Human Gene SMPDL3A (ENST00000368440.5_4) from GENCODE V47lift37
  Description: sphingomyelin phosphodiesterase acid like 3A, transcript variant 1 (from RefSeq NM_006714.5)
Gencode Transcript: ENST00000368440.5_4
Gencode Gene: ENSG00000172594.13_7
Transcript (Including UTRs)
   Position: hg19 chr6:123,110,403-123,130,865 Size: 20,463 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr6:123,110,492-123,130,553 Size: 20,062 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:123,110,403-123,130,865)mRNA (may differ from genome)Protein (453 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ASM3A_HUMAN
DESCRIPTION: RecName: Full=Acid sphingomyelinase-like phosphodiesterase 3a; Short=ASM-like phosphodiesterase 3a; EC=3.1.4.-; Flags: Precursor;
SUBCELLULAR LOCATION: Secreted (By similarity).
SIMILARITY: Belongs to the acid sphingomyelinase family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D000082 Acetaminophen
  • D004958 Estradiol
  • D004997 Ethinyl Estradiol
  • D013749 Tetrachlorodibenzodioxin
  • C016104 sodium bichromate
  • C028474 1,4-bis(2-(3,5-dichloropyridyloxy))benzene
  • C023514 2,6-dinitrotoluene
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C009505 4,4'-diaminodiphenylmethane
  • C547126 AZM551248
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 57.82 RPKM in Cervix - Endocervix
Total median expression: 508.28 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -30.7089-0.345 Picture PostScript Text
3' UTR -55.70312-0.179 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017064 - ASM-like_Pdiesterase_prd
IPR004843 - Metallo_PEstase_dom

Pfam Domains:
PF00149 - Calcineurin-like phosphoesterase
PF19272 - Acid sphingomyelin phosphodiesterase C-terminal region

SCOP Domains:
51445 - (Trans)glycosidases
52266 - SGNH hydrolase
56300 - Metallo-dependent phosphatases

ModBase Predicted Comparative 3D Structure on Q92484
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008081 phosphoric diester hydrolase activity
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0004767 sphingomyelin phosphodiesterase activity

Biological Process:
GO:0009143 nucleoside triphosphate catabolic process
GO:0006685 sphingomyelin catabolic process

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AK096144 - Homo sapiens cDNA FLJ38825 fis, clone LIVER2008998.
LP895548 - Sequence 412 from Patent EP3253886.
AK000184 - Homo sapiens cDNA FLJ20177 fis, clone COL09966, highly similar to Y08136 H.
BC018999 - Homo sapiens sphingomyelin phosphodiesterase, acid-like 3A, mRNA (cDNA clone MGC:20681 IMAGE:3138813), complete cds.
BC066591 - Homo sapiens cDNA clone IMAGE:5591320, with apparent retained intron.
AK301365 - Homo sapiens cDNA FLJ57626 complete cds, highly similar to Acid sphingomyelinase-like phosphodiesterase 3a precursor (EC 3.1.4.-).
DQ895402 - Synthetic construct Homo sapiens clone IMAGE:100009862; FLH184051.01L; RZPDo839B09143D sphingomyelin phosphodiesterase, acid-like 3A (SMPDL3A) gene, encodes complete protein.
DQ892207 - Synthetic construct clone IMAGE:100004837; FLH184055.01X; RZPDo839B09144D sphingomyelin phosphodiesterase, acid-like 3A (SMPDL3A) gene, encodes complete protein.
CU676352 - Synthetic construct Homo sapiens gateway clone IMAGE:100019474 5' read SMPDL3A mRNA.
KJ893168 - Synthetic construct Homo sapiens clone ccsbBroadEn_02562 SMPDL3A gene, encodes complete protein.
Y08136 - H.sapiens mRNA for ASM-like phosphodiesterase 3a.
JD429060 - Sequence 410084 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ASM3A_HUMAN, ASML3A, B7Z729, ENST00000368440.1, ENST00000368440.2, ENST00000368440.3, ENST00000368440.4, NM_006714, Q8WV13, Q92484, uc318gts.1, uc318gts.2
UCSC ID: ENST00000368440.5_4
RefSeq Accession: NM_006714.5
Protein: Q92484 (aka ASM3A_HUMAN or AS3A_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.