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Smpd4 sphingomyelin phosphodiesterase 4 [ Rattus norvegicus (Norway rat) ]

Gene ID: 303790, updated on 30-Mar-2024

Summary

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Official Symbol
Smpd4provided by RGD
Official Full Name
sphingomyelin phosphodiesterase 4provided by RGD
Primary source
RGD:1310674
See related
Ensembl:ENSRNOG00000001875 AllianceGenome:RGD:1310674
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
RGD1310674
Summary
Predicted to enable sphingomyelin phosphodiesterase D activity and sphingomyelin phosphodiesterase activity. Predicted to be involved in several processes, including cellular response to tumor necrosis factor; ceramide biosynthetic process; and phospholipid catabolic process. Predicted to act upstream of or within in utero embryonic development. Predicted to be located in several cellular components, including nuclear outer membrane; sarcolemma; and trans-Golgi network. Orthologous to human SMPD4 (sphingomyelin phosphodiesterase 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Thymus (RPKM 69.7), Testes (RPKM 65.3) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Smpd4 in Genome Data Viewer
Location:
11q23
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (96866805..96890520, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (83362534..83386257, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (87522971..87546687)

Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene U6 spliceosomal RNA Neighboring gene coiled-coil domain containing 74A Neighboring gene late endosomal/lysosomal adaptor, MAPK and MTOR activator 2, pseudogene 2 Neighboring gene uncharacterized LOC108352364 Neighboring gene solute carrier family 7, member 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Loss of SMPD4 Causes a Developmental Disorder Characterized by Microcephaly and Congenital Arthrogryposis. Magini P, et al. Am J Hum Genet, 2019 Oct 3. PMID 31495489, Free PMC Article
  2. Neutral sphingomyelinase-3 is a DNA damage and nongenotoxic stress-regulated gene that is deregulated in human malignancies. Corcoran CA, et al. Mol Cancer Res, 2008 May. PMID 18505924, Free PMC Article
  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. Highly variable penetrance of abnormal phenotypes in embryonic lethal knockout mice. Wilson R, et al. Wellcome Open Res, 2016. PMID 27996060, Free PMC Article

See all (7) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
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 activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
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 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 ISO
Inferred from Sequence Orthology
more info
  
involved_in sphingomyelin catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sphingomyelin catabolic process ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus ISO
Inferred from Sequence Orthology
more info
  
located_in endoplasmic reticulum ISO
Inferred from Sequence Orthology
more info
  
located_in nuclear envelope ISO
Inferred from Sequence Orthology
more info
  
located_in nuclear outer membrane ISO
Inferred from Sequence Orthology
more info
  
located_in sarcolemma ISO
Inferred from Sequence Orthology
more info
  
located_in trans-Golgi network ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
sphingomyelin phosphodiesterase 4
Names
sphingomyelin phosphodiesterase 4, neutral membrane
NP_001161278.2

NCBI Reference Sequences (RefSeq)

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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_001167806.2 → NP_001161278.2  sphingomyelin phosphodiesterase 4

    See identical proteins and their annotated locations for NP_001161278.2

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000011
    UniProtKB/TrEMBL
    A6JSK9, F1MAK9
    Related
    ENSRNOP00000047410.6, ENSRNOT00000043545.6
    Conserved Domains (1) summary
    pfam14724
    Location:8 → 768
    mit_SMPDase; Mitochondrial-associated sphingomyelin phosphodiesterase

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086029.1 Reference GRCr8

    Range
    96866805..96890520 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001024994.1: Suppressed sequence

    Description
    NM_001024994.1: This RefSeq was suppressed temporarily based on the calculation that the encoded protein was shorter than proteins from the putative ortholog from human: FLJ20297 (GeneID:55627).
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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