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Aliases for SMPDL3A Gene

Aliases for SMPDL3A Gene

  • Sphingomyelin Phosphodiesterase Acid Like 3A 2 3
  • Sphingomyelin Phosphodiesterase Acid-Like 3A 2 3 5
  • ASM-Like Phosphodiesterase 3a 3 4
  • ASML3a 3 4
  • Acid Sphingomyelinase-Like Phosphodiesterase 3a 2
  • Sphingomyelin Phosphodiesterase, Acid-Like 3A 3
  • 0610010C24Rik 3
  • EC 3.1.4.- 4
  • YR36GH4.1 3
  • EC 3.1.4 63
  • ASM3A 3

External Ids for SMPDL3A Gene

Previous GeneCards Identifiers for SMPDL3A Gene

  • GC06P123090
  • GC06P123091
  • GC06P123152
  • GC06P120686
  • GC06P123112

Summaries for SMPDL3A Gene

GeneCards Summary for SMPDL3A Gene

SMPDL3A (Sphingomyelin Phosphodiesterase Acid Like 3A) is a Protein Coding gene. GO annotations related to this gene include hydrolase activity and sphingomyelin phosphodiesterase activity. An important paralog of this gene is SMPDL3B.

UniProtKB/Swiss-Prot for SMPDL3A Gene

  • Has in vitro nucleotide phosphodiesterase activity with nucleoside triphosphates, such as ATP (PubMed:25288789, PubMed:26783088). Has in vitro activity with p-nitrophenyl-TMP (PubMed:25288789). Has lower activity with nucleoside diphosphates, and no activity with nucleoside monophosphates (PubMed:25288789, PubMed:26783088). Has in vitro activity with CDP-choline, giving rise to CMP and phosphocholine. Has in vitro activity with CDP-ethanolamine (PubMed:26783088). Does not have sphingomyelin phosphodiesterase activity (PubMed:25288789, PubMed:26783088).

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMPDL3A Gene

Genomics for SMPDL3A Gene

Regulatory Elements for SMPDL3A Gene

Enhancers for SMPDL3A 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 SMPDL3A on UCSC Golden Path with GeneCards custom track

Promoters for SMPDL3A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SMPDL3A on UCSC Golden Path with GeneCards custom track

Genomic Location for SMPDL3A Gene

Chromosome:
6
Start:
122,788,456 bp from pter
End:
122,809,720 bp from pter
Size:
21,265 bases
Orientation:
Plus strand

Genomic View for SMPDL3A Gene

Genes around SMPDL3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMPDL3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMPDL3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMPDL3A Gene

Proteins for SMPDL3A Gene

  • Protein details for SMPDL3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92484-ASM3A_HUMAN
    Recommended name:
    Acid sphingomyelinase-like phosphodiesterase 3a
    Protein Accession:
    Q92484
    Secondary Accessions:
    • B7Z729
    • Q8WV13

    Protein attributes for SMPDL3A Gene

    Size:
    453 amino acids
    Molecular mass:
    51260 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Monomer.

    Three dimensional structures from OCA and Proteopedia for SMPDL3A Gene

    Alternative splice isoforms for SMPDL3A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMPDL3A Gene

Proteomics data for SMPDL3A Gene at MOPED

Selected DME Specific Peptides for SMPDL3A Gene

Post-translational modifications for SMPDL3A Gene

  • N-glycosylated.
  • Glycosylation at Asn 69, Asn 131, Asn 222, Asn 238, Asn 263, Asn 356, and Asn 437
  • Modification sites at PhosphoSitePlus

Other Protein References for SMPDL3A Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for SMPDL3A Gene

Protein Domains for SMPDL3A Gene

Graphical View of Domain Structure for InterPro Entry

Q92484

UniProtKB/Swiss-Prot:

ASM3A_HUMAN :
  • Belongs to the acid sphingomyelinase family.
Family:
  • Belongs to the acid sphingomyelinase family.
genes like me logo Genes that share domains with SMPDL3A: view

No data available for Gene Families for SMPDL3A Gene

Function for SMPDL3A Gene

Molecular function for SMPDL3A Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=326 uM for ATP {ECO:0000269 PubMed:26783088}; KM=306 uM for ADP {ECO:0000269 PubMed:26783088}; KM=348 uM for ADP-ribose {ECO:0000269 PubMed:26783088}; KM=390 uM for CDP-ethanolamine {ECO:0000269 PubMed:26783088}; KM=262 uM for CDP-choline {ECO:0000269 PubMed:26783088}; pH dependence: Optimum pH is 4-6. {ECO:0000269 PubMed:25288789};
UniProtKB/Swiss-Prot EnzymeRegulation:
Requires micromolar levels of Zn(2+) for activity (PubMed:26783088). Inhibited by millimolar levels of Zn(2+) (PubMed:25288789, PubMed:26783088).
UniProtKB/Swiss-Prot Function:
Has in vitro nucleotide phosphodiesterase activity with nucleoside triphosphates, such as ATP (PubMed:25288789, PubMed:26783088). Has in vitro activity with p-nitrophenyl-TMP (PubMed:25288789). Has lower activity with nucleoside diphosphates, and no activity with nucleoside monophosphates (PubMed:25288789, PubMed:26783088). Has in vitro activity with CDP-choline, giving rise to CMP and phosphocholine. Has in vitro activity with CDP-ethanolamine (PubMed:26783088). Does not have sphingomyelin phosphodiesterase activity (PubMed:25288789, PubMed:26783088).
UniProtKB/Swiss-Prot Induction:
Up-regulated in macrophages in response to cholesterol accumulation. Up-regulated by cAMP.

Enzyme Numbers (IUBMB) for SMPDL3A Gene

Gene Ontology (GO) - Molecular Function for SMPDL3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004767 NOT sphingomyelin phosphodiesterase activity IDA 26783088
GO:0005515 protein binding IPI 12442002
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with SMPDL3A: view
genes like me logo Genes that share phenotypes with SMPDL3A: view

Animal Model Products

  • Taconic Biosciences Mouse Models for SMPDL3A

CRISPR Products

miRNA for SMPDL3A Gene

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SMPDL3A Gene

Localization for SMPDL3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMPDL3A Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SMPDL3A Gene COMPARTMENTS Subcellular localization image for SMPDL3A gene
Compartment Confidence
extracellular 5
lysosome 3
vacuole 3
mitochondrion 2
nucleus 2

No data available for Gene Ontology (GO) - Cellular Components for SMPDL3A Gene

Pathways & Interactions for SMPDL3A Gene

SuperPathways for SMPDL3A Gene

No Data Available

Interacting Proteins for SMPDL3A Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000357425%0d%0a9606.ENSP00000265922%0d%0a
Selected Interacting proteins: ENSP00000357425 Q92484-ASM3A_HUMAN for SMPDL3A Gene via STRING I2D

Gene Ontology (GO) - Biological Process for SMPDL3A Gene

None

No data available for Pathways by source and SIGNOR curated interactions for SMPDL3A Gene

Drugs & Compounds for SMPDL3A Gene

No Compound Related Data Available

Transcripts for SMPDL3A Gene

Unigene Clusters for SMPDL3A Gene

Sphingomyelin phosphodiesterase, acid-like 3A:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SMPDL3A Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b
SP1: -
SP2: - - - -
SP3: - - - - - -
SP4: - - - - -
SP5: - -
SP6:
SP7: -

Relevant External Links for SMPDL3A Gene

GeneLoc Exon Structure for
SMPDL3A
ECgene alternative splicing isoforms for
SMPDL3A

Expression for SMPDL3A Gene

mRNA expression in normal human tissues for SMPDL3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SMPDL3A Gene

This gene is overexpressed in Cervix - Ectocervix (x4.1).

Protein differential expression in normal tissues from HIPED for SMPDL3A Gene

This gene is overexpressed in Serum (20.3) and Vitreous humor (10.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for SMPDL3A Gene



SOURCE GeneReport for Unigene cluster for SMPDL3A Gene Hs.486357

mRNA Expression by UniProt/SwissProt for SMPDL3A Gene

Q92484-ASM3A_HUMAN
Tissue specificity: Detected in blood serum. Detected in macrophages (at protein level).
genes like me logo Genes that share expression patterns with SMPDL3A: view

Primer Products

No data available for Protein tissue co-expression partners for SMPDL3A Gene

Orthologs for SMPDL3A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SMPDL3A Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia SMPDL3A 35
  • 86.86 (n)
  • 83.07 (a)
SMPDL3A 36
  • 82 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMPDL3A 35
  • 87.54 (n)
  • 83.19 (a)
SMPDL3A 36
  • 82 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Smpdl3a 35
  • 82.54 (n)
  • 81.04 (a)
Smpdl3a 16
Smpdl3a 36
  • 80 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SMPDL3A 35
  • 99.48 (n)
  • 98.68 (a)
SMPDL3A 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smpdl3a 35
  • 82.24 (n)
  • 81.26 (a)
oppossum
(Monodelphis domestica)
Mammalia SMPDL3A 36
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SMPDL3A 36
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMPDL3A 35
  • 71.19 (n)
  • 68.33 (a)
SMPDL3A 36
  • 64 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMPDL3A 36
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smpdl3a 35
  • 67.61 (n)
  • 65.96 (a)
zebrafish
(Danio rerio)
Actinopterygii smpdl3a 35
  • 64.21 (n)
  • 64.59 (a)
smpdl3a 36
  • 54 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG32052 36
  • 28 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ZK856.5 36
  • 7 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PPN1 36
  • 12 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 4 (a)
ManyToMany
Species with no ortholog for SMPDL3A:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)

Evolution for SMPDL3A Gene

ENSEMBL:
Gene Tree for SMPDL3A (if available)
TreeFam:
Gene Tree for SMPDL3A (if available)

Paralogs for SMPDL3A Gene

Paralogs for SMPDL3A Gene

(2) SIMAP similar genes for SMPDL3A Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with SMPDL3A: view

Variants for SMPDL3A Gene

Sequence variations from dbSNP and Humsavar for SMPDL3A Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs12523814 - 122,789,392(+) CCTGG(C/T)ACTGC upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs28385609 - 122,801,319(+) AACTG(C/T)CTGTA intron-variant, reference, missense
rs1047572 -- 122,809,402(+) CACAA(A/T)TACTA reference, missense, utr-variant-3-prime
rs1110152 -- 122,790,394(-) AGGTG(A/G)GGGCA intron-variant
rs5784724 -- 122,807,710(+) TTTTT(-/T)CTGGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SMPDL3A Gene

Variant ID Type Subtype PubMed ID
nsv830791 CNV Gain 17160897
nsv823834 CNV Gain 20364138
nsv819111 CNV Loss 19587683

Variation tolerance for SMPDL3A Gene

Residual Variation Intolerance Score: 71.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.95; 74.60% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SMPDL3A Gene

HapMap Linkage Disequilibrium report
SMPDL3A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMPDL3A Gene

Disorders for SMPDL3A Gene

Relevant External Links for SMPDL3A

Human Genome Epidemiology (HuGE) Navigator
SMPDL3A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMPDL3A

No disorders were found for SMPDL3A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SMPDL3A Gene

Publications for SMPDL3A Gene

  1. Sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A) is a novel nucleotide phosphodiesterase regulated by cholesterol in human macrophages. (PMID: 25288789) Traini M. … Kritharides L. (J. Biol. Chem. 2014) 2 3 4 67
  2. Increased expression of the acid sphingomyelinase-like protein ASML3a in bladder tumors. (PMID: 12442002) Wright K.O. … Reeder J.E. (J. Urol. 2002) 2 3 23
  3. The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a - an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity. (PMID: 26783088) Lim S.M. … Nordlund P. (FEBS J. 2016) 3
  4. In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine. (PMID: 23533145) Principe S. … Drake R.R. (Proteomics 2013) 3
  5. Regulation of sphingomyelin phosphodiesterase acid-like 3A gene (SMPDL3A) by liver X receptors. (PMID: 22810003) Noto P.B. … Lala D.S. (Mol. Pharmacol. 2012) 3

Products for SMPDL3A Gene

Sources for SMPDL3A Gene

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