Format

Send to:

Choose Destination

Links from PubMed

    • Showing Current items.

    SMPD2 sphingomyelin phosphodiesterase 2 [ Homo sapiens (human) ]

    Gene ID: 6610, updated on 8-Apr-2018
    Official Symbol
    SMPD2provided by HGNC
    Official Full Name
    sphingomyelin phosphodiesterase 2provided by HGNC
    Primary source
    HGNC:HGNC:11121
    See related
    Ensembl:ENSG00000135587 MIM:603498; Vega:OTTHUMG00000015348
    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
    ISC1; NSMASE; NSMASE1
    Summary
    This gene encodes a protein which was initially identified as a sphingomyelinase based on sequence similarity between bacterial sphingomyelinases and a yeast protein. Subsequent studies showed that its biological function is less likely to be as a sphingomyelinase and instead as a lysophospholipase. [provided by RefSeq, Oct 2009]
    Expression
    Broad expression in testis (RPKM 17.9), skin (RPKM 6.8) and 24 other tissues See more
    Orthologs
    Location:
    6q21
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (109440721..109443922)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (109761849..109765125)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 162, pseudogene Neighboring gene uncharacterized LOC101927538 Neighboring gene CD164 molecule Neighboring gene peptidylprolyl isomerase like 6 Neighboring gene uncharacterized LOC105377935 Neighboring gene microtubule associated monooxygenase, calponin and LIM domain containing 1 Neighboring gene zinc finger and BTB domain containing 24 Neighboring gene adenylate kinase 9

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Treatment of cells with sphingomyelinase inhibits viral fusion after the engagement of HIV-1 gp120 with CD4 and sphingomyelinase restricts CD4 mobility. This inhibition is dependent on CD4 expression levels 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

    • Ceramide signalling, organism-specific biosystem (from REACTOME)
      Ceramide signalling, organism-specific biosystemIn certain cell types, ligand binding to p75NTR leads to ceramide production, which can mediate either cell survival (e.g. in noecotical subplate neurons) or apoptosis (e.g. in oligodendrocytes). Low...
    • 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...
    • Signal Transduction of S1P Receptor, organism-specific biosystem (from WikiPathways)
      Signal Transduction of S1P Receptor, organism-specific biosystemMetabolism of sphingomyelin by the sphingomyelinase, ceramidase (Cer'ase) and the sphingosine kinase (SK) enzymes results in formation of S1P and receptor activation. Autocrine and paracrine modes of...
    • Signalling by NGF, organism-specific biosystem (from REACTOME)
      Signalling by NGF, organism-specific biosystemNeurotrophins (NGF, BDNF, NT-3, NT-4/5) play pivotal roles in survival, differentiation, and plasticity of neurons in the peripheral and central nervous system. They are produced, and secreted in mi...
    • 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
    • Sphingolipid signaling pathway, organism-specific biosystem (from KEGG)
      Sphingolipid signaling pathway, organism-specific biosystemSphingomyelin (SM) and its metabolic products are now known to have second messenger functions in a variety of cellular signaling pathways. Particularly, the sphingolipid metabolites, ceramide (Cer) ...
    • Sphingolipid signaling pathway, conserved biosystem (from KEGG)
      Sphingolipid signaling pathway, conserved biosystemSphingomyelin (SM) and its metabolic products are now known to have second messenger functions in a variety of cellular signaling pathways. Particularly, the sphingolipid metabolites, ceramide (Cer) ...
    • TNF alpha Signaling Pathway, organism-specific biosystem (from WikiPathways)
      TNF alpha Signaling Pathway, organism-specific biosystemTumor necrosis factor alpha (TNF?) is a proinflammatory cytokine involved in various biological processes including regulation of cell proliferation, differentiation, apoptosis and immune response. T...
    • TNF receptor signaling pathway, organism-specific biosystem (from Pathway Interaction Database)
      TNF receptor signaling pathway, organism-specific biosystem
      TNF receptor signaling pathway
    • 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...
    • p75 NTR receptor-mediated signalling, organism-specific biosystem (from REACTOME)
      p75 NTR receptor-mediated signalling, organism-specific biosystemBesides signalling through the tyrosine kinase receptors TRK A, B, and C, the mature neurotrophins NGF, BDNF, and NT3/4 signal through their common receptor p75NTR. NGF binding to p75NTR activates a ...
    • p75(NTR)-mediated signaling, organism-specific biosystem (from Pathway Interaction Database)
      p75(NTR)-mediated signaling, organism-specific biosystem
      p75(NTR)-mediated signaling
    • 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...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    phospholipase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    sphingomyelin phosphodiesterase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    sphingomyelin phosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    ceramide biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    ceramide biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    glycosphingolipid metabolic process TAS
    Traceable Author Statement
    more info
     
    intracellular signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of ceramide biosynthetic process TAS
    Traceable Author Statement
    more info
     
    response to mechanical stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    sphingolipid catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    sphingomyelin metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    sphingomyelin metabolic process TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    caveola IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    caveola IEA
    Inferred from Electronic Annotation
    more info
     
    cell periphery IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    integral component of plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    intracellular IEA
    Inferred from Electronic Annotation
    more info
     
    membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    sphingomyelin phosphodiesterase 2
    Names
    N-SMase
    lyso-PAF-PLC
    lyso-platelet-activating factor-phospholipase C
    neutral sphingomyelinase
    NP_003071.2
    XP_005267166.1
    XP_011534381.1
    XP_024302294.1
    XP_024302295.1

    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_003080.2NP_003071.2  sphingomyelin phosphodiesterase 2

      See identical proteins and their annotated locations for NP_003071.2

      Status: VALIDATED

      Source sequence(s)
      AJ222801, CA314251, DA672570
      Consensus CDS
      CCDS5075.1
      UniProtKB/Swiss-Prot
      O60906
      Related
      ENSP00000258052.3, OTTHUMP00000016965, ENST00000258052.7, OTTHUMT00000041755
      Conserved Domains (1) summary
      cl00490
      Location:14279
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    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_000006.12 Reference GRCh38.p12 Primary Assembly

      Range
      109440721..109443922
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024446526.1XP_024302294.1  sphingomyelin phosphodiesterase 2 isoform X1

      Conserved Domains (1) summary
      cl00490
      Location:14321
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
    2. XM_024446527.1XP_024302295.1  sphingomyelin phosphodiesterase 2 isoform X3

    3. XM_005267109.1XP_005267166.1  sphingomyelin phosphodiesterase 2 isoform X3

    4. XM_011536079.1XP_011534381.1  sphingomyelin phosphodiesterase 2 isoform X2

      Conserved Domains (1) summary
      cl00490
      Location:6174
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    RNA

    1. XR_942566.2 RNA Sequence

    Support Center