Format

Send to:

Choose Destination

SMPD3 sphingomyelin phosphodiesterase 3 [ Homo sapiens (human) ]

Gene ID: 55512, updated on 23-Nov-2021

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
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See SMPD3 in Genome Data Viewer
Location:
16q22.1
Exon count:
16
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (68358327..68448703, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (68392230..68482411, 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 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 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 PubChem

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
enables identical protein binding IEA
Inferred from Electronic Annotation
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 phosphatidic acid binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables phosphatidylserine binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables phospholipase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables sphingomyelin phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
 
involved_in DNA biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
involved_in G1 to G0 transition IEA
Inferred from Electronic Annotation
more info
 
involved_in bone growth IEA
Inferred from Electronic Annotation
more info
 
involved_in bone mineralization IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to hydrogen peroxide IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to magnesium ion IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to oxidised low-density lipoprotein particle stimulus IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to peptide IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to redox state IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to tumor necrosis factor IEA
Inferred from Electronic Annotation
more info
 
involved_in ceramide metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in chondrocyte development involved in endochondral bone morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in collagen metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in dentinogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in endochondral ossification IEA
Inferred from Electronic Annotation
more info
 
involved_in extracellular matrix assembly IEA
Inferred from Electronic Annotation
more info
 
involved_in hematopoietic progenitor cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in lung alveolus development IEA
Inferred from Electronic Annotation
more info
 
involved_in mitotic nuclear division IEA
Inferred from Electronic Annotation
more info
 
involved_in multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of hyaluronan biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
involved_in peptide hormone secretion IEA
Inferred from Electronic Annotation
more info
 
involved_in platelet-derived growth factor receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in polysaccharide transport IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of exosomal secretion ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of mitotic nuclear division IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of smooth muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in protein kinase B signaling IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of cartilage development IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of leukocyte migration IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of protein phosphorylation IEA
Inferred from Electronic Annotation
more info
 
involved_in sphingolipid mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in sphingomyelin catabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in sphingomyelin metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in sphingomyelin metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
located_in Golgi cis cisterna IEA
Inferred from Electronic Annotation
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
PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in 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)

NEW Try the new Transcript table

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_018667.4NP_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, ENST00000219334.10
    Conserved Domains (2) summary
    cd09078
    Location:338646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    PHA03307
    Location:171321
    PHA03307; transcriptional regulator ICP4; Provisional

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 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
    PHA03307
    Location:171321
    PHA03307; transcriptional regulator ICP4; Provisional
  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
    PHA03307
    Location:171321
    PHA03307; transcriptional regulator ICP4; Provisional
  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
    PHA03307
    Location:171321
    PHA03307; transcriptional regulator ICP4; Provisional
  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
    PHA03307
    Location:171321
    PHA03307; transcriptional regulator ICP4; Provisional
  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
    PHA03307
    Location:171321
    PHA03307; transcriptional regulator ICP4; Provisional
  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
    PHA03307
    Location:171321
    PHA03307; transcriptional regulator ICP4; Provisional
  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
    PHA03307
    Location:171321
    PHA03307; transcriptional regulator ICP4; Provisional
  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, ENST00000563226.1
    Conserved Domains (2) summary
    cd09078
    Location:338646
    nSMase; Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine
    PHA03307
    Location:171321
    PHA03307; transcriptional regulator ICP4; Provisional
  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
    PHA03307
    Location:171321
    PHA03307; transcriptional regulator ICP4; Provisional
  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