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Aliases for SMPD3 Gene

Aliases for SMPD3 Gene

  • Sphingomyelin Phosphodiesterase 3, Neutral Membrane (Neutral Sphingomyelinase II) 2 3
  • Neutral Sphingomyelinase II 3 4
  • Neutral Sphingomyelinase 2 3 4
  • NSMase-2 3 4
  • NSMASE2 3 4
  • Sphingomyelin Phosphodiesterase 3 3
  • EC 3.1.4.12 4

External Ids for SMPD3 Gene

Previous GeneCards Identifiers for SMPD3 Gene

  • GC16M059090
  • GC16M068772
  • GC16M068130
  • GC16M068171
  • GC16M066949
  • GC16M068392
  • GC16M054265

Summaries for SMPD3 Gene

GeneCards Summary for SMPD3 Gene

SMPD3 (Sphingomyelin Phosphodiesterase 3, Neutral Membrane (Neutral Sphingomyelinase II)) is a Protein Coding gene. Diseases associated with SMPD3 include dentinogenesis imperfecta. Among its related pathways are Sphingolipid metabolism and Sphingolipid metabolism. GO annotations related to this gene include sphingomyelin phosphodiesterase activity.

UniProtKB/Swiss-Prot for SMPD3 Gene

  • Catalyzes the hydrolysis of sphingomyelin to form ceramide and phosphocholine. Ceramide mediates numerous cellular functions, such as apoptosis and growth arrest, and is capable of regulating these 2 cellular events independently. Also hydrolyzes sphingosylphosphocholine. Regulates the cell cycle by acting as a growth suppressor in confluent cells. Probably acts as a regulator of postnatal development and participates in bone and dentin mineralization.

Gene Wiki entry for SMPD3 Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMPD3 Gene

Genomics for SMPD3 Gene

Regulatory Elements for SMPD3 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for SMPD3 Gene

Start:
68,358,325 bp from pter
End:
68,448,688 bp from pter
Size:
90,364 bases
Orientation:
Minus strand

Genomic View for SMPD3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SMPD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMPD3 Gene

Proteins for SMPD3 Gene

  • Protein details for SMPD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NY59-NSMA2_HUMAN
    Recommended name:
    Sphingomyelin phosphodiesterase 3
    Protein Accession:
    Q9NY59
    Secondary Accessions:
    • B7ZL82
    • Q2M1S8

    Protein attributes for SMPD3 Gene

    Size:
    655 amino acids
    Molecular mass:
    71081 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SMPD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMPD3 Gene

Proteomics data for SMPD3 Gene at MOPED

Post-translational modifications for SMPD3 Gene

  • Palmitoylated, palmitoylation-deficient proteins are targeted for lysosomal degradation.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SMPD3 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for SMPD3 Gene

Domains for SMPD3 Gene

Protein Domains for SMPD3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SMPD3 Gene

Graphical View of Domain Structure for InterPro Entry

Q9NY59

UniProtKB/Swiss-Prot:

NSMA2_HUMAN :
  • Q9NY59
Family:
  • Belongs to the neutral sphingomyelinase family.
genes like me logo Genes that share domains with SMPD3: view

No data available for Gene Families for SMPD3 Gene

Function for SMPD3 Gene

Molecular function for SMPD3 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties: pH dependence: Optimum pH is 7.5.;
UniProtKB/Swiss-Prot CatalyticActivity: Sphingomyelin + H(2)O = N-acylsphingosine + phosphocholine
UniProtKB/Swiss-Prot EnzymeRegulation: Activated by unsaturated fatty acids and phosphatidylserine.
UniProtKB/Swiss-Prot Function: Catalyzes the hydrolysis of sphingomyelin to form ceramide and phosphocholine. Ceramide mediates numerous cellular functions, such as apoptosis and growth arrest, and is capable of regulating these 2 cellular events independently. Also hydrolyzes sphingosylphosphocholine. Regulates the cell cycle by acting as a growth suppressor in confluent cells. Probably acts as a regulator of postnatal development and participates in bone and dentin mineralization.

Enzyme Numbers (IUBMB) for SMPD3 Gene

Gene Ontology (GO) - Molecular Function for SMPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004767 sphingomyelin phosphodiesterase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with SMPD3: view
genes like me logo Genes that share phenotypes with SMPD3: view

Animal Models for SMPD3 Gene

MGI Knock Outs for SMPD3:

Animal Model Products

CRISPR Products

miRNA for SMPD3 Gene

miRTarBase miRNAs that target SMPD3

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SMPD3

In Situ Assay Products

Flow Cytometry Products

No data available for Transcription Factor Targeting and HOMER Transcription for SMPD3 Gene

Localization for SMPD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMPD3 Gene

Golgi apparatus membrane; Lipid-anchor. Cell membrane; Lipid-anchor. Note=May localize to detergent-resistant subdomains of Golgi membranes of hypothalamic neurosecretory neurons. According to PubMed:15051724, it localizes to plasma membrane in confluent contact-inhibited cells.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SMPD3 Gene COMPARTMENTS Subcellular localization image for SMPD3 gene
Compartment Confidence
golgi apparatus 5
plasma membrane 5
extracellular 2
cytosol 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for SMPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000137 Golgi cis cisterna IEA --
GO:0000139 Golgi membrane IEA --
GO:0005794 Golgi apparatus --
GO:0005886 plasma membrane TAS --
genes like me logo Genes that share ontologies with SMPD3: view

Pathways for SMPD3 Gene

genes like me logo Genes that share pathways with SMPD3: view

UniProtKB/Swiss-Prot Q9NY59-NSMA2_HUMAN

  • Pathway: Lipid metabolism; sphingolipid metabolism

Interacting Proteins for SMPD3 Gene

Gene Ontology (GO) - Biological Process for SMPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002244 hematopoietic progenitor cell differentiation IEA --
GO:0006665 sphingolipid metabolic process TAS --
GO:0006684 sphingomyelin metabolic process --
GO:0006685 sphingomyelin catabolic process TAS 10823942
GO:0006687 glycosphingolipid metabolic process TAS --
genes like me logo Genes that share ontologies with SMPD3: view

Compounds for SMPD3 Gene

(277) HMDB Compounds for SMPD3 Gene

Compound Synonyms Cas Number PubMed IDs
3-O-Sulfogalactosylceramide (d18:1/12:0)
  • Sulfatide (d18:1/12:0)
852100-88-0
3-O-Sulfogalactosylceramide (d18:1/14:0)
  • Sulfatide (d18:1/14:0)
Not Available
3-O-Sulfogalactosylceramide (d18:1/16:0)
  • Sulfatide (d18:1/16:0)
862509-48-6
3-O-Sulfogalactosylceramide (d18:1/18:0)
  • Sulfatide (d18:1/18:0)
244215-65-4
3-O-Sulfogalactosylceramide (d18:1/18:1(9Z))
  • Sulfatide (d18:1/18:1(9Z))
Not Available

(1) Drugbank Compounds for SMPD3 Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Phosphatidylserine
  • 3-O-sn-Phosphatidyl-L-serine
8002-43-5 target

(6) Novoseek inferred chemical compound relationships for SMPD3 Gene

Compound -log(P) Hits PubMed IDs
ceramide 86.1 16
ceramides 80.8 1
lipid 13.8 1
cholesterol 0 1
oxygen 0 1
genes like me logo Genes that share compounds with SMPD3: view

Transcripts for SMPD3 Gene

Unigene Clusters for SMPD3 Gene

Sphingomyelin phosphodiesterase 3, neutral membrane (neutral sphingomyelinase II):
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SMPD3

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for SMPD3

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SMPD3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12
SP1: - - - - -
SP2: - - - -
SP3: -
SP4: - - -
SP5: -
SP6: -
SP7:

Relevant External Links for SMPD3 Gene

GeneLoc Exon Structure for
SMPD3
ECgene alternative splicing isoforms for
SMPD3

Expression for SMPD3 Gene

mRNA expression in normal human tissues for SMPD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SMPD3 Gene

This gene is overexpressed in Small Intestine - Terminal Ileum (5.4) and Colon - Transverse (5.2).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for SMPD3 Gene

SOURCE GeneReport for Unigene cluster for SMPD3 Gene Hs.368421

mRNA Expression by UniProt/SwissProt for SMPD3 Gene

Q9NY59-NSMA2_HUMAN
Tissue specificity: Predominantly expressed in brain.
genes like me logo Genes that share expressions with SMPD3: view

In Situ Assay Products

Orthologs for SMPD3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SMPD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMPD3 35
  • 99.39 (n)
  • 99.69 (a)
SMPD3 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SMPD3 35
  • 88.18 (n)
  • 89.91 (a)
SMPD3 36
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMPD3 35
  • 88.35 (n)
  • 89.47 (a)
SMPD3 36
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Smpd3 35
  • 86.93 (n)
  • 91.58 (a)
Smpd3 16
Smpd3 36
  • 91 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMPD3 36
  • 68 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SMPD3 36
  • 71 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smpd3 35
  • 87.17 (n)
  • 90.86 (a)
chicken
(Gallus gallus)
Aves SMPD3 35
  • 69.89 (n)
  • 73.89 (a)
SMPD3 36
  • 72 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMPD3 36
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smpd3 35
  • 67.69 (n)
  • 70.77 (a)
zebrafish
(Danio rerio)
Actinopterygii smpd3 35
  • 62.37 (n)
  • 61.01 (a)
smpd3 36
  • 54 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 28 (a)
OneToOne
Species with no ortholog for SMPD3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SMPD3 Gene

ENSEMBL:
Gene Tree for SMPD3 (if available)
TreeFam:
Gene Tree for SMPD3 (if available)

Paralogs for SMPD3 Gene

Pseudogenes.org Pseudogenes for SMPD3 Gene

genes like me logo Genes that share paralogs with SMPD3: view

No data available for Paralogs for SMPD3 Gene

Variants for SMPD3 Gene

Sequence variations from dbSNP and Humsavar for SMPD3 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type MAF
rs1750 -- 68,405,167(+) GCCTC(A/G)GGACT intron-variant
rs918787 -- 68,444,022(-) TGACT(C/T)AGGCT intron-variant
rs918788 -- 68,440,954(-) TTCAA(G/T)CCATT intron-variant
rs1019544 -- 68,420,457(+) GCTAA(C/T)AGCCT intron-variant
rs1069317 -- 68,369,035(-) tcacc(A/G)tgttg intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SMPD3 Gene

Variant ID Type Subtype PubMed ID
nsv1847 CNV Insertion 18451855
esv2714652 CNV Deletion 23290073
nsv1848 CNV Insertion 18451855

Relevant External Links for SMPD3 Gene

HapMap Linkage Disequilibrium report
SMPD3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMPD3 Gene

Disorders for SMPD3 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (1) Diseases for SMPD3 Gene including...

Search for SMPD3 Gene in MalaCards »

(4) Novoseek inferred disease relationships for SMPD3 Gene

Disease -log(P) Hits PubMed IDs
panhypopituitarism 62.8 1
dwarfism 54.7 1
necrosis 16.5 5
tumors 0 6

Relevant External Links for SMPD3

Genetic Association Database (GAD)
SMPD3
Human Genome Epidemiology (HuGE) Navigator
SMPD3
genes like me logo Genes that share disorders with SMPD3: view

No data available for UniProtKB/Swiss-Prot for SMPD3 Gene

Publications for SMPD3 Gene

  1. Hydrolysis of sphingosylphosphocholine by neutral sphingomyelinases. (PMID: 14741383) Miura Y. … Hanada K. (FEBS Lett. 2004) 3 4 23
  2. Role for mammalian neutral sphingomyelinase 2 in confluence-induced growth arrest of MCF7 cells. (PMID: 15051724) Marchesini N. … Hannun Y.A. (J. Biol. Chem. 2004) 3 4 23
  3. Analysis of membrane topology of neutral sphingomyelinase 2. (PMID: 17349629) Tani M. … Hannun Y.A. (FEBS Lett. 2007) 3 4 23
  4. Cloning and characterization of the mammalian brain-specific, Mg2+- dependent neutral sphingomyelinase. (PMID: 10823942) Hofmann K. … Stoffel W. (Proc. Natl. Acad. Sci. U.S.A. 2000) 2 3 4
  5. Novel tumor necrosis factor-responsive mammalian neutral sphingomyelinase-3 is a C-tail-anchored protein. (PMID: 16517606) Krut O. … Kroenke M. (J. Biol. Chem. 2006) 3 23 25

Products for SMPD3 Gene

Sources for SMPD3 Gene

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