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

Summary

Official Symbol: Smpd4provided by RGD
Official Full Name: sphingomyelin phosphodiesterase 4provided by RGD
Primary source: RGD:1310674
See related: EnsemblRapid: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, Nov 2024]
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

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_086029.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

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General gene information

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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

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_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

ENSRNOP00000096822.1, ENSRNOT00000107761.2

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

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

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).