PAN2 poly(A) specific ribonuclease subunit PAN2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PAN2provided by HGNC
Official Full Name: poly(A) specific ribonuclease subunit PAN2provided by HGNC
Primary source: HGNC:HGNC:20074
See related: Ensembl:ENSG00000135473 MIM:617447; AllianceGenome:HGNC:20074
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: USP52
Summary: This gene encodes a deadenylase that functions as the catalytic subunit of the polyadenylate binding protein dependent poly(A) nuclease complex. The encoded protein is a magnesium dependent 3' to 5' exoribonuclease that is involved in the degradation of cytoplasmic mRNAs. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
Expression: Ubiquitous expression in testis (RPKM 19.6), thyroid (RPKM 18.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q13.3

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (56316936..56334000, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (56284581..56301646, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (56710720..56727784, complement)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Biallelic PAN2 variants in individuals with a syndromic neurodevelopmental disorder and multiple congenital anomalies.
Title: Biallelic PAN2 variants in individuals with a syndromic neurodevelopmental disorder and multiple congenital anomalies.
USP52 inhibits cell proliferation by stabilizing PTEN protein in non-small cell lung cancer.
Title: USP52 inhibits cell proliferation by stabilizing PTEN protein in non-small cell lung cancer.
USP52 regulates DNA end resection and chemosensitivity through removing inhibitory ubiquitination from CtIP.
Title: USP52 regulates DNA end resection and chemosensitivity through removing inhibitory ubiquitination from CtIP.
USP52 is a bona fide ubiquitin-specific protease, and USP52 promotes ASF1A deubiquitination and stabilization.
Title: USP52 acts as a deubiquitinase and promotes histone chaperone ASF1A stabilization.
USP52 is a key component of P-bodies required to prevent HIF1A mRNA degradation
Title: The P-body component USP52/PAN2 is a novel regulator of HIF1A mRNA stability.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
hPan2 and hPan3 have roles in mRNA decay and exhibit cytoplasmic co-localization
Title: Identification of a human cytoplasmic poly(A) nuclease complex stimulated by poly(A)-binding protein.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

SHGC-142707 (e-PCR)
- UniSTS:182547

USP52_9019 (e-PCR)
- UniSTS:468787

RH47494 (e-PCR)
- UniSTS:70

D1S1425 (e-PCR)
- UniSTS:149621

STS-W80474 (e-PCR)
- UniSTS:11662

G64805 (e-PCR)
- UniSTS:164751

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 3'-5'-RNA exonuclease activity	IDA Inferred from Direct Assay more info	PubMed
NOT enables cysteine-type deubiquitinase activity	IKR Inferred from Key Residues more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables poly(A)-specific ribonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables poly(A)-specific ribonuclease activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in nuclear-transcribed mRNA poly(A) tail shortening	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear-transcribed mRNA poly(A) tail shortening	TAS Traceable Author Statement more info
involved_in positive regulation of cytoplasmic mRNA processing body assembly	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in P-body	IBA Inferred from Biological aspect of Ancestor more info
part_of PAN complex	IBA Inferred from Biological aspect of Ancestor more info
part_of PAN complex	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: PAN2-PAN3 deadenylation complex catalytic subunit PAN2

Names: PAB-dependent poly(A)-specific ribonuclease subunit 2; PAB-dependent poly(A)-specific ribonuclease subunit PAN2; PAB1P-dependent poly(A)-nuclease; PAB1P-dependent poly(A)-specific ribonuclease; PABP-dependent poly(A) nuclease 2; PAN deadenylation complex catalytic subunit 2; PAN deadenylation complex subunit 2; PAN2 poly(A) specific ribonuclease subunit homolog; inactive ubiquitin carboxyl-terminal hydrolase 52; poly(A)-nuclease deadenylation complex subunit 2; ubiquitin specific peptidase 52; ubiquitin specific protease 52

NP_001120932.2

EC 3.1.13.4

NP_001159751.2

EC 3.1.13.4

NP_001381628.1

EC 3.1.13.4

NP_001381629.1

EC 3.1.13.4

NP_001381630.1

EC 3.1.13.4

NP_001381631.1

EC 3.1.13.4

NP_001381632.1

EC 3.1.13.4

NP_001381633.1

EC 3.1.13.4

NP_001381634.1

EC 3.1.13.4

NP_001381635.1

EC 3.1.13.4

NP_001381636.1

EC 3.1.13.4

NP_001381637.1

EC 3.1.13.4

NP_055686.4

EC 3.1.13.4

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_001127460.4 → NP_001120932.2 PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1 and 4 both encode the same isoform (1).

Source sequence(s)

AC073896

Consensus CDS

CCDS44922.1

UniProtKB/Swiss-Prot

O75189, Q504Q3, Q76E12, Q8IVE1

Related

ENSP00000401721.2, ENST00000425394.7

Conserved Domains (3) summary

cd06143
Location:975 → 1148

PAN2_exo; DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2

pfam13423
Location:517 → 898

UCH_1; Ubiquitin carboxyl-terminal hydrolase

cl29593
Location:204 → 357

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001166279.3 → NP_001159751.2 PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AC025574, AC073896

Consensus CDS

CCDS53802.1

Related

ENSP00000257931.5, ENST00000257931.9

Conserved Domains (3) summary

cd06143
Location:974 → 1147

PAN2_exo; DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2

pfam13423
Location:517 → 897

UCH_1; Ubiquitin carboxyl-terminal hydrolase

cl29593
Location:204 → 357

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001394699.1 → NP_001381628.1 PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform 1

Status: REVIEWED

Source sequence(s)

AC025574, AC073896

Consensus CDS

CCDS44922.1

UniProtKB/Swiss-Prot

O75189, Q504Q3, Q76E12, Q8IVE1

Related

ENSP00000481859.1, ENST00000610546.4

Conserved Domains (3) summary

cd06143
Location:975 → 1148

PAN2_exo; DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2

pfam13423
Location:517 → 898

UCH_1; Ubiquitin carboxyl-terminal hydrolase

cl29593
Location:204 → 357

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001394700.1 → NP_001381629.1 PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform 3

Status: REVIEWED

Source sequence(s)

AC073896

Consensus CDS

CCDS8915.1

Conserved Domains (3) summary

cd06143
Location:971 → 1144

PAN2_exo; DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2

pfam13423
Location:517 → 894

UCH_1; Ubiquitin carboxyl-terminal hydrolase

cl29593
Location:204 → 357

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001394701.1 → NP_001381630.1 PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform 4

Status: REVIEWED

Source sequence(s)

AC025574, AC073896

Conserved Domains (3) summary

cd06143
Location:970 → 1143

PAN2_exo; DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2

cd02672
Location:502 → 916

Peptidase_C19P; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

cl29593
Location:204 → 357

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001394702.1 → NP_001381631.1 PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform 4

Status: REVIEWED

Source sequence(s)

AC073896

Related

ENST00000551359.5

Conserved Domains (3) summary

cd06143
Location:970 → 1143

PAN2_exo; DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2

cd02672
Location:502 → 916

Peptidase_C19P; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

cl29593
Location:204 → 357

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001394703.1 → NP_001381632.1 PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform 5

Status: REVIEWED

Source sequence(s)

AC025574, AC073896

Conserved Domains (3) summary

cd06143
Location:975 → 1126

PAN2_exo; DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2

cd02672
Location:502 → 921

Peptidase_C19P; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

cl29593
Location:204 → 357

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001394704.1 → NP_001381633.1 PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform 6

Status: REVIEWED

Source sequence(s)

AC025574, AC073896

Conserved Domains (3) summary

cd06143
Location:974 → 1125

PAN2_exo; DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2

cd02672
Location:502 → 920

Peptidase_C19P; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

cl29593
Location:204 → 357

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001394705.1 → NP_001381634.1 PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform 7

Status: REVIEWED

Source sequence(s)

AC025574, AC073896

Conserved Domains (3) summary

cd06143
Location:971 → 1122

PAN2_exo; DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2

cd02672
Location:502 → 917

Peptidase_C19P; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

cl29593
Location:204 → 357

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001394706.1 → NP_001381635.1 PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform 8

Status: REVIEWED

Source sequence(s)

AC025574, AC073896

Conserved Domains (3) summary

cd06143
Location:970 → 1121

PAN2_exo; DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2

cd02672
Location:502 → 916

Peptidase_C19P; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

cl29593
Location:204 → 357

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001394707.1 → NP_001381636.1 PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform 8

Status: REVIEWED

Source sequence(s)

AC073896

Conserved Domains (3) summary

cd06143
Location:970 → 1121

PAN2_exo; DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2

cd02672
Location:502 → 916

Peptidase_C19P; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

cl29593
Location:204 → 357

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001394708.1 → NP_001381637.1 PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform 9

Status: REVIEWED

Source sequence(s)

AC025574, AC073896

Conserved Domains (3) summary

cd06143
Location:832 → 1005

PAN2_exo; DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2

cd02672
Location:363 → 778

Peptidase_C19P; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

cl29593
Location:65 → 218

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_014871.6 → NP_055686.4 PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice site in the coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1. Variants 3 and 5 both encode the same isoform (3).

Source sequence(s)

AC025574, AC073896

Consensus CDS

CCDS8915.1

Related

ENSP00000388231.3, ENST00000440411.8

Conserved Domains (3) summary

cd06143
Location:971 → 1144

PAN2_exo; DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2

pfam13423
Location:517 → 894

UCH_1; Ubiquitin carboxyl-terminal hydrolase

cl29593
Location:204 → 357

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...