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SMPD2 sphingomyelin phosphodiesterase 2 [ Homo sapiens (human) ]

Gene ID: 6610, updated on 21-Dec-2019

Summary

Official Symbol
SMPD2provided by HGNC
Official Full Name
sphingomyelin phosphodiesterase 2provided by HGNC
Primary source
HGNC:HGNC:11121
See related
Ensembl:ENSG00000135587 MIM:603498
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

Genomic context

See SMPD2 in Genome Data Viewer
Location:
6q21
Exon count:
10
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 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

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
sphingomyelin phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
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
 
sphingomyelin catabolic process IEA
Inferred from Electronic Annotation
more info
 
sphingomyelin metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
caveola IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

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

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_003080.3NP_003071.2  sphingomyelin phosphodiesterase 2

    See identical proteins and their annotated locations for NP_003071.2

    Status: VALIDATED

    Source sequence(s)
    AJ222801, AL109947, CA314251, DA672570
    Consensus CDS
    CCDS5075.1
    UniProtKB/Swiss-Prot
    O60906
    Related
    ENSP00000258052.3, ENST00000258052.8
    Conserved Domains (1) summary
    cl00490
    Location:14279
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 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

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