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Smpd3 sphingomyelin phosphodiesterase 3, neutral [ Mus musculus (house mouse) ]

Gene ID: 58994, updated on 7-Feb-2023

Summary

Official Symbol
Smpd3provided by MGI
Official Full Name
sphingomyelin phosphodiesterase 3, neutralprovided by MGI
Primary source
MGI:MGI:1927578
See related
Ensembl:ENSMUSG00000031906 AllianceGenome:MGI:1927578
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
fro; nSMase2; 4631433G07Rik
Summary
Enables identical protein binding activity; neutral sphingomyelin phosphodiesterase activity; and phospholipid binding activity. Involved in sphingomyelin metabolic process. Acts upstream of or within several processes, including animal organ development; enzyme linked receptor protein signaling pathway; and sphingolipid metabolic process. Located in Golgi cis cisterna and plasma membrane. Is expressed in several structures, including alimentary system; limb; nervous system; sensory organ; and skeleton. Used to study hypopituitarism; osteogenesis imperfecta; osteogenesis imperfecta type 2; and osteogenesis imperfecta type 3. Orthologous to human SMPD3 (sphingomyelin phosphodiesterase 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in colon adult (RPKM 31.2), large intestine adult (RPKM 26.1) and 17 other tissues See more
Orthologs
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Genomic context

See Smpd3 in Genome Data Viewer
Location:
8; 8 D3
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (106979180..107064597, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (106252548..106337965, complement)

Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene solute carrier family 7, member 6 opposite strand Neighboring gene protein arginine N-methyltransferase 7 Neighboring gene RIKEN cDNA 4930506A18 gene Neighboring gene predicted gene, 39238 Neighboring gene predicted gene, 34026

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
fragilitas ossium
GeneReviews: Not available

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables neutral sphingomyelin phosphodiesterase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables phosphatidic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
enables phosphatidylserine binding IDA
Inferred from Direct Assay
more info
PubMed 
enables phospholipase activity IBA
Inferred from Biological aspect of Ancestor
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 IDA
Inferred from Direct Assay
more info
PubMed 
enables sphingomyelin phosphodiesterase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables sphingomyelin phosphodiesterase activity ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within BMP signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within DNA biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within G1 to G0 transition IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in artery smooth muscle contraction ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within bone development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within bone growth IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within bone mineralization IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within bone mineralization IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cartilage development IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within cartilage development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cell cycle IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cellular response to hydrogen peroxide IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within cellular response to magnesium ion IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within cellular response to oxidised low-density lipoprotein particle stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cellular response to peptide IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cellular response to reactive oxygen species IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cellular response to redox state IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cellular response to tumor necrosis factor IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within ceramide metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within chondrocyte development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within chondrocyte development involved in endochondral bone morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within collagen metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within dentinogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in dopamine uptake ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within endochondral ossification IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within extracellular matrix assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within hematopoietic progenitor cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within lipid metabolic process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within lung alveolus development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within lung development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within mitotic nuclear division IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within multicellular organism growth IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within multicellular organism growth IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of cytosolic calcium ion concentration ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of hyaluronan biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within ossification IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within peptide hormone secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within platelet-derived growth factor receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within polysaccharide transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of NIK/NF-kappaB signaling ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of ceramide biosynthetic process ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of exosomal secretion ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of mitotic nuclear division IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of nitric oxide biosynthetic process ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of smooth muscle cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within protein kinase B signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within regulation of cartilage development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within regulation of hyaluronan biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within regulation of leukocyte migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within regulation of protein phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within respiratory system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within signal transduction IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within signal transduction TAS
Traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within skeletal system development IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within skeletal system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within sphingolipid mediated signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within sphingolipid metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within sphingomyelin catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in sphingomyelin catabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in sphingomyelin metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within sphingomyelin metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
involved_in sphingomyelin metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
located_in Golgi cis cisterna IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
located_in membrane ISO
Inferred from Sequence Orthology
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
sphingomyelin phosphodiesterase 3
Names
nSMase-2
neutral sphingomyelinase 2
neutral sphingomyelinase II
NP_067466.1
XP_006531304.1
XP_011246764.1
XP_011246765.1

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_021491.4NP_067466.1  sphingomyelin phosphodiesterase 3

    See identical proteins and their annotated locations for NP_067466.1

    Status: VALIDATED

    Source sequence(s)
    AC124544, AC134615
    Consensus CDS
    CCDS22634.1
    UniProtKB/Swiss-Prot
    Q3UTQ5, Q9JJY3
    Related
    ENSMUSP00000069255.8, ENSMUST00000067512.8
    Conserved Domains (2) summary
    cd09078
    Location:336646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    PRK12372
    Location:181305
    PRK12372; ribonuclease III; Reviewed

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000074.7 Reference GRCm39 C57BL/6J

    Range
    106979180..107064597 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006531241.5XP_006531304.1  sphingomyelin phosphodiesterase 3 isoform X1

    See identical proteins and their annotated locations for XP_006531304.1

    UniProtKB/Swiss-Prot
    Q3UTQ5, Q9JJY3
    Conserved Domains (2) summary
    cd09078
    Location:336646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    PRK12372
    Location:181305
    PRK12372; ribonuclease III; Reviewed
  2. XM_011248462.1XP_011246764.1  sphingomyelin phosphodiesterase 3 isoform X1

    See identical proteins and their annotated locations for XP_011246764.1

    UniProtKB/Swiss-Prot
    Q3UTQ5, Q9JJY3
    Related
    ENSMUSP00000148282.2, ENSMUST00000212896.2
    Conserved Domains (2) summary
    cd09078
    Location:336646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    PRK12372
    Location:181305
    PRK12372; ribonuclease III; Reviewed
  3. XM_011248463.4XP_011246765.1  sphingomyelin phosphodiesterase 3 isoform X1

    See identical proteins and their annotated locations for XP_011246765.1

    UniProtKB/Swiss-Prot
    Q3UTQ5, Q9JJY3
    Conserved Domains (2) summary
    cd09078
    Location:336646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    PRK12372
    Location:181305
    PRK12372; ribonuclease III; Reviewed