Format

Send to:

Choose Destination

SMPD3 sphingomyelin phosphodiesterase 3 [ Homo sapiens (human) ]

Gene ID: 55512, updated on 3-Oct-2018

Summary

Official Symbol
SMPD3provided by HGNC
Official Full Name
sphingomyelin phosphodiesterase 3provided by HGNC
Primary source
HGNC:HGNC:14240
See related
Ensembl:ENSG00000103056 MIM:605777; Vega:OTTHUMG00000137559
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NSMASE2
Expression
Biased expression in duodenum (RPKM 22.0), small intestine (RPKM 21.4) and 11 other tissues See more
Orthologs

Genomic context

See SMPD3 in Genome Data Viewer
Location:
16q22.1
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (68358327..68448703, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (68392230..68482409, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene solute carrier family 7 member 6 Neighboring gene solute carrier family 7 member 6 opposite strand Neighboring gene protein arginine methyltransferase 7 Neighboring gene RNA, U4 small nuclear 30, pseudogene Neighboring gene ribosomal protein L35a pseudogene 33 Neighboring gene uncharacterized LOC105371321

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env A redox-regulated translocation of neutral sphingomyelinase-2 to the plasma membrane is required for HIV-1 gp120-induced enlargement and stabilization of the structure of lipid microdomains on dendrites PubMed
env HIV-1 gp120 binding to CXCR4 induces NADPH oxidase-mediated production of superoxide radicals in neurons, which is involved in the activation of neutral sphingomyelinase PubMed
env In human primary neurons, HIV-1 gp120 induces the activation of sphingomyelinases (primarily neutral sphingomyelinase); antisense knockdown of neutral sphingomyelinase markedly inhibits gp120-mediated apoptosis and cell death of primary neurons PubMed
Nef nef HIV-1 Nef inhibits sphingomyelinase activity in human podocyte PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Ceramide signaling pathway, organism-specific biosystem (from Pathway Interaction Database)
    Ceramide signaling pathway, organism-specific biosystem
    Ceramide signaling pathway
  • Death Receptor Signalling, organism-specific biosystem (from REACTOME)
    Death Receptor Signalling, organism-specific biosystemThe death receptors, all cell-surface receptors, begin the process of caspase activation. The common feature of these type 1 transmembrane proteins is the "death-domain" a conserved cytoplasmic motif...
  • Glycosphingolipid metabolism, organism-specific biosystem (from REACTOME)
    Glycosphingolipid metabolism, organism-specific biosystemThe steps involved in the synthesis of glycosphingolipids (sphingolipids with one or more sugars attached) are annotated here (Gault et al. 2010).
  • Metabolic pathways, organism-specific biosystem (from KEGG)
    Metabolic pathways, organism-specific biosystem
    Metabolic pathways
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Sphingolipid metabolism, organism-specific biosystem (from KEGG)
    Sphingolipid metabolism, organism-specific biosystem
    Sphingolipid metabolism
  • Sphingolipid metabolism, organism-specific biosystem (from REACTOME)
    Sphingolipid metabolism, organism-specific biosystemSphingolipids are derivatives of long chain sphingoid bases such as sphingosine (trans-1,3-dihydroxy 2-amino-4-octadecene), an 18-carbon unsaturated amino alcohol which is the most abundant sphingoid...
  • Sphingolipid metabolism, conserved biosystem (from KEGG)
    Sphingolipid metabolism, conserved biosystem
    Sphingolipid metabolism
  • TNF signaling, organism-specific biosystem (from REACTOME)
    TNF signaling, organism-specific biosystemThe inflammatory cytokine tumor necrosis factor alpha (TNF-alpha) is expressed in immune and nonimmune cell types including macrophages, T cells, mast cells, granulocytes, natural killer (NK) cells, ...
  • TNFR1-mediated ceramide production, organism-specific biosystem (from REACTOME)
    TNFR1-mediated ceramide production, organism-specific biosystemTNF-alpha activates sphingomyelinase (SMASE) proteins to catalyze hydrolysis of sphingomyeline into ceramide. Two types of SMASE can be distinguished downstream of TNFR1 signaling, acid and neutral S...
  • sphingomyelin metabolism/ceramide salvage, organism-specific biosystem (from BIOCYC)
    sphingomyelin metabolism/ceramide salvage, organism-specific biosystemSphingomyelin is found in all tissues and lipoproteins; for example, it accounts for ~5% of the lipid phosphate in liver and 25% in pancreas . Sphingomyelin has a function in signal transduction . Th...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ22593, MGC138443

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sphingomyelin phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sphingomyelin phosphodiesterase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cell cycle IEA
Inferred from Electronic Annotation
more info
 
hematopoietic progenitor cell differentiation IEA
Inferred from Electronic Annotation
more info
 
peptide hormone secretion IEA
Inferred from Electronic Annotation
more info
 
positive regulation of ceramide biosynthetic process TAS
Traceable Author Statement
more info
 
positive regulation of exosomal secretion ISS
Inferred from Sequence or Structural Similarity
more info
 
sphingomyelin catabolic process TAS
Traceable Author Statement
more info
PubMed 
sphingomyelin metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
Golgi cis cisterna IEA
Inferred from Electronic Annotation
more info
 
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
sphingomyelin phosphodiesterase 3
Names
nSMase-2
neutral sphingomyelinase 2
neutral sphingomyelinase II
NP_061137.1
XP_005256088.1
XP_005256089.1
XP_011521509.1
XP_011521510.1
XP_011521511.1
XP_011521512.1
XP_016878894.1
XP_016878895.1
XP_016878896.1
XP_016878897.1

NCBI Reference Sequences (RefSeq)

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_018667.3NP_061137.1  sphingomyelin phosphodiesterase 3

    See identical proteins and their annotated locations for NP_061137.1

    Status: VALIDATED

    Source sequence(s)
    AC099521, AK289651, BC112238
    Consensus CDS
    CCDS10867.1
    UniProtKB/Swiss-Prot
    Q9NY59
    UniProtKB/TrEMBL
    A8K0T6
    Related
    ENSP00000219334.5, OTTHUMP00000174866, ENST00000219334.9, OTTHUMT00000268895
    Conserved Domains (2) summary
    cd09078
    Location:338646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    cl28033
    Location:171321
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region

RefSeqs of Annotated Genomes: Homo sapiens 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 GRCh38.p12 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

    Range
    68358327..68448703 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017023406.1XP_016878895.1  sphingomyelin phosphodiesterase 3 isoform X1

    UniProtKB/Swiss-Prot
    Q9NY59
    Conserved Domains (2) summary
    cd09078
    Location:338646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    cl28033
    Location:171321
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
  2. XM_011523207.1XP_011521509.1  sphingomyelin phosphodiesterase 3 isoform X1

    See identical proteins and their annotated locations for XP_011521509.1

    UniProtKB/Swiss-Prot
    Q9NY59
    Conserved Domains (2) summary
    cd09078
    Location:338646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    cl28033
    Location:171321
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
  3. XM_005256031.4XP_005256088.1  sphingomyelin phosphodiesterase 3 isoform X1

    See identical proteins and their annotated locations for XP_005256088.1

    UniProtKB/Swiss-Prot
    Q9NY59
    Conserved Domains (2) summary
    cd09078
    Location:338646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    cl28033
    Location:171321
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
  4. XM_017023405.1XP_016878894.1  sphingomyelin phosphodiesterase 3 isoform X1

    UniProtKB/Swiss-Prot
    Q9NY59
    Conserved Domains (2) summary
    cd09078
    Location:338646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    cl28033
    Location:171321
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
  5. XM_017023408.1XP_016878897.1  sphingomyelin phosphodiesterase 3 isoform X1

    UniProtKB/Swiss-Prot
    Q9NY59
    Conserved Domains (2) summary
    cd09078
    Location:338646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    cl28033
    Location:171321
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
  6. XM_017023407.1XP_016878896.1  sphingomyelin phosphodiesterase 3 isoform X1

    UniProtKB/Swiss-Prot
    Q9NY59
    Conserved Domains (2) summary
    cd09078
    Location:338646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    cl28033
    Location:171321
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
  7. XM_005256032.3XP_005256089.1  sphingomyelin phosphodiesterase 3 isoform X1

    See identical proteins and their annotated locations for XP_005256089.1

    UniProtKB/Swiss-Prot
    Q9NY59
    Conserved Domains (2) summary
    cd09078
    Location:338646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    cl28033
    Location:171321
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
  8. XM_011523209.2XP_011521511.1  sphingomyelin phosphodiesterase 3 isoform X1

    See identical proteins and their annotated locations for XP_011521511.1

    UniProtKB/Swiss-Prot
    Q9NY59
    Related
    ENSP00000455955.1, OTTHUMP00000256335, ENST00000563226.1, OTTHUMT00000436207
    Conserved Domains (2) summary
    cd09078
    Location:338646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    cl28033
    Location:171321
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
  9. XM_011523208.2XP_011521510.1  sphingomyelin phosphodiesterase 3 isoform X1

    See identical proteins and their annotated locations for XP_011521510.1

    UniProtKB/Swiss-Prot
    Q9NY59
    Conserved Domains (2) summary
    cd09078
    Location:338646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    cl28033
    Location:171321
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
  10. XM_011523210.2XP_011521512.1  sphingomyelin phosphodiesterase 3 isoform X2

    Conserved Domains (1) summary
    cl00490
    Location:338441
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

RNA

  1. XR_933371.2 RNA Sequence

Support Center