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Ppp4r3a protein phosphatase 4 regulatory subunit 3A [ Mus musculus (house mouse) ]

Gene ID: 68734, updated on 18-Apr-2024

Summary

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Official Symbol
Ppp4r3aprovided by MGI
Official Full Name
protein phosphatase 4 regulatory subunit 3Aprovided by MGI
Primary source
MGI:MGI:1915984
See related
Ensembl:ENSMUSG00000041846 AllianceGenome:MGI:1915984
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
Smek1; mKIAA2010; 1110034C04Rik
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 several structures, including central nervous system; heart; and retina nuclear layer. Orthologous to human PPP4R3A (protein phosphatase 4 regulatory subunit 3A). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 18.5), placenta adult (RPKM 11.4) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
12 E; 12 51.17 cM
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (101005668..101051721, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (101039409..101083737, complement)

Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 88C Neighboring gene STARR-positive B cell enhancer ABC_E7169 Neighboring gene predicted gene, 36756 Neighboring gene STARR-seq mESC enhancer starr_33081 Neighboring gene STARR-positive B cell enhancer ABC_E8502 Neighboring gene microRNA 1190 Neighboring gene predicted gene, 47639 Neighboring gene RIKEN cDNA D130020L05 gene Neighboring gene STARR-seq mESC enhancer starr_33083 Neighboring gene STARR-seq mESC enhancer starr_33084 Neighboring gene myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 pseudogene 2 Neighboring gene kinesin family member 4, pseudogene

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. Ppp4r3a deficiency leads to depression-like behaviors in mice by modulating the synthesis of synaptic proteins. Gao F, et al. Dis Model Mech, 2022 Jun 1. PMID 35314861, Free PMC Article
  2. Protein phosphatase 4 and Smek complex negatively regulate Par3 and promote neuronal differentiation of neural stem/progenitor cells. Lyu J, et al. Cell Rep, 2013 Nov 14. PMID 24209749, Free PMC Article
  3. 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
  4. Smek1 deficiency exacerbates experimental autoimmune encephalomyelitis by activating proinflammatory microglia and suppressing the IDO1-AhR pathway. Duan RN, et al. J Neuroinflammation, 2021 Jun 28. PMID 34183017, Free PMC Article
  5. 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

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Ppp4r3a deficiency leads to depression-like behaviors in mice by modulating the synthesis of synaptic proteins.
    Title: Ppp4r3a deficiency leads to depression-like behaviors in mice by modulating the synthesis of synaptic proteins.
  2. Smek1 deficiency exacerbates experimental autoimmune encephalomyelitis by activating proinflammatory microglia and suppressing the IDO1-AhR pathway.
    Title: Smek1 deficiency exacerbates experimental autoimmune encephalomyelitis by activating proinflammatory microglia and suppressing the IDO1-AhR pathway.
  3. 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.
  4. 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.
  5. Authors identify the cell polarity protein Par3, a negative regulator of neuronal differentiation, as a Smek1 substrate and demonstrate that Smek1 suppresses its activity.
    Title: Protein phosphatase 4 and Smek complex negatively regulate Par3 and promote neuronal differentiation of neural stem/progenitor cells.
  6. 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)

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 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 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
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 

General protein information

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Preferred Names
serine/threonine-protein phosphatase 4 regulatory subunit 3A
Names
SMEK homolog 1, 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_001160214.1 → NP_001153686.1  serine/threonine-protein phosphatase 4 regulatory subunit 3A isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame donor splice site at one of the coding exons compared to variant 1, resulting in a longer isoform (2) with an internal protein segment not found in isoform 1.
    Source sequence(s)
    AK053668, AK054087, AK152480, BC064465
    Consensus CDS
    CCDS49142.1
    UniProtKB/TrEMBL
    E9Q481
    Related
    ENSMUSP00000129654.2, ENSMUST00000163095.9
    Conserved Domains (3) summary
    pfam04802
    Location:166 → 357
    SMK-1; Component of IIS longevity pathway SMK-1
    cl17171
    Location:7 → 65
    PH-like; Pleckstrin homology-like domain
    cl26969
    Location:325 → 402
    Vitellogenin_N; Lipoprotein amino terminal region

  2. NM_211355.2 → NP_997594.1  serine/threonine-protein phosphatase 4 regulatory subunit 3A isoform 1

    See identical proteins and their annotated locations for NP_997594.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript, and encodes isoform 1.
    Source sequence(s)
    AK053668, AK054087, BC064465
    Consensus CDS
    CCDS26111.1
    UniProtKB/Swiss-Prot
    Q3UF79, Q69Z35, Q6P2K6, Q80VS2, Q8BKP7
    Related
    ENSMUSP00000041667.9, ENSMUST00000048305.10
    Conserved Domains (3) summary
    pfam04802
    Location:166 → 357
    SMK-1; Component of IIS longevity pathway SMK-1
    cl17171
    Location:7 → 65
    PH-like; Pleckstrin homology-like domain
    cl26969
    Location:325 → 402
    Vitellogenin_N; Lipoprotein amino terminal region

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_000078.7 Reference GRCm39 C57BL/6J

    Range
    101005668..101051721 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017315173.2 → XP_017170662.1  serine/threonine-protein phosphatase 4 regulatory subunit 3A isoform X1

    Conserved Domains (3) summary
    pfam04802
    Location:166 → 357
    SMK-1; Component of IIS longevity pathway SMK-1
    pfam09747
    Location:626 → 741
    DUF2052; Coiled-coil domain containing protein (DUF2052)
    cl17171
    Location:7 → 65
    PH-like; Pleckstrin homology-like domain

  2. XM_017315174.3 → XP_017170663.1  serine/threonine-protein phosphatase 4 regulatory subunit 3A isoform X2

    Conserved Domains (4) summary
    pfam04802
    Location:166 → 357
    SMK-1; Component of IIS longevity pathway SMK-1
    pfam09747
    Location:613 → 728
    DUF2052; Coiled-coil domain containing protein (DUF2052)
    cl17171
    Location:7 → 65
    PH-like; Pleckstrin homology-like domain
    cl26969
    Location:325 → 402
    Vitellogenin_N; Lipoprotein amino terminal region

RNA

  1. XR_003950076.2 RNA Sequence

  2. XR_001780474.3 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6P2K6.1 GenPept UniProtKB/Swiss-Prot:Q6P2K6

Gene LinkOut

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