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

Gene ID: 104570, updated on 21-Apr-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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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)
  • Targeted (2) 
  • Endonuclease-mediated (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

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