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

Summary

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: mouse all
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Genomic context

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

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.
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.
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.
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.
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.

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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

PMC156606P1 (e-PCR)
- UniSTS:271408

D8S2279 (e-PCR)
- UniSTS:473907

RH64826 (e-PCR)
- UniSTS:91742

A006B41 (e-PCR)
- UniSTS:17518

D1S1423 (e-PCR)
- UniSTS:149619

RH41617 (e-PCR)
- UniSTS:90488

D11S3114 (e-PCR)
- UniSTS:152207

RH80630 (e-PCR)
- UniSTS:90793

G32319 (e-PCR)
- UniSTS:116912

G43493 (e-PCR)
- UniSTS:94953

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)

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
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
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
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
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
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
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

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
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
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
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
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
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
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
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
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
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