Human Gene SMPD4 (ENST00000680298.1_9) from GENCODE V47lift37
  Description: sphingomyelin phosphodiesterase 4, transcript variant 2 (from RefSeq NM_017951.5)
Gencode Transcript: ENST00000680298.1_9
Gencode Gene: ENSG00000136699.20_18
Transcript (Including UTRs)
   Position: hg19 chr2:130,908,981-130,939,175 Size: 30,195 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr2:130,910,128-130,934,165 Size: 24,038 Coding Exon Count: 19 

Page IndexSequence and LinksPrimersCTDGene AllelesMicroarray Expression
RNA StructureOther SpeciesmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:130,908,981-130,939,175)mRNA (may differ from genome)Protein (827 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  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

+  Common Gene Haplotype Alleles
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+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -36.60118-0.310 Picture PostScript Text
3' UTR -433.601147-0.378 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.

-  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   
      
      

-  Descriptions from all associated GenBank mRNAs
  AF052134 - Homo sapiens clone 23585 mRNA sequence.
AL136737 - Homo sapiens mRNA; cDNA DKFZp434A1711 (from clone DKFZp434A1711).
BC040941 - Homo sapiens, Similar to hypothetical protein FLJ20297, clone IMAGE:5590452, mRNA.
BC064947 - Homo sapiens sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3), mRNA (cDNA clone MGC:70674 IMAGE:6023304), complete cds.
AK000304 - Homo sapiens cDNA FLJ20297 fis, clone HEP05942.
AK001227 - Homo sapiens cDNA FLJ10365 fis, clone NT2RM2001393.
AK126920 - Homo sapiens cDNA FLJ44972 fis, clone BRAWH3001053.
AK000763 - Homo sapiens cDNA FLJ20756 fis, clone HEP01556.
AK056501 - Homo sapiens cDNA FLJ31939 fis, clone NT2RP7006547.
AB037839 - Homo sapiens KIAA1418 mRNA for KIAA1418 protein.
JD439500 - Sequence 420524 from Patent EP1572962.
JD137696 - Sequence 118720 from Patent EP1572962.
JD359282 - Sequence 340306 from Patent EP1572962.
JD378943 - Sequence 359967 from Patent EP1572962.
JD245641 - Sequence 226665 from Patent EP1572962.
JD487883 - Sequence 468907 from Patent EP1572962.
JD219697 - Sequence 200721 from Patent EP1572962.
JD426522 - Sequence 407546 from Patent EP1572962.
JD022883 - Sequence 3907 from Patent EP1572962.
JD035324 - Sequence 16348 from Patent EP1572962.
JD029092 - Sequence 10116 from Patent EP1572962.
JD019219 - Sequence 243 from Patent EP1572962.
JD380070 - Sequence 361094 from Patent EP1572962.
JD513418 - Sequence 494442 from Patent EP1572962.
JD052242 - Sequence 33266 from Patent EP1572962.
JD103241 - Sequence 84265 from Patent EP1572962.
JD470659 - Sequence 451683 from Patent EP1572962.
JD288003 - Sequence 269027 from Patent EP1572962.
JD090862 - Sequence 71886 from Patent EP1572962.
JD023152 - Sequence 4176 from Patent EP1572962.
JD029909 - Sequence 10933 from Patent EP1572962.
JD498147 - Sequence 479171 from Patent EP1572962.
AK301576 - Homo sapiens cDNA FLJ58546 complete cds, highly similar to Homo sapiens sphingomyelin phosphodiesterase 4, neutral membrane, transcript variant 1, mRNA.
JD094785 - Sequence 75809 from Patent EP1572962.
JD561252 - Sequence 542276 from Patent EP1572962.
JD361654 - Sequence 342678 from Patent EP1572962.
JD201753 - Sequence 182777 from Patent EP1572962.
AK299185 - Homo sapiens cDNA FLJ59395 complete cds, highly similar to Homo sapiens sphingomyelin phosphodiesterase 4, neutral membrane, transcript variant 1, mRNA.
JD190506 - Sequence 171530 from Patent EP1572962.
AK303519 - Homo sapiens cDNA FLJ54527 complete cds, highly similar to Homo sapiens sphingomyelin phosphodiesterase 4, neutral membrane, transcript variant 1, mRNA.
AK298609 - Homo sapiens cDNA FLJ53156 complete cds, highly similar to Homo sapiens sphingomyelin phosphodiesterase 4, neutral membrane, transcript variant 2, mRNA.
JD407178 - Sequence 388202 from Patent EP1572962.
JD073901 - Sequence 54925 from Patent EP1572962.
AK297257 - Homo sapiens cDNA FLJ59341 complete cds, highly similar to Homo sapiens sphingomyelin phosphodiesterase 4, neutral membrane, transcript variant 1, mRNA.
CR533550 - Homo sapiens full open reading frame cDNA clone RZPDo834H0919D for gene FLJ20297, hypothetical protein FLJ20297; complete cds, incl. stopcodon.
AK303427 - Homo sapiens cDNA FLJ53260 complete cds, highly similar to Homo sapiens sphingomyelin phosphodiesterase 4, neutral membrane, transcript variant 2, mRNA.
JD214552 - Sequence 195576 from Patent EP1572962.
JD104412 - Sequence 85436 from Patent EP1572962.
JD208053 - Sequence 189077 from Patent EP1572962.
JD343494 - Sequence 324518 from Patent EP1572962.
JD287684 - Sequence 268708 from Patent EP1572962.
JD162970 - Sequence 143994 from Patent EP1572962.
JD287685 - Sequence 268709 from Patent EP1572962.
JD364784 - Sequence 345808 from Patent EP1572962.
JD214586 - Sequence 195610 from Patent EP1572962.
EU367941 - Homo sapiens SKNY protein mRNA, complete cds.
KJ902844 - Synthetic construct Homo sapiens clone ccsbBroadEn_12238 SMPD4 gene, encodes complete protein.
JD162109 - Sequence 143133 from Patent EP1572962.
JD243813 - Sequence 224837 from Patent EP1572962.
JD163916 - Sequence 144940 from Patent EP1572962.
JD163917 - Sequence 144941 from Patent EP1572962.
JD556974 - Sequence 537998 from Patent EP1572962.
JD478206 - Sequence 459230 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-7277 - sphingolipid biosynthesis (mammals)
PWY3DJ-11281 - sphingomyelin metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: A0A7P0TB24, A0A7P0TB24_HUMAN, NM_017951, SMPD4 , uc330gtr.1, uc330gtr.2
UCSC ID: ENST00000680298.1_9
RefSeq Accession: NM_017951.5

-  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.