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PPP4R2 protein phosphatase 4 regulatory subunit 2 [ Homo sapiens (human) ]

Gene ID: 151987, updated on 2-Nov-2024

Summary

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Official Symbol
PPP4R2provided by HGNC
Official Full Name
protein phosphatase 4 regulatory subunit 2provided by HGNC
Primary source
HGNC:HGNC:18296
See related
Ensembl:ENSG00000163605 MIM:613822; AllianceGenome:HGNC:18296
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
PP4R2
Summary
The protein encoded by this gene is a regulatory subunit of the serine/threonine-protein phosphatase 4 complex. In addition to being required for efficient DNA double strand break repair, this complex plays a role in organization of microtubules at centrosomes and processing of spliceosomal snRNPs. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]
Expression
Ubiquitous expression in bone marrow (RPKM 21.8), testis (RPKM 13.7) and 25 other tissues See more
Orthologs
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Genomic context

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See PPP4R2 in Genome Data Viewer
Location:
3p13
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (72996743..73069198)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (73038643..73110702)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (73045894..73118349)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14531 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14532 Neighboring gene lysosomal protein transmembrane 4 beta pseudogene 2 Neighboring gene glucoside xylosyltransferase 2 Neighboring gene ferritin heavy chain 1 pseudogene 23 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20094 Neighboring gene Sharpr-MPRA regulatory region 10271 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14533 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20095 Neighboring gene uncharacterized LOC124909395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20096 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20097 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:73077426-73077926 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:73077927-73078427 Neighboring gene RNA, U7 small nuclear 19 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:73097059-73097560 Neighboring gene Sharpr-MPRA regulatory region 10785 Neighboring gene MPRA-validated peak4698 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20098 Neighboring gene endogenous Bornavirus like nucleoprotein 2 Neighboring gene small nucleolar RNA U13 Neighboring gene RNA, U6 small nuclear 557, 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
  • 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?
  1. Results from a study on gene expression variability markers in early-stage human embryos shows that PPP4R2 is a putative expression variability marker for the 3-day, 8-cell embryo stage.
    Title: Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.
  2. PPP4R2 affects the survival of neuronal cells in response to DNA damage.
    Title: PPP4R2 regulates neuronal cell differentiation and survival, functionally cooperating with SMN.
  3. PP4R2, a regulatory subunit of PP4, mediates the DNA damage-dependent association between RPA2 and the PP4C catalytic subunit.
    Title: A PP4 phosphatase complex dephosphorylates RPA2 to facilitate DNA repair via homologous recombination.
  4. A three-protein PP4 phosphatase complex in mammalian cells, containing PP4C, PP4R2, and PP4R3beta, specifically dephosphorylates ATR-mediated gamma-H2AX generated during DNA replication.
    Title: A PP4-phosphatase complex dephosphorylates gamma-H2AX generated during DNA replication.
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)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC131930

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein phosphatase regulator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein phosphatase regulator activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein-macromolecule adaptor activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA splicing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in protein modification process TAS
Traceable Author Statement
more info
 PubMed 
involved_in regulation of double-strand break repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of double-strand break repair via homologous recombination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in centrosome IEA
Inferred from Electronic Annotation
more info
  
located_in chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
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 
part_of protein phosphatase 4 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of protein phosphatase 4 complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of protein phosphatase 4 complex IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
serine/threonine-protein phosphatase 4 regulatory subunit 2

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_001318025.2 → NP_001304954.1  serine/threonine-protein phosphatase 4 regulatory subunit 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC098481, AC103559
    UniProtKB/Swiss-Prot
    Q9NY27
    Conserved Domains (2) summary
    pfam09184
    Location:9 → 202
    PPP4R2; PPP4R2
    cl26761
    Location:141 → 360
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

  2. NM_001318026.2 → NP_001304955.1  serine/threonine-protein phosphatase 4 regulatory subunit 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate first exon compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC098481, AC103559
    UniProtKB/TrEMBL
    A0AA34QVI2
    Conserved Domains (1) summary
    pfam09184
    Location:1 → 220
    PPP4R2; PPP4R2

  3. NM_001318027.2 → NP_001304956.1  serine/threonine-protein phosphatase 4 regulatory subunit 2 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate exon and uses an alternate splice junction compared to variant 1. The resulting isoform (4) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC098481, AC103559
    UniProtKB/Swiss-Prot
    Q9NY27
    Conserved Domains (1) summary
    COG5271
    Location:27 → 246
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

  4. NM_001318028.2 → NP_001304957.1  serine/threonine-protein phosphatase 4 regulatory subunit 2 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains two alternate exons in place of the last seven exons compared to variant 1. The resulting isoform (5) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC098481, BX089727, DB469745
    Consensus CDS
    CCDS82805.1
    UniProtKB/TrEMBL
    C9IZF4
    Related
    ENSP00000418675.1, ENST00000495566.1
    Conserved Domains (1) summary
    pfam09184
    Location:9 → 57
    PPP4R2; PPP4R2

  5. NM_174907.4 → NP_777567.1  serine/threonine-protein phosphatase 4 regulatory subunit 2 isoform 1

    See identical proteins and their annotated locations for NP_777567.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC098481, AC103559
    Consensus CDS
    CCDS2917.1
    UniProtKB/Swiss-Prot
    A8K1I6, Q2TAJ9, Q498B8, Q8WXX6, Q9NY27
    UniProtKB/TrEMBL
    A0AA34QVI2
    Related
    ENSP00000349124.5, ENST00000356692.10
    Conserved Domains (2) summary
    pfam09184
    Location:9 → 259
    PPP4R2; PPP4R2
    cl26761
    Location:198 → 417
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

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
    72996743..73069198
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    73038643..73110702
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NY27.3 GenPept UniProtKB/Swiss-Prot:Q9NY27

Gene LinkOut

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