Smpdl3b sphingomyelin phosphodiesterase, acid-like 3B [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Smpdl3bprovided by MGI
Official Full Name: sphingomyelin phosphodiesterase, acid-like 3Bprovided by MGI
Primary source: MGI:MGI:1916022
See related: Ensembl:ENSMUSG00000028885 AllianceGenome:MGI:1916022
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Asml3b; 1110054A24Rik
Summary: Enables phosphoric diester hydrolase activity and zinc ion binding activity. Involved in membrane lipid catabolic process; negative regulation of inflammatory response; and negative regulation of toll-like receptor signaling pathway. Located in plasma membrane. Orthologous to human SMPDL3B (sphingomyelin phosphodiesterase acid like 3B). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in small intestine adult (RPKM 61.1), duodenum adult (RPKM 49.2) and 7 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4 D2.3; 4 65.82 cM

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (132460277..132484558, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (132732966..132757171, complement)

Chromosome 4 - NC_000070.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

SMPDL3B is palmitoylated and stabilized by ZDHHC5, and its silencing aggravates diabetic retinopathy of db/db mice: Activation of NLRP3/NF-kappaB pathway.
Title: SMPDL3B is palmitoylated and stabilized by ZDHHC5, and its silencing aggravates diabetic retinopathy of db/db mice: Activation of NLRP3/NF-κB pathway.
SMPDL3b modulates radiation-induced DNA damage response in renal podocytes.
Title: SMPDL3b modulates radiation-induced DNA damage response in renal podocytes.
Study reports that Smpdl3b excess, as observed in podocytes in diabetic kidney disease, impairs insulin receptor isoform B-dependent pro-survival insulin signaling by interfering with insulin receptor isoforms binding to caveolin-1 in the plasma membrane.
Title: SMPDL3b modulates insulin receptor signaling in diabetic kidney disease.
These results demonstrate that radiation injury induces early cytoskeletal remodeling, down-regulation of SMPDL3b, and elevation of cellular ceramide levels. Overexpression of SMPDL3b and pretreatment with rituximab confer a radioprotective effect in cultured podocytes.
Title: Sphingomyelinase-like phosphodiesterase 3b mediates radiation-induced damage of renal podocytes.
Although a potential substrate for SMPDL3B is sphingomyelin, we identify other possible substrates such as CDP-choline, ATP, and ADP.
Title: Crystal Structure of the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3B Provides Insights into Determinants of Substrate Specificity.
our results identify the membrane-modulating enzyme SMPDL3B as a negative regulator of TLR signaling that functions at the interface of membrane biology and innate immunity.
Title: The Lipid-Modifying Enzyme SMPDL3B Negatively Regulates Innate Immunity.
SMPDL3b may be an important modulator of podocyte function by shifting suPAR-mediated podocyte injury from a migratory phenotype to an apoptotic phenotype and that it represents a novel therapeutic glomerular disease target
Title: Sphingomyelinase-like phosphodiesterase 3b expression levels determine podocyte injury phenotypes in glomerular disease.

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Variation

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Alleles

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

Endonuclease-mediated (3)
Gene trapped (1)
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AU045240 (e-PCR)
- UniSTS:159301

Smpdl3b (e-PCR), detects polymorphism
- UniSTS:507237

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity, acting on glycosyl bonds	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables phosphoric diester hydrolase activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphoric diester hydrolase activity	IDA Inferred from Direct Assay more info	PubMed
enables phosphoric diester hydrolase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables phosphoric diester hydrolase activity	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sphingomyelin phosphodiesterase activity	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within immune system process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within inflammatory response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within innate immune response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lipid catabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lipid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in membrane lipid catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within metabolic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of inflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of innate immune response	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of toll-like receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sphingomyelin catabolic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in extracellular region	IEA Inferred from Electronic Annotation more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in side of membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: acid sphingomyelinase-like phosphodiesterase 3b

Names: ASM-like phosphodiesterase 3b

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_133888.2 → NP_598649.1 acid sphingomyelinase-like phosphodiesterase 3b precursor

See identical proteins and their annotated locations for NP_598649.1

Status: PROVISIONAL

Source sequence(s)

AL627130

Consensus CDS

CCDS18733.1

UniProtKB/Swiss-Prot

P58242

UniProtKB/TrEMBL

Q3TLX9

Related

ENSMUSP00000030709.9, ENSMUST00000030709.9

Conserved Domains (2) summary

cd00842
Location:23 → 323

MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain

pfam00149
Location:22 → 281

Metallophos; Calcineurin-like phosphoesterase

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_000070.7 Reference GRCm39 C57BL/6J

Range

132460277..132484558 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036163553.1 → XP_036019446.1 acid sphingomyelinase-like phosphodiesterase 3b isoform X1

Conserved Domains (1) summary

cd00842
Location:23 → 323

MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain