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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
    mouse all
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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 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)

    Genotypes

    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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