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Sgms2 sphingomyelin synthase 2 [ Rattus norvegicus (Norway rat) ]

Gene ID: 310849, updated on 2-Nov-2024

Summary

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Official Symbol
Sgms2provided by RGD
Official Full Name
sphingomyelin synthase 2provided by RGD
Primary source
RGD:1305778
See related
EnsemblRapid:ENSRNOG00000011284 AllianceGenome:RGD:1305778
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
spermatin; RGD1305778
Summary
Predicted to enable ceramide cholinephosphotransferase activity; ceramide phosphoethanolamine synthase activity; and sphingomyelin synthase activity. Predicted to be involved in ceramide biosynthetic process; regulation of bone mineralization; and sphingomyelin biosynthetic process. Predicted to act upstream of or within ceramide phosphoethanolamine biosynthetic process. Located in plasma membrane. Human ortholog(s) of this gene implicated in calvarial doughnut lesions with bone fragility. Orthologous to human SGMS2 (sphingomyelin synthase 2). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Kidney (RPKM 131.9), Testes (RPKM 74.2) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Sgms2 in Genome Data Viewer
Location:
2q43
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (222567661..222641804, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (219889809..219967704, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (236458276..236530667, complement)

Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134485686 Neighboring gene cytochrome P450, family 2, subfamily u, polypeptide 1 Neighboring gene aminoacyl tRNA synthetase complex-interacting multifunctional protein 1, pseudogene 1 Neighboring gene uncharacterized LOC108350108 Neighboring gene uncharacterized LOC134485969 Neighboring gene uncharacterized LOC120100944 Neighboring gene uncharacterized LOC134485970 Neighboring gene 3'-phosphoadenosine 5'-phosphosulfate synthase 1

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 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. Cellular localization of sphingomyelin synthase 2 in the seminiferous epithelium of adult rat testes. Lee NP, et al. J Endocrinol, 2007 Jan. PMID 17210739
  2. Osteoporosis and skeletal dysplasia caused by pathogenic variants in SGMS2. Pekkinen M, et al. JCI Insight, 2019 Apr 4. PMID 30779713, Free PMC Article
  3. Developmental stage-specific expression of genes for sphingomyelin synthase in rat brain. Filippenkov IB, et al. Cell Tissue Res, 2018 Apr. PMID 29294205
  4. Sphingomyelin synthases regulate protein trafficking and secretion. Subathra M, et al. PLoS One, 2011. PMID 21980337, Free PMC Article
  5. Functional characterization of enzymes catalyzing ceramide phosphoethanolamine biosynthesis in mice. Bickert A, et al. J Lipid Res, 2015 Apr. PMID 25667419, Free PMC Article

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables ceramide cholinephosphotransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ceramide cholinephosphotransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables ceramide cholinephosphotransferase activity ISO
Inferred from Sequence Orthology
more info
  
enables ceramide phosphoethanolamine synthase activity IEA
Inferred from Electronic Annotation
more info
  
enables ceramide phosphoethanolamine synthase activity ISO
Inferred from Sequence Orthology
more info
  
enables kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables phosphotransferase activity, for other substituted phosphate groups IEA
Inferred from Electronic Annotation
more info
  
enables sphingomyelin synthase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables sphingomyelin synthase activity IEA
Inferred from Electronic Annotation
more info
  
enables sphingomyelin synthase activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in ceramide biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ceramide biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within ceramide biosynthetic process ISO
Inferred from Sequence Orthology
more info
  
involved_in ceramide phosphoethanolamine biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within ceramide phosphoethanolamine biosynthetic process ISO
Inferred from Sequence Orthology
more info
  
involved_in phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of bone mineralization IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of bone mineralization ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of bone mineralization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in sphingolipid metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in sphingomyelin biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sphingomyelin biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within sphingomyelin biosynthetic process ISO
Inferred from Sequence Orthology
more info
  
involved_in sphingomyelin biosynthetic process ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus ISO
Inferred from Sequence Orthology
more info
  
is_active_in Golgi membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi membrane IEA
Inferred from Electronic Annotation
more info
  
located_in Golgi membrane ISO
Inferred from Sequence Orthology
more info
  
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
phosphatidylcholine:ceramide cholinephosphotransferase 2
NP_001014065.1
XP_006233373.1
XP_017446423.1
XP_038958378.1
XP_038958379.1
XP_038958380.1
XP_038958381.1
XP_063138026.1
XP_063138027.1

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_001014043.1 → NP_001014065.1  phosphatidylcholine:ceramide cholinephosphotransferase 2

    See identical proteins and their annotated locations for NP_001014065.1

    Status: PROVISIONAL

    Source sequence(s)
    BC085803
    UniProtKB/TrEMBL
    A0A0G2JSK7, A0A8I5ZQ87, A6HVS9
    Related
    ENSRNOP00000015020.5, ENSRNOT00000015020.7
    Conserved Domains (1) summary
    pfam14360
    Location:220 → 293
    PAP2_C; PAP2 superfamily C-terminal

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_086020.1 Reference GRCr8

    Range
    222567661..222641804 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039102450.2 → XP_038958378.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

    UniProtKB/TrEMBL
    A0A0G2JSK7, A0A8I5ZQ87, A6HVS9
    Conserved Domains (1) summary
    pfam14360
    Location:220 → 293
    PAP2_C; PAP2 superfamily C-terminal

  2. XM_039102451.2 → XP_038958379.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

    UniProtKB/TrEMBL
    A0A0G2JSK7, A0A8I5ZQ87, A6HVS9
    Conserved Domains (1) summary
    pfam14360
    Location:220 → 293
    PAP2_C; PAP2 superfamily C-terminal

  3. XM_017590934.3 → XP_017446423.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

    UniProtKB/TrEMBL
    A0A0G2JSK7, A0A8I5ZQ87, A6HVS9
    Conserved Domains (1) summary
    pfam14360
    Location:220 → 293
    PAP2_C; PAP2 superfamily C-terminal

  4. XM_063281956.1 → XP_063138026.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

    UniProtKB/TrEMBL
    A0A0G2JSK7, A6HVS9

  5. XM_039102452.2 → XP_038958380.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

    UniProtKB/TrEMBL
    A0A0G2JSK7, A0A8I5ZQ87, A6HVS9
    Conserved Domains (1) summary
    pfam14360
    Location:220 → 293
    PAP2_C; PAP2 superfamily C-terminal

  6. XM_039102453.2 → XP_038958381.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

    UniProtKB/TrEMBL
    A0A0G2JSK7, A0A8I5ZQ87, A6HVS9
    Conserved Domains (1) summary
    pfam14360
    Location:220 → 293
    PAP2_C; PAP2 superfamily C-terminal

  7. XM_006233311.5 → XP_006233373.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

    See identical proteins and their annotated locations for XP_006233373.1

    UniProtKB/TrEMBL
    A0A0G2JSK7, A0A8I5ZQ87, A6HVS9
    Conserved Domains (1) summary
    pfam14360
    Location:220 → 293
    PAP2_C; PAP2 superfamily C-terminal

  8. XM_063281957.1 → XP_063138027.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X2

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q4JM44.2 GenPept UniProtKB/Swiss-Prot:Q4JM44

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