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

Summary

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

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_086020.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

in contrast to Sgms1, Sgms2 does not contain the multi-exon 5'-UTR but encodes circRNAs, which are composed of the coding region of the gene and are expressed at a low level.
Title: Developmental stage-specific expression of genes for sphingomyelin synthase in rat brain.
SMS1 and SMS2 are capable of regulating TGN-mediated protein trafficking and secretion
Title: Sphingomyelin synthases regulate protein trafficking and secretion.

Submit: New GeneRIF Correction

General gene information

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Markers

MGI:3693554 (e-PCR)
- UniSTS:498418

UniSTS:498418 (e-PCR)
- UniSTS:498418

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

EC 2.7.8.27

XP_006233373.1

EC 2.7.8.27

XP_017446423.1

EC 2.7.8.27

XP_038958378.1

EC 2.7.8.27

XP_038958379.1

EC 2.7.8.27

XP_038958380.1

EC 2.7.8.27

XP_038958381.1

EC 2.7.8.27

XP_063138026.1

EC 2.7.8.27

XP_063138027.1

EC 2.7.8.27

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)

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

NC_086020.1 Reference GRCr8

Range

222567661..222641804 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A0G2JSK7, A6HVS9
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
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
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
XM_063281957.1 → XP_063138027.1 phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X2