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PPP4R1 protein phosphatase 4 regulatory subunit 1 [ Homo sapiens (human) ]

Gene ID: 9989, updated on 3-Apr-2024

Summary

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Official Symbol
PPP4R1provided by HGNC
Official Full Name
protein phosphatase 4 regulatory subunit 1provided by HGNC
Primary source
HGNC:HGNC:9320
See related
Ensembl:ENSG00000154845 MIM:604908; AllianceGenome:HGNC:9320
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
MEG1; PP4R1; PP4(Rmeg)
Summary
This gene encodes one of several alternate regulatory subunits of serine/threonine protein phosphatase 4 (PP4). The protein features multiple HEAT repeats. This protein forms a complex with PP4RC. This complex may have a distinct role from other PP4 complexes, including regulation of HDAC3 (Zhang et al., PMID: 15805470). There is also a transcribed pseudogene on chromosome 20. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]
Expression
Ubiquitous expression in esophagus (RPKM 39.0), testis (RPKM 25.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
18p11.22
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (9546794..9617199, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (9710190..9781391, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (9546792..9614557, complement)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene ralA binding protein 1 Neighboring gene iroquois homeobox 4 pseudogene 1 Neighboring gene RNA, U2 small nuclear 27, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr18:9570108-9570290 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:9574228-9574738 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:9574739-9575249 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9284 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9285 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9286 Neighboring gene PPP4R1 antisense RNA 1 Neighboring gene RNA, U6 small nuclear 903, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:9643443-9644016 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:9644964-9645470 Neighboring gene long intergenic non-protein coding RNA 2856

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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Related articles in PubMed

  1. PP4R1 interacts with HMGA2 to promote non-small-cell lung cancer migration and metastasis via activating MAPK/ERK-induced epithelial-mesenchymal transition. Wang B, et al. Mol Carcinog, 2020 May. PMID 32077156
  2. The PP4R1 sub-unit of protein phosphatase PP4 is essential for inhibition of NF-κB by merkel polyomavirus small tumour antigen. Abdul-Sada H, et al. Oncotarget, 2017 Apr 11. PMID 28445980, Free PMC Article
  3. A PP4 holoenzyme balances physiological and oncogenic nuclear factor-kappa B signaling in T lymphocytes. Brechmann M, et al. Immunity, 2012 Oct 19. PMID 23084358
  4. Cloning and characterization of a novel subunit of protein serine/threonine phosphatase 4 from mesangial cells. Wada T, et al. J Am Soc Nephrol, 2001 Dec. PMID 11729228
  5. The PP4R1 subunit of protein phosphatase PP4 targets TRAF2 and TRAF6 to mediate inhibition of NF-κB activation. Hadweh P, et al. Cell Signal, 2014 Dec. PMID 25134449

See all (45) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PP4R1 promotes glycolysis and gallbladder cancer progression through facilitating ERK1/2 mediated PKM2 nuclear translocation.
    Title: PP4R1 promotes glycolysis and gallbladder cancer progression through facilitating ERK1/2 mediated PKM2 nuclear translocation.
  2. PP4R1 accelerates the malignant progression of NSCLC via up-regulating HSPA6 expression and HSPA6-mediated ER stress.
    Title: PP4R1 accelerates the malignant progression of NSCLC via up-regulating HSPA6 expression and HSPA6-mediated ER stress.
  3. PP4R1 interacts with HMGA2 to promote non-small-cell lung cancer migration and metastasis via activating MAPK/ERK-induced epithelial-mesenchymal transition.
    Title: PP4R1 interacts with HMGA2 to promote non-small-cell lung cancer migration and metastasis via activating MAPK/ERK-induced epithelial-mesenchymal transition.
  4. Data identify PP4R1 as a novel target for virus subversion of the host anti-viral response.
    Title: The PP4R1 sub-unit of protein phosphatase PP4 is essential for inhibition of NF-κB by merkel polyomavirus small tumour antigen.
  5. PP4R1 could mediate the dephosphorylation of TRAF2 Ser11.
    Title: The PP4R1 subunit of protein phosphatase PP4 targets TRAF2 and TRAF6 to mediate inhibition of NF-κB activation.
  6. PP4R1 expression was triggered upon activation and proliferation of primary human T lymphocytes and deficiency for PP4R1 caused sustained and increased IKK activity, T cell hyperactivation, and aberrant NF-kappaB signaling in NF-kappaB-addicted T cell lymphomas
    Title: A PP4 holoenzyme balances physiological and oncogenic nuclear factor-kappa B signaling in T lymphocytes.
  7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to phosphoprotein phosphatase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
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 NAS
Non-traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in protein dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein phosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in signal transduction NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of protein phosphatase 4 complex ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
serine/threonine-protein phosphatase 4 regulatory subunit 1
Names
serine/threonine phosphatase 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)

  1. NM_001042388.3 → NP_001035847.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform a

    See identical proteins and their annotated locations for NP_001035847.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer protein (isoform a).
    Source sequence(s)
    AF100744, AK027064, BC060829, DR006046
    Consensus CDS
    CCDS42412.1
    UniProtKB/Swiss-Prot
    Q8TF05, Q99774, Q9UNQ7
    UniProtKB/TrEMBL
    A8K923, B2RCG9
    Related
    ENSP00000383402.3, ENST00000400556.8
    Conserved Domains (2) summary
    pfam15017
    Location:449 → 473
    AF1Q; Drug resistance and apoptosis regulator
    sd00044
    Location:133 → 157
    HEAT; HEAT repeat [structural motif]

  2. NM_001382562.1 → NP_001369491.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform c

    Status: REVIEWED

    Source sequence(s)
    AP000902, AP001381
    UniProtKB/TrEMBL
    A8K923, B2RCG9
    Conserved Domains (2) summary
    sd00044
    Location:44 → 68
    HEAT; HEAT repeat [structural motif]
    pfam15017
    Location:364 → 382
    WRNPLPNID; Putative WW-binding domain and destruction box

  3. NM_005134.4 → NP_005125.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform b

    See identical proteins and their annotated locations for NP_005125.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site compared to variant 1.This results in a shorter protein (isoform b), compared to isoform a.
    Source sequence(s)
    AF100744, BC060829
    Consensus CDS
    CCDS42413.1
    UniProtKB/TrEMBL
    A8K923, B2RCG9
    Related
    ENSP00000383401.3, ENST00000400555.7
    Conserved Domains (2) summary
    pfam15017
    Location:432 → 456
    AF1Q; Drug resistance and apoptosis regulator
    sd00044
    Location:116 → 140
    HEAT; HEAT repeat [structural motif]

RNA

  1. NR_052003.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI621152, AK293869, AK295533, AP001381, DR006046

  2. NR_168403.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP000902, AP001381

  3. NR_168404.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP000902, AP001381

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    9546794..9617199 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047437976.1 → XP_047293932.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X8

  2. XM_047437973.1 → XP_047293929.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X4

  3. XM_011525776.2 → XP_011524078.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X2

    UniProtKB/TrEMBL
    A8K923, B2RCG9
    Conserved Domains (2) summary
    pfam15017
    Location:484 → 508
    AF1Q; Drug resistance and apoptosis regulator
    sd00044
    Location:168 → 192
    HEAT; HEAT repeat [structural motif]

  4. XM_011525779.4 → XP_011524081.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X6

    UniProtKB/TrEMBL
    A8K923, B2RCG9
    Conserved Domains (1) summary
    sd00044
    Location:605 → 633
    HEAT; HEAT repeat [structural motif]

  5. XM_017026105.3 → XP_016881594.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X3

    UniProtKB/TrEMBL
    A8K923, B2RCG9

  6. XM_011525775.4 → XP_011524077.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X1

    UniProtKB/TrEMBL
    A8K923, B2RCG9
    Conserved Domains (2) summary
    pfam15017
    Location:501 → 525
    AF1Q; Drug resistance and apoptosis regulator
    sd00044
    Location:185 → 209
    HEAT; HEAT repeat [structural motif]

  7. XM_047437979.1 → XP_047293935.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X11

  8. XM_047437975.1 → XP_047293931.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X7

  9. XM_047437978.1 → XP_047293934.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X10

    Conserved Domains (2) summary
    sd00044
    Location:553 → 581
    HEAT; HEAT repeat [structural motif]
    pfam15017
    Location:342 → 360
    WRNPLPNID; Putative WW-binding domain and destruction box

  10. XM_047437974.1 → XP_047293930.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X5

  11. XM_047437977.1 → XP_047293933.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X9

  12. XM_047437980.1 → XP_047293936.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X12

RNA

  1. XR_007066261.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    9710190..9781391 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054319424.1 → XP_054175399.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X8

  2. XM_054319420.1 → XP_054175395.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X4

  3. XM_054319418.1 → XP_054175393.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X2

  4. XM_054319422.1 → XP_054175397.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X6

  5. XM_054319419.1 → XP_054175394.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X3

  6. XM_054319417.1 → XP_054175392.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X1

  7. XM_054319427.1 → XP_054175402.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X11

  8. XM_054319423.1 → XP_054175398.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X7

  9. XM_054319426.1 → XP_054175401.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X10

  10. XM_054319421.1 → XP_054175396.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X5

  11. XM_054319425.1 → XP_054175400.1  serine/threonine-protein phosphatase 4 regulatory subunit 1 isoform X9

RNA

  1. XR_008485037.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TF05.1 GenPept UniProtKB/Swiss-Prot:Q8TF05

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