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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 3 4
  • NSMASE-3 3 4
  • NSMASE3 3 4
  • Neutral Sphingomyelinase-3 2
  • 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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
- Elite enhancer/Elite enhancer-gene association

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

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

Animal Models for SMPD4 Gene

MGI Knock Outs for SMPD4:

Animal Model Products

CRISPR Products

miRNA for SMPD4 Gene

miRTarBase miRNAs that target SMPD4

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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: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 & 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:0006685 sphingomyelin catabolic process IDA 16517606
GO:0006687 glycosphingolipid metabolic process TAS --
GO:0046475 glycerophospholipid catabolic process IDA 16517606
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

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphatidyl serine Approved Nutra Target 0
Water Approved Pharma 0
PHOSPHATIDYLSERINE 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:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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, MaxQB, and MOPED for SMPD4 Gene



Protein tissue co-expression partners for SMPD4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SMPD4 Gene:

SMPD4

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

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 34
  • 83.58 (n)
  • 87.17 (a)
SMPD4 35
  • 86 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMPD4 34
  • 88.52 (n)
  • 91.21 (a)
SMPD4 35
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Smpd4 34
  • 85.6 (n)
  • 90.27 (a)
Smpd4 16
Smpd4 35
  • 90 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SMPD4 34
  • 96.41 (n)
  • 95.95 (a)
rat
(Rattus norvegicus)
Mammalia Smpd4 34
  • 86.37 (n)
  • 90.88 (a)
oppossum
(Monodelphis domestica)
Mammalia SMPD4 35
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 70 (a)
OneToMany
-- 35
  • 73 (a)
OneToMany
chicken
(Gallus gallus)
Aves SMPD4 34
  • 70.63 (n)
  • 75.15 (a)
SMPD4 35
  • 74 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMPD4 35
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smpd4 34
  • 66.12 (n)
  • 67.43 (a)
Str.6070 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.4713 34
zebrafish
(Danio rerio)
Actinopterygii smpd4 34
  • 64.59 (n)
  • 63.96 (a)
wufb22d05 34
smpd4 35
  • 63 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4009 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000405 34
  • 48.41 (n)
  • 33.7 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG6962 34
  • 43.27 (n)
  • 29.53 (a)
CG6962 35
  • 25 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 32 (a)
OneToOne
Species where no ortholog for SMPD4 was found in the sources mined by GeneCards:
  • 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
rs6985 -- 130,151,488(-) CTGAG(A/C/G/T)ATAAT nc-transcript-variant, utr-variant-3-prime
rs2261286 -- 130,154,583(+) GAGCC(A/C)TGACC intron-variant
rs4511676 -- 130,153,274(+) GGGAC(A/G)GGTCA intron-variant
rs2290296 -- 130,157,224(+) GGCAG(C/T)GGTGG 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
dgv2032n106 OTHER inversion 24896259
dgv4072n100 CNV loss 25217958
dgv4073n100 CNV gain 25217958
dgv7079n54 CNV loss 21841781
esv2751826 CNV gain 17911159
esv2759092 CNV gain+loss 17122850
esv2760631 CNV gain+loss 21179565
esv2763387 CNV loss 21179565
esv3584065 CNV loss 25503493
esv3592440 CNV loss 21293372
esv3592441 CNV gain 21293372
esv3893326 CNV gain 25118596
nsv1001337 CNV loss 25217958
nsv1004301 CNV loss 25217958
nsv1005664 CNV loss 25217958
nsv1008911 CNV gain 25217958
nsv1008970 CNV loss 25217958
nsv1011360 CNV loss 25217958
nsv428403 CNV loss 18775914
nsv459274 CNV loss 19166990
nsv482053 CNV gain 20164927
nsv520559 CNV gain+loss 19592680
nsv583046 CNV loss 21841781
nsv583113 CNV gain 21841781
nsv7327 OTHER inversion 18451855
nsv821629 CNV loss 15273396
nsv834375 CNV loss 17160897
nsv961882 CNV duplication 23825009
nsv998333 CNV gain+loss 25217958

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)

Relevant External Links for SMPD4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
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
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 65
  2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 46 65
  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 65
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 65
  5. 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 65

Products for SMPD4 Gene

Sources for SMPD4 Gene

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