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Aliases for SMPD4 Gene

Aliases for SMPD4 Gene

  • Sphingomyelin Phosphodiesterase 4, Neutral Membrane (Neutral Sphingomyelinase-3) 2 3
  • NSMASE3 3 4 6
  • Neutral Sphingomyelinase III 3 4
  • Neutral Sphingomyelinase 3 3 4
  • NSMASE-3 3 4
  • KIAA1418 4 6
  • Sphingomyelin Phosphodiesterase 4 3
  • SKNY Protein 3
  • EC 3.1.4.12 4
  • NET13 3

External Ids for SMPD4 Gene

Summaries for SMPD4 Gene

Entrez Gene Summary for SMPD4 Gene

  • Sphingomyelinases (EC 3.1.4.12), such as SMPD4, catalyze the hydrolysis of membrane sphingomyelin to form phosphorylcholine and ceramide (Krut et al., 2006 [PubMed 16517606]).[supplied by OMIM, Mar 2008]

GeneCards Summary for SMPD4 Gene

SMPD4 (Sphingomyelin Phosphodiesterase 4, Neutral Membrane (Neutral Sphingomyelinase-3)) is a Protein Coding gene. Among its related pathways are Sphingolipid metabolism and Sphingolipid metabolism. GO annotations related to this gene include sphingomyelin phosphodiesterase activity and sphingomyelin phosphodiesterase D activity.

UniProtKB/Swiss-Prot for SMPD4 Gene

  • Catalyzes the hydrolysis of membrane sphingomyelin to form phosphorylcholine and ceramide.

Gene Wiki entry for SMPD4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMPD4 Gene

Genomics for SMPD4 Gene

Genomic Location for SMPD4 Gene

Start:
130,151,392 bp from pter
End:
130,182,750 bp from pter
Size:
31,359 bases
Orientation:
Minus strand

Genomic View for SMPD4 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SMPD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMPD4 Gene

Regulatory Elements for SMPD4 Gene

Proteins for SMPD4 Gene

  • Protein details for SMPD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NXE4-NSMA3_HUMAN
    Recommended name:
    Sphingomyelin phosphodiesterase 4
    Protein Accession:
    Q9NXE4
    Secondary Accessions:
    • B4DM23
    • B4DQ31
    • B4DRB8
    • B4DWK7
    • B4E0L6
    • E7ESA2
    • E9PCE6
    • Q6FI76
    • Q6P1P7
    • Q6ZT43
    • Q9H0M2
    • Q9NW20
    • Q9NWL2
    • Q9P2C9

    Protein attributes for SMPD4 Gene

    Size:
    827 amino acids
    Molecular mass:
    93352 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA91368.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA91567.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA92656.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SMPD4 Gene

neXtProt entry for SMPD4 Gene

Proteomics data for SMPD4 Gene at MOPED

Post-translational modifications for SMPD4 Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys106, Lys238, Lys461, Lys529, Lys541, Lys565, and Lys621

No data available for DME Specific Peptides for SMPD4 Gene

Domains for SMPD4 Gene

Protein Domains for SMPD4 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SMPD4: view

No data available for Gene Families and UniProtKB/Swiss-Prot for SMPD4 Gene

Function for SMPD4 Gene

Molecular function for SMPD4 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties: pH dependence: Optimum pH is 7.0. {ECO:0000269 PubMed:16517606};
UniProtKB/Swiss-Prot CatalyticActivity: Sphingomyelin + H(2)O = N-acylsphingosine + phosphocholine
UniProtKB/Swiss-Prot EnzymeRegulation: Activated by phosphatidylserine and tumor necrosis factor (TNF). Inhibited by scyphostatin.
UniProtKB/Swiss-Prot Function: Catalyzes the hydrolysis of membrane sphingomyelin to form phosphorylcholine and ceramide.

Enzyme Numbers (IUBMB) for SMPD4 Gene

Gene Ontology (GO) - Molecular Function for SMPD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004767 sphingomyelin phosphodiesterase activity TAS --
GO:0046872 metal ion binding IEA --
GO:0050290 sphingomyelin phosphodiesterase D activity IDA 16517606
genes like me logo Genes that share ontologies with SMPD4: view

miRNA for SMPD4 Gene

miRTarBase miRNAs that target SMPD4

No data available for Phenotypes , Animal Models , Transcription Factor Targeting and HOMER Transcription for SMPD4 Gene

Localization for SMPD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMPD4 Gene

Endoplasmic reticulum membrane; Single-pass membrane protein. Golgi apparatus membrane; Single-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SMPD4 Gene COMPARTMENTS Subcellular localization image for SMPD4 gene
Compartment Confidence
endoplasmic reticulum 5
golgi apparatus 5
plasma membrane 3
lysosome 1
mitochondrion 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for SMPD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005783 endoplasmic reticulum IDA 16517606
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0005794 Golgi apparatus IDA 16517606
GO:0005802 trans-Golgi network IDA 16517606
genes like me logo Genes that share ontologies with SMPD4: view

Pathways for SMPD4 Gene

genes like me logo Genes that share pathways with SMPD4: view

Pathways by source for SMPD4 Gene

Gene Ontology (GO) - Biological Process for SMPD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006665 sphingolipid metabolic process TAS --
GO:0006685 sphingomyelin catabolic process IDA 16517606
GO:0006687 glycosphingolipid metabolic process TAS --
GO:0008152 metabolic process --
GO:0044281 small molecule metabolic process TAS --
genes like me logo Genes that share ontologies with SMPD4: view

Compounds for SMPD4 Gene

(277) HMDB Compounds for SMPD4 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 SMPD4 Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Phosphatidylserine
  • 3-O-sn-Phosphatidyl-L-serine
8002-43-5 target
genes like me logo Genes that share compounds with SMPD4: view

Transcripts for SMPD4 Gene

Unigene Clusters for SMPD4 Gene

Sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SMPD4 Gene

No ASD Table

Relevant External Links for SMPD4 Gene

GeneLoc Exon Structure for
SMPD4
ECgene alternative splicing isoforms for
SMPD4

Expression for SMPD4 Gene

mRNA expression in normal human tissues for SMPD4 Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for SMPD4 Gene

SOURCE GeneReport for Unigene cluster for SMPD4 Gene Hs.516450

mRNA Expression by UniProt/SwissProt for SMPD4 Gene

Q9NXE4-NSMA3_HUMAN
Tissue specificity: Widely expressed, with highest levels in heart and skeletal muscle.
genes like me logo Genes that share expressions with SMPD4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for SMPD4 Gene

Orthologs for SMPD4 Gene

This gene was present in the common ancestor of animals.

Orthologs for SMPD4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMPD4 35
  • 96.41 (n)
  • 95.95 (a)
cow
(Bos Taurus)
Mammalia SMPD4 35
  • 83.58 (n)
  • 87.17 (a)
SMPD4 36
  • 86 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMPD4 35
  • 88.52 (n)
  • 91.21 (a)
SMPD4 36
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Smpd4 35
  • 85.6 (n)
  • 90.27 (a)
Smpd4 16
Smpd4 36
  • 90 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMPD4 36
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 70 (a)
OneToMany
-- 36
  • 73 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Smpd4 35
  • 86.37 (n)
  • 90.88 (a)
chicken
(Gallus gallus)
Aves SMPD4 35
  • 70.63 (n)
  • 75.15 (a)
SMPD4 36
  • 74 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMPD4 36
  • 61 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.4713 35
tropical clawed frog
(Silurana tropicalis)
Amphibia smpd4 35
  • 66.12 (n)
  • 67.43 (a)
Str.6070 35
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4009 35
zebrafish
(Danio rerio)
Actinopterygii smpd4 35
  • 64.59 (n)
  • 63.96 (a)
smpd4 36
  • 63 (a)
OneToOne
wufb22d05 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000405 35
  • 48.41 (n)
  • 33.7 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG6962 35
  • 43.27 (n)
  • 29.53 (a)
CG6962 36
  • 25 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 32 (a)
OneToOne
Species with no ortholog for SMPD4:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • 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 SMPD4 Gene

ENSEMBL:
Gene Tree for SMPD4 (if available)
TreeFam:
Gene Tree for SMPD4 (if available)

Paralogs for SMPD4 Gene

genes like me logo Genes that share paralogs with SMPD4: view

No data available for Paralogs for SMPD4 Gene

Variants for SMPD4 Gene

Sequence variations from dbSNP and Humsavar for SMPD4 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type MAF
rs6985 -- 130,151,488(-) CTGAG(A/C)ATAAT utr-variant-3-prime, nc-transcript-variant
rs2084784 -- 130,158,842(+) GGCCC(A/G)GCCTC intron-variant
rs2122970 -- 130,174,953(-) GCAGT(C/G)GCAAG frameshift-variant, nc-transcript-variant, utr-variant-5-prime
rs2261286 -- 130,154,583(+) GAGCC(A/C)TGACC intron-variant
rs2313836 -- 130,150,956(-) AGCGG(A/G)GGGCA downstream-variant-500B

Structural Variations from Database of Genomic Variants (DGV) for SMPD4 Gene

Variant ID Type Subtype PubMed ID
nsv821629 CNV Loss 15273396
nsv459274 CNV Loss 19166990
dgv1247e1 CNV Complex 17122850
esv2751826 CNV Gain 17911159
dgv1249e1 CNV Complex 17122850
dgv1250e1 CNV Complex 17122850
nsv428403 CNV Loss 18775914
dgv4305n71 CNV Gain 21882294
dgv4306n71 CNV Gain 21882294
essv1878 CNV CNV 17122850
nsv875061 CNV Gain 21882294
nsv834375 CNV Loss 17160897
nsv7327 OTHER Inversion 18451855
nsv875074 CNV Gain 21882294
dgv4307n71 CNV Gain 21882294
nsv520559 CNV Gain+Loss 19592680
nsv875084 CNV Gain+Loss 21882294
nsv482053 CNV Gain 20164927
nsv875086 CNV Gain 21882294
nsv875087 CNV Gain 21882294
dgv4308n71 CNV Gain 21882294

Relevant External Links for SMPD4 Gene

HapMap Linkage Disequilibrium report
SMPD4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMPD4 Gene

Disorders for SMPD4 Gene

Relevant External Links for SMPD4

Genetic Association Database (GAD)
SMPD4
Human Genome Epidemiology (HuGE) Navigator
SMPD4
genes like me logo Genes that share disorders with SMPD4: view

No data available for UniProtKB/Swiss-Prot for SMPD4 Gene

Publications for SMPD4 Gene

  1. 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) 2 3 4 25
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  3. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier L.W. … Wilson R.K. (Nature 2005) 3 4
  4. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10718198) Nagase T. … Ohara O. (DNA Res. 2000) 3 4
  5. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S. … Poustka A. (Genome Res. 2001) 3 4

Products for SMPD4 Gene

Sources for SMPD4 Gene

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