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

Summary

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

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_000078.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (1) 1 citation
Endonuclease-mediated (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G36391 (e-PCR)
- UniSTS:29769

BB044704 (e-PCR)
- UniSTS:185951

MARC_16316-16317:1017431376:1 (e-PCR)
- UniSTS:267999

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)

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
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

NC_000078.7 Reference GRCm39 C57BL/6J

Range

101005668..101051721 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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