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PPP4R3B protein phosphatase 4 regulatory subunit 3B [ Homo sapiens (human) ]

Gene ID: 57223, updated on 3-Apr-2024

Summary

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Official Symbol
PPP4R3Bprovided by HGNC
Official Full Name
protein phosphatase 4 regulatory subunit 3Bprovided by HGNC
Primary source
HGNC:HGNC:29267
See related
Ensembl:ENSG00000275052 MIM:610352; AllianceGenome:HGNC:29267
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
Also known as
PSY2; smk1; FLFL2; SMEK2; PP4R3B
Summary
Predicted to act upstream of or within positive regulation of gluconeogenesis and protein dephosphorylation. Located in centrosome and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 19.2), lymph node (RPKM 17.8) and 25 other tissues See more
Orthologs
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Genomic context

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See PPP4R3B in Genome Data Viewer
Location:
2p16.1
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (55547292..55617622, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (55544479..55614812, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (55774428..55844757, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 634, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15781 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15782 Neighboring gene cilia and flagella associated protein 36 Neighboring gene small nucleolar RNA SNORA12 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:55794160-55794660 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:55843714-55844639 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:55844640-55845564 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11500 Neighboring gene PPP4R3B divergent transcript Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:55877194-55877806 Neighboring gene polyribonucleotide nucleotidyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15786

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. Phosphoproteomic analysis reveals that PP4 dephosphorylates KAP-1 impacting the DNA damage response. Lee DH, et al. EMBO J, 2012 May 16. PMID 22491012, Free PMC Article
  2. Loss of SMEK, a novel, conserved protein, suppresses MEK1 null cell polarity, chemotaxis, and gene expression defects. Mendoza MC, et al. Mol Cell Biol, 2005 Sep. PMID 16107728, Free PMC Article
  3. An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Kittler R, et al. Nature, 2004 Dec 23. PMID 15616564
  4. A PP4-phosphatase complex dephosphorylates gamma-H2AX generated during DNA replication. Chowdhury D, et al. Mol Cell, 2008 Jul 11. PMID 18614045, Free PMC Article
  5. Suppressor of MEK null (SMEK)/protein phosphatase 4 catalytic subunit (PP4C) is a key regulator of hepatic gluconeogenesis. Yoon YS, et al. Proc Natl Acad Sci U S A, 2010 Oct 12. PMID 20876121, Free PMC Article

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

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

EBI GWAS Catalog

Description
Genome-wide screen for metabolic syndrome susceptibility Loci reveals strong lipid gene contribution but no evidence for common genetic basis for clustering of metabolic syndrome traits.
EBI GWAS Catalog

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

  • FLJ31474, FLJ41002, KIAA1387

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein phosphatase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in DNA damage response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in gluconeogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of gluconeogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in protein dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of double-strand break repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in centrosome IDA
Inferred from Direct Assay
more info
  
part_of chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear speck IDA
Inferred from Direct Assay
more info
  
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
part_of protein phosphatase 4 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
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 3B
Names
SMEK homolog 2, suppressor of mek1

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_001122964.3 → NP_001116436.3  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC015982, KF510821
    Consensus CDS
    CCDS46289.1
    UniProtKB/Swiss-Prot
    Q5MIZ7, Q6P9B0, Q86XB8, Q9BQJ0, Q9BRK2, Q9H913, Q9P2G0
    UniProtKB/TrEMBL
    B4DKA9
    Related
    ENSP00000483228.1, ENST00000616407.2

  2. NM_001282850.2 → NP_001269779.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform 3

    See identical proteins and their annotated locations for NP_001269779.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an in-frame exon in the coding region, compared to variant 1. The resulting isoform (3) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AC015982, BC006215, BE535214, DB261776
    Consensus CDS
    CCDS62913.1
    UniProtKB/TrEMBL
    B4DKA9
    Related
    ENSP00000484116.1, ENST00000616288.4
    Conserved Domains (3) summary
    pfam04802
    Location:168 → 359
    SMK-1; Component of IIS longevity pathway SMK-1
    pfam08365
    Location:645 → 682
    IGF2_C; Insulin-like growth factor II E-peptide
    cl17171
    Location:7 → 65
    PH-like; Pleckstrin homology-like domain

  3. NM_020463.4 → NP_065196.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform 2

    See identical proteins and their annotated locations for NP_065196.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two in-frame exons in the coding region, compared to variant 1. The resulting isoform (2) lacks two internal segments, compared to isoform 1.
    Source sequence(s)
    AC015982, BC060855, BE535214, DB261776
    Consensus CDS
    CCDS1855.1
    UniProtKB/TrEMBL
    B4DKA9
    Related
    ENSP00000478677.1, ENST00000611717.4
    Conserved Domains (3) summary
    pfam04802
    Location:168 → 359
    SMK-1; Component of IIS longevity pathway SMK-1
    pfam08365
    Location:592 → 629
    IGF2_C; Insulin-like growth factor II E-peptide
    cl17171
    Location:7 → 65
    PH-like; Pleckstrin homology-like domain

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    55547292..55617622 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017004536.3 → XP_016860025.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X14

  2. XM_017004535.3 → XP_016860024.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X13

    Conserved Domains (1) summary
    cl17171
    Location:7 → 65
    PH-like; Pleckstrin homology-like domain

  3. XM_017004534.3 → XP_016860023.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X10

  4. XM_017004533.3 → XP_016860022.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X9

  5. XM_047445153.1 → XP_047301109.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X12

  6. XM_047445152.1 → XP_047301108.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X11

  7. XM_017004532.3 → XP_016860021.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X8

  8. XM_005264447.4 → XP_005264504.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X7

    Conserved Domains (3) summary
    pfam04802
    Location:98 → 151
    SMK-1; Component of IIS longevity pathway SMK-1
    pfam08365
    Location:469 → 506
    IGF2_C; Insulin-like growth factor II E-peptide
    cl17171
    Location:7 → 65
    PH-like; Pleckstrin homology-like domain

  9. XM_005264446.4 → XP_005264503.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X5

    UniProtKB/TrEMBL
    B4DKA9
    Conserved Domains (2) summary
    pfam04802
    Location:168 → 359
    SMK-1; Component of IIS longevity pathway SMK-1
    cl17171
    Location:7 → 65
    PH-like; Pleckstrin homology-like domain

  10. XM_017004531.3 → XP_016860020.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X2

    UniProtKB/TrEMBL
    B4DKA9
    Conserved Domains (2) summary
    pfam04802
    Location:168 → 359
    SMK-1; Component of IIS longevity pathway SMK-1
    cl17171
    Location:7 → 65
    PH-like; Pleckstrin homology-like domain

  11. XM_005264445.4 → XP_005264502.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X4

    UniProtKB/TrEMBL
    B4DKA9
    Conserved Domains (2) summary
    pfam04802
    Location:168 → 359
    SMK-1; Component of IIS longevity pathway SMK-1
    cl17171
    Location:7 → 65
    PH-like; Pleckstrin homology-like domain

  12. XM_005264444.4 → XP_005264501.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X3

    UniProtKB/TrEMBL
    B4DKA9
    Conserved Domains (3) summary
    pfam04802
    Location:168 → 359
    SMK-1; Component of IIS longevity pathway SMK-1
    pfam08365
    Location:624 → 661
    IGF2_C; Insulin-like growth factor II E-peptide
    cl17171
    Location:7 → 65
    PH-like; Pleckstrin homology-like domain

  13. XM_005264442.4 → XP_005264499.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X1

    UniProtKB/TrEMBL
    B4DKA9
    Conserved Domains (2) summary
    pfam04802
    Location:168 → 359
    SMK-1; Component of IIS longevity pathway SMK-1
    cl17171
    Location:7 → 65
    PH-like; Pleckstrin homology-like domain

  14. XM_047445155.1 → XP_047301111.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X16

  15. XM_047445154.1 → XP_047301110.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X15

  16. XM_047445151.1 → XP_047301107.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    55544479..55614812 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054343115.1 → XP_054199090.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X14

  2. XM_054343114.1 → XP_054199089.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X13

  3. XM_054343111.1 → XP_054199086.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X10

  4. XM_054343110.1 → XP_054199085.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X9

  5. XM_054343113.1 → XP_054199088.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X12

  6. XM_054343112.1 → XP_054199087.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X11

  7. XM_054343109.1 → XP_054199084.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X8

  8. XM_054343108.1 → XP_054199083.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X7

  9. XM_054343106.1 → XP_054199081.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X5

  10. XM_054343103.1 → XP_054199078.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X2

  11. XM_054343105.1 → XP_054199080.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X4

  12. XM_054343104.1 → XP_054199079.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X3

  13. XM_054343102.1 → XP_054199077.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X1

  14. XM_054343117.1 → XP_054199092.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X16

  15. XM_054343116.1 → XP_054199091.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X15

  16. XM_054343107.1 → XP_054199082.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5MIZ7.2 GenPept UniProtKB/Swiss-Prot:Q5MIZ7

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