Smpd1 sphingomyelin phosphodiesterase 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Smpd1provided by RGD
Official Full Name: sphingomyelin phosphodiesterase 1provided by RGD
Primary source: RGD:1549719
See related: EnsemblRapid:ENSRNOG00000017977 AllianceGenome:RGD:1549719
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
Summary: Predicted to enable acid sphingomyelin phosphodiesterase activity and zinc ion binding activity. Involved in several processes, including ceramide biosynthetic process; positive regulation of apoptotic process; and response to cocaine. Located in extracellular space and lamellar body. Used to study Wilson disease. Human ortholog(s) of this gene implicated in Niemann-Pick disease; Niemann-Pick disease type A; and Niemann-Pick disease type B. Orthologous to human SMPD1 (sphingomyelin phosphodiesterase 1). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Biased expression in Liver (RPKM 433.6), Heart (RPKM 374.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q32

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (169304772..169308615)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (159892946..159896789)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (170383682..170387525)

Chromosome 1 - NC_086019.1 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?

summary, the data above strongly suggest that the age-dependent up-regulation of ASMase plays an important role in the modulation of ceramide and SM contents in rat tissues and that imipramine and zoledronic acid are useful tools for SM turnover.
Title: Role of acid sphingomyelinase in the age-dependent dysregulation of sphingolipids turnover in the tissues of rats.

Submit: New GeneRIF Correction

General gene information

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Markers

AF206720 (e-PCR)
- UniSTS:208174

Smpd1 (e-PCR), detects polymorphism
- UniSTS:144444

Smpd1 (e-PCR), detects polymorphism
- UniSTS:507234

RH134756 (e-PCR)
- UniSTS:218034

UniSTS:235734 (e-PCR)
- UniSTS:235734

RH130448 (e-PCR)
- UniSTS:213732

SMPD1_855 (e-PCR)
- UniSTS:277756

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables acid sphingomyelin phosphodiesterase activity	IBA Inferred from Biological aspect of Ancestor more info
enables acid sphingomyelin phosphodiesterase activity	ISO Inferred from Sequence Orthology more info
enables hydrolase activity, acting on glycosyl bonds	IEA Inferred from Electronic Annotation more info
enables sphingomyelin phosphodiesterase activity	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cellular response to UV	ISO Inferred from Sequence Orthology more info
involved_in cellular response to calcium ion	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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ceramide biosynthetic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ceramide metabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cholesterol metabolic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of MAP kinase activity	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of MAP kinase activity	ISO Inferred from Sequence Orthology more info
involved_in plasma membrane repair	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of endocytosis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of viral entry into host cell	IEA Inferred from Electronic Annotation more info
involved_in response to cocaine	IDA Inferred from Direct Assay more info	PubMed
involved_in response to interleukin-1	ISO Inferred from Sequence Orthology more info
involved_in response to ionizing radiation	ISO Inferred from Sequence Orthology more info
involved_in response to tumor necrosis factor	ISO Inferred from Sequence Orthology more info
involved_in response to type I interferon	ISO Inferred from Sequence Orthology more info
involved_in response to virus	ISO Inferred from Sequence Orthology more info
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in sphingomyelin catabolic process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within sphingomyelin catabolic process	ISO Inferred from Sequence Orthology more info
involved_in sphingomyelin catabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of symbiont entry into host cell	ISO Inferred from Sequence Orthology more info
acts_upstream_of_positive_effect symbiont entry into host cell	ISO Inferred from Sequence Orthology more info
involved_in symbiont entry into host cell	ISO Inferred from Sequence Orthology more info
involved_in termination of signal transduction	ISO Inferred from Sequence Orthology more info
involved_in wound healing	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in endolysosome	ISO Inferred from Sequence Orthology more info
located_in endosome	ISO Inferred from Sequence Orthology more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
is_active_in extracellular space	ISO Inferred from Sequence Orthology more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info
located_in lamellar body	IDA Inferred from Direct Assay more info	PubMed
is_active_in lysosome	IBA Inferred from Biological aspect of Ancestor more info
is_active_in lysosome	ISO Inferred from Sequence Orthology more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: sphingomyelin phosphodiesterase

Names: sphingomyelin phosphodiesterase 1, acid lysosomal

NP_001006998.1

EC 3.1.4.12

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_001006997.1 → NP_001006998.1 sphingomyelin phosphodiesterase

See identical proteins and their annotated locations for NP_001006998.1

Status: PROVISIONAL

Source sequence(s)

BC083780

UniProtKB/TrEMBL

F7ETC0, Q5XIA6

Related

ENSRNOP00000024224.4, ENSRNOT00000024224.6

Conserved Domains (3) summary

smart00741
Location:85 → 158

SapB; Saposin (B) Domains

cd00842
Location:199 → 494

MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain

pfam00149
Location:252 → 459

Metallophos; Calcineurin-like phosphoesterase