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Aliases for SMPD4 Gene

Aliases for SMPD4 Gene

  • Sphingomyelin Phosphodiesterase 4 2 3 5
  • Sphingomyelin Phosphodiesterase 4, Neutral Membrane (Neutral Sphingomyelinase-3) 2 3
  • Neutral Sphingomyelinase III 3 4
  • Neutral Sphingomyelinase-3 2 3
  • Neutral Sphingomyelinase 3 3 4
  • NSMASE-3 3 4
  • NSMASE3 3 4
  • SKNY Protein 3
  • EC 3.1.4.12 4
  • KIAA1418 4
  • NET13 3

External Ids for SMPD4 Gene

Previous GeneCards Identifiers for SMPD4 Gene

  • GC02M130626
  • GC02M130908
  • GC02M123204

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) is a Protein Coding gene. Among its related pathways are Sphingolipid metabolism and 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

Regulatory Elements for SMPD4 Gene

Enhancers for SMPD4 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around SMPD4 on UCSC Golden Path with GeneCards custom track

Promoters for SMPD4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SMPD4 on UCSC Golden Path with GeneCards custom track

Genomic Location for SMPD4 Gene

Chromosome:
2
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

Genes around SMPD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMPD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMPD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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

  • Ubiquitination at Lys 106, Lys 238, Lys 461, Lys 529, Lys 541, Lys 565, and Lys 621
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SMPD4 Gene

Domains & Families 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:0050290 sphingomyelin phosphodiesterase D activity IEA,IDA 16517606
genes like me logo Genes that share ontologies with SMPD4: view
genes like me logo Genes that share phenotypes with SMPD4: view

Animal Models for SMPD4 Gene

MGI Knock Outs for SMPD4:

Animal Model Products

miRNA for SMPD4 Gene

miRTarBase miRNAs that target SMPD4

No data available for Human Phenotype Ontology , Transcription Factor Targets 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 4
plasma membrane 3
lysosome 1
mitochondrion 1
nucleus 1
peroxisome 1
vacuole 1

Gene Ontology (GO) - Cellular Components for SMPD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SMPD4: view

Pathways & Interactions 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:0008152 metabolic process IEA --
GO:0044281 small molecule metabolic process TAS --
GO:0046513 ceramide biosynthetic process IDA 16517606
GO:0071356 cellular response to tumor necrosis factor IDA 16517606
genes like me logo Genes that share ontologies with SMPD4: view

No data available for SIGNOR curated interactions for SMPD4 Gene

Drugs & Compounds for SMPD4 Gene

(3) Drugs for SMPD4 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphatidylserine Approved Nutra Target 0
Phosphocholine Experimental Pharma 0
Magnesium Nutra 0

(246) Additional Compounds for SMPD4 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
3-O-Sulfogalactosylceramide (d18:1/12:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
852100-88-0
3-O-Sulfogalactosylceramide (d18:1/14:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
3-O-Sulfogalactosylceramide (d18:1/16:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
862509-48-6
3-O-Sulfogalactosylceramide (d18:1/18:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
244215-65-4
3-O-Sulfogalactosylceramide (d18:1/18:1(9Z))
  • 3'-O-Sulphogalactosylceramide
  • 3-O-Sulfo-beta-D-galactosylceramide
  • 3-O-Sulfo-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
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

Protein differential expression in normal tissues from HIPED for SMPD4 Gene

This gene is overexpressed in Bone (8.8) and Peripheral blood mononuclear cells (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with SMPD4: view

Protein tissue co-expression partners for SMPD4 Gene

- Elite partner

Primer Products

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
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
chimpanzee
(Pan troglodytes)
Mammalia SMPD4 35
  • 96.41 (n)
  • 95.95 (a)
rat
(Rattus norvegicus)
Mammalia Smpd4 35
  • 86.37 (n)
  • 90.88 (a)
oppossum
(Monodelphis domestica)
Mammalia SMPD4 36
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 70 (a)
OneToMany
-- 36
  • 73 (a)
OneToMany
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
tropical clawed frog
(Silurana tropicalis)
Amphibia smpd4 35
  • 66.12 (n)
  • 67.43 (a)
Str.6070 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.4713 35
zebrafish
(Danio rerio)
Actinopterygii smpd4 35
  • 64.59 (n)
  • 63.96 (a)
wufb22d05 35
smpd4 36
  • 63 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4009 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
rs2897670 -- 130,151,003(+) ATCCT(C/T)AGAGC downstream-variant-500B
rs2897674 -- 130,171,406(+) CCTAC(A/G)TATAT intron-variant
rs2923817 -- 130,158,055(+) ggatc(A/T)cttca intron-variant
rs3100091 -- 130,151,282(-) CCTGG(A/G)CCTCT downstream-variant-500B
rs3192414 -- 130,152,309(-) CAGCG(C/G)CGGCC nc-transcript-variant, utr-variant-3-prime

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

Variation tolerance for SMPD4 Gene

Residual Variation Intolerance Score: 40.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.24; 52.56% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for SMPD4 Gene

Disorders for SMPD4 Gene

Relevant External Links for SMPD4

Genetic Association Database (GAD)
SMPD4
Human Genome Epidemiology (HuGE) Navigator
SMPD4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMPD4

No disorders were found for SMPD4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas 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 26 67
  2. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. (PMID: 25609649) Li X. … Chen J. (Mol. Syst. Biol. 2015) 3
  3. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 3
  4. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein M.Y. … Mann M. (Cell 2015) 3
  5. A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface. (PMID: 26638075) Gupta G.D. … Pelletier L. (Cell 2015) 3

Products for SMPD4 Gene

Sources for SMPD4 Gene

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