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

    Gene ID: 57223, updated on 28-Oct-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 enable protein phosphatase activator activity. Involved in regulation of double-strand break repair. Located in centrosome and nuclear speck. Part of chromatin and protein phosphatase 4 complex. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 19.2), lymph node (RPKM 17.8) and 25 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (55547292..55617622, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (55544479..55614812, complement)
    RS_2024_09 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 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. An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Kittler R, et al. Nature, 2004 Dec 23. PMID 15616564
    2. 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
    3. 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
    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 (49) 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 regulation of double-strand break repair 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
    		  
    located_in 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_2024_08

    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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