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Aliases for SMPDL3B Gene

Aliases for SMPDL3B Gene

  • Sphingomyelin Phosphodiesterase Acid Like 3B 2 3 5
  • Acid Sphingomyelinase-Like Phosphodiesterase 3b 3 4
  • ASM-Like Phosphodiesterase 3b 3 4
  • ASML3B 3 4
  • Sphingomyelin Phosphodiesterase, Acid-Like 3B 2
  • Sphingomyelin Phosphodiesterase Acid-Like 3B 2
  • EC 3.1.4.- 4
  • ASMLPD 4

External Ids for SMPDL3B Gene

Previous GeneCards Identifiers for SMPDL3B Gene

  • GC01P027867
  • GC01P028134
  • GC01P028261
  • GC01P026518

Summaries for SMPDL3B Gene

GeneCards Summary for SMPDL3B Gene

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

UniProtKB/Swiss-Prot for SMPDL3B Gene

  • Lipid-modulating phosphodiesterase (PubMed:26095358). Active on the surface of macrophages and dendritic cells and strongly influences macrophage lipid composition and membrane fluidity. Acts as a negative regulator of Toll-like receptor signaling (By similarity). Has in vitro phosphodiesterase activity, but the physiological substrate is unknown (PubMed:26095358). Lacks activity with phosphocholine-containing lipids, but can cleave CDP-choline, and can release phosphate from ATP and ADP (in vitro) (By similarity).

Additional gene information for SMPDL3B Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMPDL3B Gene

Genomics for SMPDL3B Gene

GeneHancer (GH) Regulatory Elements for SMPDL3B Gene

Promoters and enhancers for SMPDL3B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J027934 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 645.6 +1.3 1271 3.6 SP1 ZNF121 ZSCAN21 MAFK ZNF548 ZNF404 MZF1 EGR1 IKZF1 GLIS2 SMPDL3B TRNAU1AP TMEM222 GMEB1 SNHG12 MAP3K6 ACTG1P20 RPA2 FAM76A YTHDF2
GH01J027941 Enhancer 1.3 FANTOM5 ENCODE 39.7 +8.2 8211 3.1 ELF3 CBFA2T2 ZNF148 CEBPG RERE MAFK TFE3 TRIM24 HNF1A PPARG SMPDL3B THEMIS2 PTAFR FGR XKR8 RPA2 SESN2 MED18 EYA3 WASF2
GH01J027881 Promoter/Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 22.1 -47.1 -47137 11.7 CEBPG ZNF687 RELA SP1 CREM MLLT1 ZBED1 IKZF1 ZBTB33 PKNOX1 RPA2 XKR8 THEMIS2 SMPDL3B ENSG00000227050 EYA3 SCARNA1 PPP1R8 RNU6-1245P FGR
GH01J027932 Promoter 0.8 Ensembl 43 -2.6 -2647 0.2 NFIB NFIC NFE2 NFIA POLR2A GC01M027930 SMPDL3B RPA2
GH01J027904 Enhancer 0.8 ENCODE dbSUPER 28.1 -30.1 -30144 0.3 SP1 RXRA RFX1 CEBPB YY1 RAD21 CEBPG HNF4A ZBTB33 POLR2A SMPDL3B THEMIS2 PPP1R8 SCARNA1 RNU6-1245P ATP5IF1 DNAJC8 RPA2 GC01M027883
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SMPDL3B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SMPDL3B gene promoter:
  • c-Myb
  • C/EBPalpha
  • C/EBPbeta
  • CREB
  • deltaCREB
  • IRF-1
  • PPAR-alpha
  • SRF
  • SRF (504 AA)

Genomic Locations for SMPDL3B Gene

Genomic Locations for SMPDL3B Gene
chr1:27,934,948-27,959,157
(GRCh38/hg38)
Size:
24,210 bases
Orientation:
Plus strand
chr1:28,261,504-28,285,668
(GRCh37/hg19)
Size:
24,165 bases
Orientation:
Plus strand

Genomic View for SMPDL3B Gene

Genes around SMPDL3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMPDL3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMPDL3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMPDL3B Gene

Proteins for SMPDL3B Gene

  • Protein details for SMPDL3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92485-ASM3B_HUMAN
    Recommended name:
    Acid sphingomyelinase-like phosphodiesterase 3b
    Protein Accession:
    Q92485
    Secondary Accessions:
    • B7ZB35
    • Q5T0Z0
    • Q96CB7

    Protein attributes for SMPDL3B Gene

    Size:
    455 amino acids
    Molecular mass:
    50814 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Interacts with TLR4, TLR7, TLR8 and TLR9.

    Alternative splice isoforms for SMPDL3B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMPDL3B Gene

Post-translational modifications for SMPDL3B Gene

No data available for DME Specific Peptides for SMPDL3B Gene

Domains & Families for SMPDL3B Gene

Gene Families for SMPDL3B Gene

Human Protein Atlas (HPA):
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for SMPDL3B Gene

GenScript: Design optimal peptide antigens:
  • Acid sphingomyelinase-like phosphodiesterase 3b (ASM3B_HUMAN)
  • cDNA FLJ57705, highly similar to Acid sphingomyelinase-like phosphodiesterase 3b (EC 3.1.4.-) (B4DE65_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q92485

UniProtKB/Swiss-Prot:

ASM3B_HUMAN :
  • Belongs to the acid sphingomyelinase family.
Family:
  • Belongs to the acid sphingomyelinase family.
genes like me logo Genes that share domains with SMPDL3B: view

Function for SMPDL3B Gene

Molecular function for SMPDL3B Gene

UniProtKB/Swiss-Prot Function:
Lipid-modulating phosphodiesterase (PubMed:26095358). Active on the surface of macrophages and dendritic cells and strongly influences macrophage lipid composition and membrane fluidity. Acts as a negative regulator of Toll-like receptor signaling (By similarity). Has in vitro phosphodiesterase activity, but the physiological substrate is unknown (PubMed:26095358). Lacks activity with phosphocholine-containing lipids, but can cleave CDP-choline, and can release phosphate from ATP and ADP (in vitro) (By similarity).

Enzyme Numbers (IUBMB) for SMPDL3B Gene

Phenotypes From GWAS Catalog for SMPDL3B Gene

Gene Ontology (GO) - Molecular Function for SMPDL3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004767 sphingomyelin phosphodiesterase activity IEA --
GO:0008081 phosphoric diester hydrolase activity ISS --
GO:0008270 zinc ion binding ISS --
GO:0016787 hydrolase activity IEA --
GO:0016798 hydrolase activity, acting on glycosyl bonds IEA --
genes like me logo Genes that share ontologies with SMPDL3B: view
genes like me logo Genes that share phenotypes with SMPDL3B: view

Animal Models for SMPDL3B Gene

MGI Knock Outs for SMPDL3B:
  • Smpdl3b Smpdl3b<tm1a(EUCOMM)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for SMPDL3B

CRISPR Products

Clone Products

  • Applied Biological Materials (abm): Clones for SMPDL3B - Now 50% OFF >
  • * SMPDL3B as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * SMPDL3B tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SMPDL3B Gene

Localization for SMPDL3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMPDL3B Gene

Secreted. Cell membrane; Lipid-anchor, GPI-anchor.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SMPDL3B gene
Compartment Confidence
plasma membrane 4
lysosome 3
golgi apparatus 2
peroxisome 1
cytosol 1
extracellular 0
mitochondrion 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SMPDL3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IBA,IEA 21873635
GO:0005886 plasma membrane ISS --
GO:0016020 membrane IEA --
GO:0031225 anchored component of membrane IEA --
genes like me logo Genes that share ontologies with SMPDL3B: view

Pathways & Interactions for SMPDL3B Gene

PathCards logo

SuperPathways for SMPDL3B Gene

No Data Available

Interacting Proteins for SMPDL3B Gene

STRING Interaction Network Preview (showing top 5 STRING interactants - click image to see top 25)
https://version11.string-db.org/api/image/network?species=9606&limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000363001%0d9606.ENSP00000378046%0d9606.ENSP00000385410%0d9606.ENSP00000420443%0d9606.ENSP00000377015%0d9606.ENSP00000400459%0d
Selected Interacting proteins: ENSP00000363001 Q92485-ASM3B_HUMAN for SMPDL3B Gene via STRING IID

Gene Ontology (GO) - Biological Process for SMPDL3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006685 sphingomyelin catabolic process IEA --
GO:0006954 inflammatory response IEA --
GO:0008150 biological_process ND --
GO:0008152 metabolic process IEA --
genes like me logo Genes that share ontologies with SMPDL3B: view

No data available for Pathways by source and SIGNOR curated interactions for SMPDL3B Gene

Drugs & Compounds for SMPDL3B Gene

No Compound Related Data Available

Transcripts for SMPDL3B Gene

Unigene Clusters for SMPDL3B Gene

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

CRISPR Products

Clone Products

  • Applied Biological Materials (abm): Clones for SMPDL3B - Now 50% OFF >
  • * SMPDL3B as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * SMPDL3B tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

Alternative Splicing Database (ASD) splice patterns (SP) for SMPDL3B Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12a · 12b ^ 13
SP1: - - - - -
SP2: -
SP3: - - - -
SP4: -
SP5: - - - - - - -
SP6: - - - -
SP7: - - -

Relevant External Links for SMPDL3B Gene

GeneLoc Exon Structure for
SMPDL3B
ECgene alternative splicing isoforms for
SMPDL3B

Expression for SMPDL3B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SMPDL3B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SMPDL3B Gene

This gene is overexpressed in Pancreas (x10.6), Colon - Transverse (x8.7), and Stomach (x4.5).

Protein differential expression in normal tissues from HIPED for SMPDL3B Gene

This gene is overexpressed in Adipocyte (26.2) and Cervix (10.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SMPDL3B Gene



NURSA nuclear receptor signaling pathways regulating expression of SMPDL3B Gene:

SMPDL3B

SOURCE GeneReport for Unigene cluster for SMPDL3B Gene:

Hs.123659

Evidence on tissue expression from TISSUES for SMPDL3B Gene

  • Intestine(4.3)
genes like me logo Genes that share expression patterns with SMPDL3B: view

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SMPDL3B Gene

Orthologs for SMPDL3B Gene

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

Orthologs for SMPDL3B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMPDL3B 34 35
  • 99.34 (n)
dog
(Canis familiaris)
Mammalia SMPDL3B 35 34
  • 86.45 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SMPDL3B 35 34
  • 84.79 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Smpdl3b 17 35 34
  • 80.97 (n)
rat
(Rattus norvegicus)
Mammalia Smpdl3b 34
  • 80.67 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SMPDL3B 35
  • 61 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMPDL3B 35
  • 60 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMPDL3B 34 35
  • 65.58 (n)
lizard
(Anolis carolinensis)
Reptilia SMPDL3B 35
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smpdl3b 34
  • 61.6 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC564392 34
  • 62.33 (n)
smpdl3b 35
  • 52 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6438 34
fruit fly
(Drosophila melanogaster)
Insecta CG32052 35 34
  • 51.64 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005806 34
  • 49.22 (n)
worm
(Caenorhabditis elegans)
Secernentea ZK856.5 34
  • 47.33 (n)
asm-3 35
  • 15 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PPN1 35 37
  • 12 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 43 (a)
OneToMany
-- 35
  • 40 (a)
OneToMany
Species where no ortholog for SMPDL3B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 SMPDL3B Gene

ENSEMBL:
Gene Tree for SMPDL3B (if available)
TreeFam:
Gene Tree for SMPDL3B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SMPDL3B: view image

Paralogs for SMPDL3B Gene

Paralogs for SMPDL3B Gene

(1) SIMAP similar genes for SMPDL3B Gene using alignment to 4 proteins:

  • ASM3B_HUMAN
  • F8VWW8_HUMAN
  • F8VXS3_HUMAN
  • Q5T0Y8_HUMAN
genes like me logo Genes that share paralogs with SMPDL3B: view

Variants for SMPDL3B Gene

Sequence variations from dbSNP and Humsavar for SMPDL3B Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000106172 -- 27,955,086(+) G/A intron_variant
rs1000116390 -- 27,936,024(+) C/A genic_upstream_transcript_variant, intron_variant
rs1000128062 -- 27,946,542(+) C/T intron_variant
rs1000175325 -- 27,935,669(+) A/C genic_upstream_transcript_variant, intron_variant
rs1000333192 -- 27,942,194(+) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SMPDL3B Gene

Variant ID Type Subtype PubMed ID
esv3585564 CNV loss 21293372
esv3585565 CNV gain 21293372

Variation tolerance for SMPDL3B Gene

Residual Variation Intolerance Score: 77.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.82; 79.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SMPDL3B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMPDL3B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMPDL3B Gene

Disorders for SMPDL3B Gene

Additional Disease Information for SMPDL3B

No disorders were found for SMPDL3B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SMPDL3B Gene

Publications for SMPDL3B Gene

  1. The Lipid-Modifying Enzyme SMPDL3B Negatively Regulates Innate Immunity. (PMID: 26095358) Heinz LX … Superti-Furga G (Cell reports 2015) 2 3 4 58
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Quantitative mapping of RNA-mediated nuclear estrogen receptor β interactome in human breast cancer cells. (PMID: 29509190) Giurato G … Tarallo R (Scientific data 2018) 3 58
  5. Sphingomyelinase-like phosphodiesterase 3b mediates radiation-induced damage of renal podocytes. (PMID: 27836988) Ahmad A … Zeidan YH (FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2017) 3 58

Products for SMPDL3B Gene

Sources for SMPDL3B Gene

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