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    Ppp4r3b protein phosphatase 4 regulatory subunit 3B [ Mus musculus (house mouse) ]

    Gene ID: 104570, updated on 8-May-2024

    Summary

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    Official Symbol
    Ppp4r3bprovided by MGI
    Official Full Name
    protein phosphatase 4 regulatory subunit 3Bprovided by MGI
    Primary source
    MGI:MGI:2144474
    See related
    Ensembl:ENSMUSG00000020463 AllianceGenome:MGI:2144474
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Smek2; mKIAA1387
    Summary
    Acts upstream of or within positive regulation of gluconeogenesis and protein dephosphorylation. Located in cytoplasm and nucleus. Part of protein phosphatase 4 complex. Is expressed in central nervous system and retina. Orthologous to human PPP4R3B (protein phosphatase 4 regulatory subunit 3B). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 9.9), CNS E14 (RPKM 7.1) and 27 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ppp4r3b in Genome Data Viewer
    Location:
    11 A3.3; 11 16.46 cM
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (29118053..29170797)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (29172976..29220797)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene ribosomal protein SA, pseudogene 5 Neighboring gene STARR-seq mESC enhancer starr_29016 Neighboring gene STARR-seq mESC enhancer starr_29017 Neighboring gene STARR-seq mESC enhancer starr_29018 Neighboring gene STARR-seq mESC enhancer starr_29020 Neighboring gene RIKEN cDNA A630052C17 gene Neighboring gene polyribonucleotide nucleotidyltransferase 1 Neighboring gene STARR-positive B cell enhancer ABC_E1136 Neighboring gene predicted gene, 51940 Neighboring gene STARR-positive B cell enhancer ABC_E5213 Neighboring gene cilia and flagella associated protein 36 Neighboring gene STARR-seq mESC enhancer starr_29022 Neighboring gene fibrillarin pseudogene Neighboring gene predicted gene, 23109

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Dephosphorylation enables the recruitment of 53BP1 to double-strand DNA breaks. Lee DH, et al. Mol Cell, 2014 May 8. PMID 24703952, Free PMC Article
    2. Smek promotes histone deacetylation to suppress transcription of Wnt target gene brachyury in pluripotent embryonic stem cells. Lyu J, et al. Cell Res, 2011 Jun. PMID 21423269, Free PMC Article
    3. Smek promotes corticogenesis through regulating Mbd3's stability and Mbd3/NuRD complex recruitment to genes associated with neurogenesis. Moon BS, et al. PLoS Biol, 2017 May. PMID 28467410, Free PMC Article
    4. Smek1/2 is a nuclear chaperone and cofactor for cleaved Wnt receptor Ryk, regulating cortical neurogenesis. Chang WH, et al. Proc Natl Acad Sci U S A, 2017 Dec 12. PMID 29180410, 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 (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Smek1 and Smek2 (Smek1/2) are key factors in the Ryk signaling pathway
      Title: Smek1/2 is a nuclear chaperone and cofactor for cleaved Wnt receptor Ryk, regulating cortical neurogenesis.
    2. Smek/Mbd3 interaction regulates neuronal gene expression and neuronal differentiation during cortical development.
      Title: Smek promotes corticogenesis through regulating Mbd3's stability and Mbd3/NuRD complex recruitment to genes associated with neurogenesis.
    3. the Smek-containing protein phosphatase 4 complex represses transcription of Wnt-responsive development-related genes through histone deacetylation, and that this complex is essential for embryonic stem cell pluripotency maintenance
      Title: Smek promotes histone deacetylation to suppress transcription of Wnt target gene brachyury in pluripotent embryonic stem cells.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (2) 

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1387

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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
    		  
    acts_upstream_of gluconeogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of gluconeogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein dephosphorylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within protein dephosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of double-strand break repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  

    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_001363358.1 → NP_001350287.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform 2

      Status: VALIDATED

      Source sequence(s)
      BX000351, BX294116
      UniProtKB/TrEMBL
      Q3V166
      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

    2. NM_001363359.1 → NP_001350288.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform 3

      Status: VALIDATED

      Source sequence(s)
      BX000351, BX294116
      UniProtKB/TrEMBL
      Q3V166
      Conserved Domains (3) summary
      pfam08365
      Location:631 → 668
      IGF2_C; Insulin-like growth factor II E-peptide
      pfam04802
      Location:168 → 359
      SMK-1; Component of IIS longevity pathway SMK-1
      cl17171
      Location:7 → 65
      PH-like; Pleckstrin homology-like domain

    3. NM_001363360.1 → NP_001350289.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform 4

      Status: VALIDATED

      Source sequence(s)
      BX000351, BX294116
      UniProtKB/TrEMBL
      Q3V166
      Conserved Domains (3) summary
      pfam08365
      Location:619 → 656
      IGF2_C; Insulin-like growth factor II E-peptide
      pfam04802
      Location:168 → 333
      SMK-1; Component of IIS longevity pathway SMK-1
      cl17171
      Location:7 → 65
      PH-like; Pleckstrin homology-like domain

    4. NM_001363361.1 → NP_001350290.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform 5

      Status: VALIDATED

      Source sequence(s)
      BX000351, BX294116
      UniProtKB/TrEMBL
      Q3V166
      Conserved Domains (3) summary
      pfam08365
      Location:549 → 586
      IGF2_C; Insulin-like growth factor II E-peptide
      pfam04802
      Location:168 → 263
      SMK-1; Component of IIS longevity pathway SMK-1
      cl17171
      Location:7 → 65
      PH-like; Pleckstrin homology-like domain

    5. NM_001363362.1 → NP_001350291.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform 6

      Status: VALIDATED

      Source sequence(s)
      BX000351, BX294116
      Related
      ENSMUSP00000099920.3, ENSMUST00000102856.9
      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

    6. NM_134034.3 → NP_598795.2  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform 1

      See identical proteins and their annotated locations for NP_598795.2

      Status: VALIDATED

      Source sequence(s)
      AK037253, AK133211, BE692419, CD350450
      Consensus CDS
      CCDS24492.1
      UniProtKB/Swiss-Prot
      Q3V0E4, Q5M6V9, Q5RJC0, Q5RJC1, Q6ZPS5, Q8BTK2, Q8BY94, Q8BYY0, Q922R5
      UniProtKB/TrEMBL
      Q3V166
      Related
      ENSMUSP00000020755.6, ENSMUST00000020755.12
      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

    RNA

    1. NR_156485.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      BX000351, BX294116

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      29118053..29170797
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036156203.1 → XP_036012096.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X1

      UniProtKB/TrEMBL
      Q3V166
      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

    2. XM_036156204.1 → XP_036012097.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X2

      UniProtKB/TrEMBL
      Q3V166
      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

    3. XM_036156205.1 → XP_036012098.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X3

      UniProtKB/TrEMBL
      Q3V166
      Conserved Domains (2) summary
      pfam04802
      Location:168 → 263
      SMK-1; Component of IIS longevity pathway SMK-1
      cl17171
      Location:7 → 65
      PH-like; Pleckstrin homology-like domain

    4. XM_036156206.1 → XP_036012099.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X4

      UniProtKB/TrEMBL
      Q3V166
      Conserved Domains (2) summary
      pfam04802
      Location:168 → 263
      SMK-1; Component of IIS longevity pathway SMK-1
      cl17171
      Location:7 → 65
      PH-like; Pleckstrin homology-like domain

    5. XM_036156207.1 → XP_036012100.1  serine/threonine-protein phosphatase 4 regulatory subunit 3B isoform X5

      Conserved Domains (1) summary
      pfam04802
      Location:12 → 63
      SMK-1; Component of IIS longevity pathway SMK-1

    RNA

    1. XR_004936677.1 RNA Sequence

    2. XR_004936679.1 RNA Sequence

    3. XR_004936678.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q922R5.2 GenPept UniProtKB/Swiss-Prot:Q922R5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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