U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Smpd4 sphingomyelin phosphodiesterase 4 [ Mus musculus (house mouse) ]

    Gene ID: 77626, updated on 3-Apr-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Smpd4provided by MGI
    Official Full Name
    sphingomyelin phosphodiesterase 4provided by MGI
    Primary source
    MGI:MGI:1924876
    See related
    Ensembl:ENSMUSG00000005899 AllianceGenome:MGI:1924876
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    4122402O22Rik
    Summary
    Enables sphingomyelin phosphodiesterase activity. Involved in cellular response to tumor necrosis factor; ceramide biosynthetic process; and sphingomyelin catabolic process. Acts upstream of or within in utero embryonic development. Located in endoplasmic reticulum; nuclear envelope; and sarcolemma. Is expressed in cranium; hemolymphoid system; nervous system; respiratory system; and urinary system. Orthologous to human SMPD4 (sphingomyelin phosphodiesterase 4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis adult (RPKM 25.1), cortex adult (RPKM 16.4) and 28 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    16 A3; 16 10.92 cM
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (17437218..17462694)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (17619354..17644830)

    Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_40257 Neighboring gene purinergic receptor P2X, ligand-gated ion channel, 6 Neighboring gene solute carrier family 7 (cationic amino acid transporter, y+ system), member 4 Neighboring gene STARR-seq mESC enhancer starr_40258 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:17619324-17619507 Neighboring gene STARR-seq mESC enhancer starr_40259 Neighboring gene coiled-coil domain containing 74A Neighboring gene mediator complex subunit 15 Neighboring gene calcyclin binding protein pseudogene

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Neutral sphingomyelinase-3 mediates TNF-stimulated oxidant activity in skeletal muscle. Moylan JS, et al. Redox Biol, 2014. PMID 25180167, Free PMC Article
    2. Ceramide triggers budding of exosome vesicles into multivesicular endosomes. Trajkovic K, et al. Science, 2008 Feb 29. PMID 18309083
    3. Novel tumor necrosis factor-responsive mammalian neutral sphingomyelinase-3 is a C-tail-anchored protein. Krut O, et al. J Biol Chem, 2006 May 12. PMID 16517606
    4. Identification of new transmembrane proteins concentrated at the nuclear envelope using organellar proteomics of mesenchymal cells. Cheng LC, et al. Nucleus, 2019 Dec. PMID 31142202, Free PMC Article
    5. A staging system for correct phenotype interpretation of mouse embryos harvested on embryonic day 14 (E14.5). Geyer SH, et al. J Anat, 2017 May. PMID 28185240, Free PMC Article

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (3) 
    • Endonuclease-mediated (2) 

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • KIAA1418

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sphingomyelin phosphodiesterase D activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables sphingomyelin phosphodiesterase D activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables sphingomyelin phosphodiesterase D activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables sphingomyelin phosphodiesterase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to tumor necrosis factor IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cellular response to tumor necrosis factor ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in ceramide biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ceramide biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ceramide biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endoplasmic reticulum organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in glycerophospholipid catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in glycerophospholipid catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within in utero embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in sphingomyelin catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sphingomyelin catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in sphingomyelin catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in sphingomyelin catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear envelope IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear outer membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in sarcolemma IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in trans-Golgi network ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in trans-Golgi network ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 

    General protein information

    Go to the top of the page Help
    Preferred Names
    sphingomyelin phosphodiesterase 4
    Names
    nSMase3
    neutral membrane (neutral sphingomyelinase-3)
    neutral sphingomyelinase 3
    neutral sphingomyelinase III
    NP_001158081.1
    NP_001158082.1
    NP_001158083.1
    NP_001390351.1
    NP_084221.2
    XP_006522783.1
    XP_006522784.1
    XP_006522785.1
    XP_006522788.1
    XP_017172649.1
    XP_030105190.1
    XP_030105191.1
    XP_036016072.1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001164609.2 → NP_001158081.1  sphingomyelin phosphodiesterase 4 isoform 4

      See identical proteins and their annotated locations for NP_001158081.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 4, which is shorter than isoform 1.
      Source sequence(s)
      AC115733
      Consensus CDS
      CCDS49780.1
      UniProtKB/TrEMBL
      A0A338P695
      Related
      ENSMUSP00000087620.5, ENSMUST00000090159.13
      Conserved Domains (1) summary
      pfam14724
      Location:8 → 752
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

    2. NM_001164610.2 → NP_001158082.1  sphingomyelin phosphodiesterase 4 isoform 3

      See identical proteins and their annotated locations for NP_001158082.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 3, which is shorter than isoform 1.
      Source sequence(s)
      AC115733
      Consensus CDS
      CCDS49781.1
      UniProtKB/TrEMBL
      A0A338P695
      Related
      ENSMUSP00000131867.2, ENSMUST00000163476.10
      Conserved Domains (1) summary
      pfam14724
      Location:8 → 739
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

    3. NM_001164611.2 → NP_001158083.1  sphingomyelin phosphodiesterase 4 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AC115733
      Consensus CDS
      CCDS49779.1
      UniProtKB/TrEMBL
      A0A338P695
      Related
      ENSMUSP00000130720.2, ENSMUST00000165363.10
      Conserved Domains (1) summary
      pfam14724
      Location:8 → 738
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

    4. NM_001403422.1 → NP_001390351.1  sphingomyelin phosphodiesterase 4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC115733

    5. NM_029945.4 → NP_084221.2  sphingomyelin phosphodiesterase 4 isoform 1

      See identical proteins and their annotated locations for NP_084221.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC115733
      Consensus CDS
      CCDS28009.1
      UniProtKB/Swiss-Prot
      Q3TPE0, Q3TPP1, Q6ZPR5, Q8CBJ5, Q8CD12, Q8CD83, Q8R0J3, Q9CX74
      UniProtKB/TrEMBL
      A0A338P695
      Related
      ENSMUSP00000006053.7, ENSMUST00000006053.13
      Conserved Domains (1) summary
      pfam14724
      Location:8 → 768
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

    RNA

    1. NR_175375.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC115733

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000082.7 Reference GRCm39 C57BL/6J

      Range
      17437218..17462694
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006522725.3 → XP_006522788.1  sphingomyelin phosphodiesterase 4 isoform X4

      UniProtKB/TrEMBL
      A0A338P735
      Related
      ENSMUSP00000156215.2, ENSMUST00000232271.2
      Conserved Domains (1) summary
      pfam14724
      Location:81 → 533
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

    2. XM_030249331.2 → XP_030105191.1  sphingomyelin phosphodiesterase 4 isoform X5

      Conserved Domains (1) summary
      pfam14724
      Location:35 → 389
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

    3. XM_030249330.1 → XP_030105190.1  sphingomyelin phosphodiesterase 4 isoform X4

      UniProtKB/TrEMBL
      A0A338P735
      Conserved Domains (1) summary
      pfam14724
      Location:81 → 533
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

    4. XM_006522722.3 → XP_006522785.1  sphingomyelin phosphodiesterase 4 isoform X3

      See identical proteins and their annotated locations for XP_006522785.1

      UniProtKB/Swiss-Prot
      Q3TPE0, Q3TPP1, Q6ZPR5, Q8CBJ5, Q8CD12, Q8CD83, Q8R0J3, Q9CX74
      UniProtKB/TrEMBL
      A0A338P695
      Conserved Domains (1) summary
      pfam14724
      Location:8 → 768
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

    5. XM_006522721.4 → XP_006522784.1  sphingomyelin phosphodiesterase 4 isoform X2

      UniProtKB/TrEMBL
      A0A338P695
      Related
      ENSMUSP00000155897.2, ENSMUST00000231436.2
      Conserved Domains (1) summary
      pfam14724
      Location:38 → 769
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

    6. XM_036160179.1 → XP_036016072.1  sphingomyelin phosphodiesterase 4 isoform X3

      UniProtKB/Swiss-Prot
      Q3TPE0, Q3TPP1, Q6ZPR5, Q8CBJ5, Q8CD12, Q8CD83, Q8R0J3, Q9CX74
      UniProtKB/TrEMBL
      A0A338P695
      Conserved Domains (1) summary
      pfam14724
      Location:8 → 768
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

    7. XM_006522720.4 → XP_006522783.1  sphingomyelin phosphodiesterase 4 isoform X1

      UniProtKB/TrEMBL
      A0A338P695
      Conserved Domains (1) summary
      pfam14724
      Location:38 → 798
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

    8. XM_017317160.3 → XP_017172649.1  sphingomyelin phosphodiesterase 4 isoform X5

      Conserved Domains (1) summary
      pfam14724
      Location:35 → 389
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

    RNA

    1. XR_001781871.3 RNA Sequence

    2. XR_001781872.3 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZPR5.2 GenPept UniProtKB/Swiss-Prot:Q6ZPR5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous