Smpd3 sphingomyelin phosphodiesterase 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Smpd3provided by RGD
Official Full Name: sphingomyelin phosphodiesterase 3provided by RGD
Primary source: RGD:619754
See related: EnsemblRapid:ENSRNOG00000000257 AllianceGenome:RGD:619754
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: cca1
Summary: Predicted to enable identical protein binding activity; neutral sphingomyelin phosphodiesterase activity; and phospholipid binding activity. Involved in several processes, including positive regulation of biosynthetic process; positive regulation of exosomal secretion; and positive regulation of non-canonical NF-kappaB signal transduction. Predicted to be located in Golgi cis cisterna and plasma membrane. Predicted to be active in cytoplasm. Used to study pulmonary hypertension and transient cerebral ischemia. Biomarker of chronic obstructive pulmonary disease. Orthologous to human SMPD3 (sphingomyelin phosphodiesterase 3). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Brain (RPKM 79.6), Adrenal (RPKM 26.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 19q12

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	19	NC_086037.1 (51072209..51155639, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	19	NC_051354.1 (34162337..34245786, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	19	NC_005118.4 (38237963..38321572, complement)

Chromosome 19 - NC_086037.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Characterization of neutral sphingomyelinase activity and isoform expression in rodent skeletal muscle mitochondria.
Title: Characterization of neutral sphingomyelinase activity and isoform expression in rodent skeletal muscle mitochondria.
nSMase2 is a novel regulator of autophagy and provide evidence that Golgi-localized ceramides participate in cytoprotective autophagy against starvation.
Title: Activation of neutral sphingomyelinase 2 by starvation induces cell-protective autophagy via an increase in Golgi-localized ceramide.
These results indicate an important function of nSMase2 in the striatum.
Title: Enriched Expression of Neutral Sphingomyelinase 2 in the Striatum is Essential for Regulation of Lipid Raft Content and Motor Coordination.
The results of this study reveal that cerebral ischemia induced the activation of the nSMase2/ceramide pathway in astrocytes, but not neurons in the rat hippocampus
Title: Early activation of nSMase2/ceramide pathway in astrocytes is involved in ischemia-associated neuronal damage via inflammation in rat hippocampi.
NSMase-2- and PP2A-dependent regulation of IRAK-1 degradation is a novel mechanism to fine tune the magnitude of IL-1beta response.
Title: Protein phosphatase 2A and neutral sphingomyelinase 2 regulate IRAK-1 protein ubiquitination and degradation in response to interleukin-1beta.
nSMase2 has a role in ceramide generation, aberrant apoptosis, and lung injury under cigarette smoke exposure
Title: Neutral sphingomyelinase 2: a novel target in cigarette smoke-induced apoptosis and lung injury.
nSMase2 may increase dopamine uptake through inducing ceramide production and thereby decreasing intracellular calcium levels.
Title: Neutral sphingomyelinase 2 induces dopamine uptake through regulation of intracellular calcium.
sphingomyelin phosphodiesterase 3 is critical for tumor necrosis factor (TNF) alpha-induced trafficking of NMDA receptors and synaptic plasticity
Title: Tumor necrosis factor-alpha-induced neutral sphingomyelinase-2 modulates synaptic plasticity by controlling the membrane insertion of NMDA receptors.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Smpd3 (e-PCR), detects polymorphism
- UniSTS:498449

RH141370 (e-PCR)
- UniSTS:223366

D19Got24 (e-PCR)
- UniSTS:113801

Smpd3 (e-PCR), detects polymorphism
- UniSTS:502672

Smpd3 (e-PCR), detects polymorphism
- UniSTS:261276

UniSTS:498356 (e-PCR)
- UniSTS:498356

Smpd3 (e-PCR), detects polymorphism
- UniSTS:498356

D19Got57 (e-PCR)
- UniSTS:115184

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables neutral sphingomyelin phosphodiesterase activity	IEA Inferred from Electronic Annotation more info
enables neutral sphingomyelin phosphodiesterase activity	ISO Inferred from Sequence Orthology more info
enables phosphatidic acid binding	IEA Inferred from Electronic Annotation more info
enables phosphatidic acid binding	ISO Inferred from Sequence Orthology more info
enables phosphatidic acid binding	ISS Inferred from Sequence or Structural Similarity more info
enables phosphatidylserine binding	IEA Inferred from Electronic Annotation more info
enables phosphatidylserine binding	ISO Inferred from Sequence Orthology more info
enables phosphatidylserine binding	ISS Inferred from Sequence or Structural Similarity more info
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	IBA Inferred from Biological aspect of Ancestor more info
enables sphingomyelin phosphodiesterase activity	IEA Inferred from Electronic Annotation more info
enables sphingomyelin phosphodiesterase activity	ISO Inferred from Sequence Orthology more info
enables sphingomyelin phosphodiesterase activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in BMP signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within BMP signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in DNA biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in G1 to G0 transition	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within G1 to G0 transition	ISO Inferred from Sequence Orthology more info
involved_in artery smooth muscle contraction	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within bone development	ISO Inferred from Sequence Orthology more info
involved_in bone growth	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within bone growth	ISO Inferred from Sequence Orthology more info
involved_in bone mineralization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within bone mineralization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cartilage development	ISO Inferred from Sequence Orthology more info
involved_in cellular response to hydrogen peroxide	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to hydrogen peroxide	ISO Inferred from Sequence Orthology more info
involved_in cellular response to interleukin-1	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to magnesium ion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to magnesium ion	ISO Inferred from Sequence Orthology more info
involved_in cellular response to oxidised low-density lipoprotein particle stimulus	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to oxidised low-density lipoprotein particle stimulus	ISO Inferred from Sequence Orthology more info
involved_in cellular response to peptide	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to peptide	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to reactive oxygen species	ISO Inferred from Sequence Orthology more info
involved_in cellular response to redox state	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to redox state	ISO Inferred from Sequence Orthology more info
involved_in cellular response to tumor necrosis factor	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to tumor necrosis factor	ISO Inferred from Sequence Orthology more info
involved_in ceramide metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within ceramide metabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chondrocyte development	ISO Inferred from Sequence Orthology more info
involved_in chondrocyte development involved in endochondral bone morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chondrocyte development involved in endochondral bone morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in collagen metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within collagen metabolic process	ISO Inferred from Sequence Orthology more info
involved_in dentinogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within dentinogenesis	ISO Inferred from Sequence Orthology more info
involved_in dopamine uptake	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endochondral ossification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within endochondral ossification	ISO Inferred from Sequence Orthology more info
involved_in extracellular matrix assembly	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within extracellular matrix assembly	ISO Inferred from Sequence Orthology more info
involved_in hematopoietic progenitor cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within hematopoietic progenitor cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in lung alveolus development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lung alveolus development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lung development	ISO Inferred from Sequence Orthology more info
involved_in mitotic nuclear division	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mitotic nuclear division	ISO Inferred from Sequence Orthology more info
involved_in multicellular organism growth	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within multicellular organism growth	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cytosolic calcium ion concentration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of hyaluronan biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of hyaluronan biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ossification	ISO Inferred from Sequence Orthology more info
involved_in peptide hormone secretion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within peptide hormone secretion	ISO Inferred from Sequence Orthology more info
involved_in platelet-derived growth factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within platelet-derived growth factor receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in polysaccharide transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within polysaccharide transport	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of ceramide biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of exosomal secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of mitotic nuclear division	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of mitotic nuclear division	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of nitric oxide biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of non-canonical NF-kappaB signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of smooth muscle cell proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of smooth muscle cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in regulation of cartilage development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of cartilage development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of hyaluronan biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of leukocyte migration	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of leukocyte migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within respiratory system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within signal transduction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal system development	ISO Inferred from Sequence Orthology more info
involved_in sphingolipid mediated signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within sphingolipid mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in sphingolipid metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within sphingolipid metabolic process	ISO Inferred from Sequence Orthology more info
involved_in sphingomyelin catabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within sphingomyelin catabolic process	ISO Inferred from Sequence Orthology more info
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
acts_upstream_of_or_within sphingomyelin metabolic process	ISO Inferred from Sequence Orthology more info
involved_in sphingomyelin metabolic process	ISO Inferred from Sequence Orthology more info
involved_in sphingomyelin metabolic process	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in Golgi cis cisterna	IEA Inferred from Electronic Annotation more info
located_in Golgi cis cisterna	ISO Inferred from Sequence Orthology more info
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: sphingomyelin phosphodiesterase 3

Names: confluent 3Y1 cell-associated 1; confluent 3Y1 cell-associated protein 1; nSMase-2; nSMase2; neutral sphingomyelin phosphodiesterase 3; neutral sphingomyelinase 2; neutral sphingomyelinase II; sphingomyelin phosphodiesterase 3, neutral membrane

NP_446057.2

EC 3.1.4.12

XP_006255605.1

EC 3.1.4.12

XP_017456885.1

EC 3.1.4.12

XP_063134406.1

EC 3.1.4.12

XP_063134407.1

EC 3.1.4.12

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_053605.2 → NP_446057.2 sphingomyelin phosphodiesterase 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000019

UniProtKB/Swiss-Prot

O35049

UniProtKB/TrEMBL

A6IYW6, D4A8L3

Related

ENSRNOP00000030458.5, ENSRNOT00000031977.6

Conserved Domains (2) summary

cd09078
Location:336 → 646

nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine

cl11081
Location:172 → 321

dermokine

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086037.1 Reference GRCr8

Range

51072209..51155639 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006255543.5 → XP_006255605.1 sphingomyelin phosphodiesterase 3 isoform X1

See identical proteins and their annotated locations for XP_006255605.1

UniProtKB/Swiss-Prot

O35049

UniProtKB/TrEMBL

A6IYW6, D4A8L3

Conserved Domains (2) summary

cd09078
Location:336 → 646

nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine

cl11081
Location:172 → 321

dermokine
XM_063278337.1 → XP_063134407.1 sphingomyelin phosphodiesterase 3 isoform X1

UniProtKB/Swiss-Prot

O35049

UniProtKB/TrEMBL

A6IYW6, D4A8L3
XM_063278336.1 → XP_063134406.1 sphingomyelin phosphodiesterase 3 isoform X1

UniProtKB/Swiss-Prot

O35049

UniProtKB/TrEMBL

A6IYW6, D4A8L3
XM_017601396.3 → XP_017456885.1 sphingomyelin phosphodiesterase 3 isoform X1

UniProtKB/Swiss-Prot

O35049

UniProtKB/TrEMBL

A6IYW6, D4A8L3

Conserved Domains (2) summary

cd09078
Location:336 → 646

nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine

cl11081
Location:172 → 321

dermokine