PCNP is a novel regulator of proliferation, migration, and invasion in human thyroid cancer.
  2. TIPE2 and PCNP expression abnormalities in peripheral blood mononuclear cells associated with disease activity in rheumatoid arthritis: a meta-analysis.
    Title: TIPE2 and PCNP expression abnormalities in peripheral blood mononuclear cells associated with disease activity in rheumatoid arthritis: a meta-analysis.
  3. PCNP promotes ovarian cancer progression by accelerating beta-catenin nuclear accumulation and triggering EMT transition.
    Title: PCNP promotes ovarian cancer progression by accelerating β-catenin nuclear accumulation and triggering EMT transition.
  4. PCNP mediates the proliferation, migration, and invasion of human neuroblastoma cells through mitogen-activated protein kinase and PI3K/AKT/mTOR signaling pathways, implying that PCNP is a therapeutic target for patients with neuroblastoma.
    Title: PEST-containing nuclear protein mediates the proliferation, migration, and invasion of human neuroblastoma cells through MAPK and PI3K/AKT/mTOR signaling pathways.
  5. NIRF has ubiquitination activity, the hallmark of a ubiquitin ligase. PCNP was readily ubiquitinated in 293 and COS-7 cells, and NIRF ubiquitinated PCNP in vitro as well as in vivo.
    Title: NIRF is a ubiquitin ligase that is capable of ubiquitinating PCNP, a PEST-containing nuclear protein.
Submit: New GeneRIF Correction

Phenotypes

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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)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp781I24156

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in nuclear body IDA
Inferred from Direct Assay
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
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
PEST proteolytic signal-containing nuclear protein
Names
PEST-containing nuclear protein

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)

  1. NM_001320395.1 → NP_001307324.1  PEST proteolytic signal-containing nuclear protein isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate coding exon compared to variant 1, that causes a frameshift. The resulting isoform (b) has a shorter and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AB037675, BC013916, BU608892, DA304502
    UniProtKB/Swiss-Prot
    Q8WW12
    Conserved Domains (1) summary
    pfam15473
    Location:23 → 118
    PCNP; PEST, proteolytic signal-containing nuclear protein family

  2. NM_001320397.1 → NP_001307326.1  PEST proteolytic signal-containing nuclear protein isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame segment compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AB037675, BU608892, DA304502, DB060329
    UniProtKB/Swiss-Prot
    Q8WW12
    Conserved Domains (1) summary
    pfam15473
    Location:24 → 138
    PCNP; PEST, proteolytic signal-containing nuclear protein family

  3. NM_001320398.1 → NP_001307327.1  PEST proteolytic signal-containing nuclear protein isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (d) has the same N- and C-termini but is 1 aa shorter compared to isoform a.
    Source sequence(s)
    AB037675, BF541732, BU608892, CD696085, DA304502
    UniProtKB/Swiss-Prot
    Q8WW12
    Conserved Domains (1) summary
    pfam15473
    Location:24 → 170
    PCNP; PEST, proteolytic signal-containing nuclear protein family

  4. NM_001320399.1 → NP_001307328.1  PEST proteolytic signal-containing nuclear protein isoform e

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate 5' exon and uses an alternate splice junction compared to variant 1. The resulting isoform (e) has a shorter and distinct N-terminus compared to isoform a.
    Source sequence(s)
    AB037675, AC073861, BI596913, BU608892, DA304502
    UniProtKB/Swiss-Prot
    Q8WW12
    Conserved Domains (1) summary
    pfam15473
    Location:20 → 151
    PCNP; PEST, proteolytic signal-containing nuclear protein family

  5. NM_001320400.1 → NP_001307329.1  PEST proteolytic signal-containing nuclear protein isoform f

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks two alternate coding exons compared to variant 1, that causes a frameshift. The resulting isoform (f) has a shorter and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AB037675, AC073861, BF244508, BU608892, DA304502
    UniProtKB/Swiss-Prot
    Q8WW12
    Conserved Domains (1) summary
    pfam15473
    Location:24 → 94
    PCNP; PEST, proteolytic signal-containing nuclear protein family

  6. NM_001320401.1 → NP_001307330.1  PEST proteolytic signal-containing nuclear protein isoform g

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (g) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AB037675, BU608892, DA304502, DA710370
    UniProtKB/Swiss-Prot
    Q8WW12
    Conserved Domains (1) summary
    pfam15473
    Location:24 → 146
    PCNP; PEST, proteolytic signal-containing nuclear protein family

  7. NM_020357.3 → NP_065090.1  PEST proteolytic signal-containing nuclear protein isoform a

    See identical proteins and their annotated locations for NP_065090.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AC073861
    Consensus CDS
    CCDS2942.1
    UniProtKB/Swiss-Prot
    B2RBE7, D3DN52, Q53GF3, Q6AI44, Q8WW12, Q96CU3, Q9NS81
    Related
    ENSP00000265260.3, ENST00000265260.8
    Conserved Domains (1) summary
    pfam15473
    Location:24 → 171
    PCNP; PEST, proteolytic signal-containing nuclear protein family

RNA

  1. NR_135223.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB037675, BU608892, DA304502
    Related
    ENST00000460231.5

  2. NR_135224.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (9) uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AB037675, BU608892, DA304502, DB032930
    Related
    ENST00000469941.5

  3. NR_135225.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (10) uses two alternate splice junctions compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB037675, AC073861, BU608892, DA304502, DA817951

  4. NR_135226.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (11) uses an alternate splice junction and lacks two alternate exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB037675, BU608892, DA304502, DA821754

  5. NR_135227.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (12) uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB037675, AC073861, BI547939, BU608892, DA304502

  6. NR_135228.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (13) uses an alternate splice junction and lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB037675, BU608892, DA041324, DA304502

  7. NR_135229.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (14) lacks an alternate exon and contains another alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB037675, AC073861, BI913146, BU608892, DA304502

  8. NR_135230.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (15) uses an alternate splice junction and lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB037675, BU608892, DA304502, DB481581

  9. NR_135231.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (16) lacks two alternate exons compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AB037675, BU608892, DA304502, HY051831

  10. NR_135232.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (17) contains an alternate exon and uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB037675, AC073861, BU608892, CN482876, DA304502

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    101574094..101594465
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    104286707..104307080
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054347352.1 → XP_054203327.1  PEST proteolytic signal-containing nuclear protein isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WW12.2 GenPept UniProtKB/Swiss-Prot:Q8WW12

Gene LinkOut

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

Chemical Information
Molecular Biology Databases
Research Materials
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