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

    Gene ID: 77626, updated on 28-Aug-2018

    Summary

    Official Symbol
    Smpd4provided by MGI
    Official Full Name
    sphingomyelin phosphodiesterase 4provided by MGI
    Primary source
    MGI:MGI:1924876
    See related
    Ensembl:ENSMUSG00000005899 Vega:OTTMUSG00000035764
    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
    Expression
    Ubiquitous expression in testis adult (RPKM 25.1), cortex adult (RPKM 16.4) and 28 other tissues See more
    Orthologs

    Genomic context

    See Smpd4 in Genome Data Viewer
    Location:
    16; 16 A3
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 16 NC_000082.6 (17619354..17644830)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 16 NC_000082.5 (17619447..17644923)

    Chromosome 16 - NC_000082.6Genomic Context describing neighboring genes 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 coiled-coil domain containing 74A Neighboring gene mediator complex subunit 15 Neighboring gene calcyclin binding protein pseudogene

    Genomic regions, transcripts, and products

    Expression

    • 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

    Variation

    Alleles

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

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA1418

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
     
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    sphingomyelin phosphodiesterase D activity ISO
    Inferred from Sequence Orthology
    more info
     
    sphingomyelin phosphodiesterase D activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    sphingomyelin phosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    cellular response to tumor necrosis factor ISO
    Inferred from Sequence Orthology
    more info
     
    ceramide biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
     
    glycerophospholipid catabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    sphingomyelin catabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    sphingomyelin catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    Component Evidence Code Pubs
    Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
     
    Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
     
    endoplasmic reticulum ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    membrane IEA
    Inferred from Electronic Annotation
    more info
     
    trans-Golgi network ISO
    Inferred from Sequence Orthology
    more info
     
    trans-Golgi network ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 

    General protein information

    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_084221.2
    XP_006522783.1
    XP_006522784.1
    XP_006522785.1
    XP_006522788.1
    XP_017172649.1

    NCBI Reference Sequences (RefSeq)

    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_001164609.1NP_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)
      AI415105, AK019466, AK031685, AK164234
      Consensus CDS
      CCDS49780.1
      UniProtKB/Swiss-Prot
      Q6ZPR5
      Related
      ENSMUSP00000087620.4, OTTMUSP00000050403, ENSMUST00000090159.12, OTTMUST00000091498
      Conserved Domains (1) summary
      pfam14724
      Location:8752
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase
    2. NM_001164610.1NP_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)
      AI415105, AK019466, AK031685, AK035892
      Consensus CDS
      CCDS49781.1
      UniProtKB/Swiss-Prot
      Q6ZPR5
      Related
      ENSMUSP00000131867.1, OTTMUSP00000050402, ENSMUST00000163476.9, OTTMUST00000091496
      Conserved Domains (1) summary
      pfam14724
      Location:8739
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase
    3. NM_001164611.1NP_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)
      AI415105, AK019466, AK031029, AK031685, AK035892
      Consensus CDS
      CCDS49779.1
      UniProtKB/Swiss-Prot
      Q6ZPR5
      Related
      ENSMUSP00000130720.1, OTTMUSP00000050421, ENSMUST00000165363.9, OTTMUST00000091524
      Conserved Domains (1) summary
      pfam14724
      Location:8738
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase
    4. NM_029945.3NP_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)
      AI415105, AK019466, AK031685
      Consensus CDS
      CCDS28009.1
      UniProtKB/Swiss-Prot
      Q6ZPR5
      Related
      ENSMUSP00000006053.6, OTTMUSP00000050401, ENSMUST00000006053.12, OTTMUST00000091495
      Conserved Domains (1) summary
      pfam14724
      Location:8768
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000082.6 Reference GRCm38.p4 C57BL/6J

      Range
      17619354..17644830
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006522722.2XP_006522785.1  sphingomyelin phosphodiesterase 4 isoform X3

      See identical proteins and their annotated locations for XP_006522785.1

      UniProtKB/Swiss-Prot
      Q6ZPR5
      Conserved Domains (1) summary
      pfam14724
      Location:8768
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase
    2. XM_006522725.2XP_006522788.1  sphingomyelin phosphodiesterase 4 isoform X4

      Related
      ENSMUSP00000156215.1, OTTMUSP00000050405, ENSMUST00000232271.1, OTTMUST00000091501
      Conserved Domains (1) summary
      pfam14724
      Location:81533
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase
    3. XM_006522720.3XP_006522783.1  sphingomyelin phosphodiesterase 4 isoform X1

      Conserved Domains (1) summary
      pfam14724
      Location:38798
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase
    4. XM_006522721.3XP_006522784.1  sphingomyelin phosphodiesterase 4 isoform X2

      Related
      ENSMUSP00000155897.1, OTTMUSP00000050408, ENSMUST00000231436.1, OTTMUST00000091504
      Conserved Domains (1) summary
      pfam14724
      Location:38769
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase
    5. XM_017317160.1XP_017172649.1  sphingomyelin phosphodiesterase 4 isoform X5

      Conserved Domains (1) summary
      pfam14724
      Location:50389
      mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

    RNA

    1. XR_001781871.1 RNA Sequence

    2. XR_001781872.1 RNA Sequence

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