Sptlc1 serine palmitoyltransferase, long chain base subunit 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Sptlc1provided by MGI
Official Full Name: serine palmitoyltransferase, long chain base subunit 1provided by MGI
Primary source: MGI:MGI:1099431
See related: Ensembl:ENSMUSG00000021468 AllianceGenome:MGI:1099431
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Lcb1; SPT1; E030036H05
Summary: Enables serine C-palmitoyltransferase activity. Involved in regulation of fat cell apoptotic process and sphingomyelin biosynthetic process. Acts upstream of or within ceramide biosynthetic process; sphinganine biosynthetic process; and sphingosine biosynthetic process. Located in endoplasmic reticulum membrane. Is expressed in brain and liver. Human ortholog(s) of this gene implicated in hereditary sensory and autonomic neuropathy type 1A. Orthologous to human SPTLC1 (serine palmitoyltransferase long chain base subunit 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in bladder adult (RPKM 10.7), placenta adult (RPKM 10.3) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 13 B1; 13 27.68 cM

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	13	NC_000079.7 (53486784..53531401, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	13	NC_000079.6 (53332748..53377417, complement)

Chromosome 13 - NC_000079.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Murine endothelial serine palmitoyltransferase 1 (SPTLC1) is required for vascular development and systemic sphingolipid homeostasis.
Title: Murine endothelial serine palmitoyltransferase 1 (SPTLC1) is required for vascular development and systemic sphingolipid homeostasis.
mice with an adipocyte-specific deletion of Sptlc1 show that de novo sphingolipid biosynthesis is required for adipocyte cell viability and normal metabolic function and that reduced de novo sphingolipid biosynthesis within adipocytes is associated with adipocyte death, adipose tissue remodeling, and metabolic dysfunction
Title: De Novo Sphingolipid Biosynthesis Is Required for Adipocyte Survival and Metabolic Homeostasis.
Data suggest that overexpression of serine palmitoyltransferase (Sptlc1, serine palmitoyltransferase long chain base subunit 1) to elevate de novo sphingolipid biosynthesis induces autophagy in the liver.
Title: Autophagy regulates sphingolipid levels in the liver.
Sptlc1 deficient mice absorb less cholesterol.
Title: Serine palmitoyltransferase (SPT) deficient mice absorb less cholesterol.
Physical interaction of ABCA1 and SPTLC1 results in reduction of ABCA1 activity and that inhibition of this interaction produces enhanced cholesterol efflux.
Title: SPTLC1 binds ABCA1 to negatively regulate trafficking and cholesterol efflux activity of the transporter.
Both Sptlc1 and Sptlc2 interactions are necessary for Serine palmitoyl-CoA transferase (SPT) activity in vivo and SPT activity directly influences plasma sphingolipid levels
Title: Serine palmitoyl-CoA transferase (SPT) deficiency and sphingolipid levels in mice.
The expression and activities of SPT in mouse liver increased significantly following fumonisin B1 treatment
Title: Ceramide synthase inhibition by fumonisin B1 treatment activates sphingolipid-metabolizing systems in mouse liver.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (2)
Targeted (2) 1 citation
Endonuclease-mediated (7) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW552086 (e-PCR)
- UniSTS:180534

Sptlc1 (e-PCR), detects polymorphism
- UniSTS:547151

RH126236 (e-PCR)
- UniSTS:162944

Sptlc1 (e-PCR), detects polymorphism
- UniSTS:527566

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables acyltransferase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables pyridoxal phosphate binding	IEA Inferred from Electronic Annotation more info
enables serine C-palmitoyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
NOT enables serine C-palmitoyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables serine C-palmitoyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
contributes_to serine C-palmitoyltransferase activity	ISO Inferred from Sequence Orthology more info	PubMed
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in ceramide biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within ceramide biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within ceramide biosynthetic process	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within lipid metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of lipophagy	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of lipophagy	ISO Inferred from Sequence Orthology more info
involved_in regulation of fat cell apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within sphinganine biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within sphingolipid biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in sphingolipid metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sphingomyelin biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within sphingomyelin biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within sphingomyelin biosynthetic process	ISA Inferred from Sequence Alignment more info	PubMed
involved_in sphingosine biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within sphingosine biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sphingosine biosynthetic process	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of SPOTS complex	ISO Inferred from Sequence Orthology more info	PubMed
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
part_of serine C-palmitoyltransferase complex	ISA Inferred from Sequence Alignment more info	PubMed
part_of serine C-palmitoyltransferase complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: serine palmitoyltransferase 1

Names: long chain base biosynthesis protein 1; serine-palmitoyl-CoA transferase 1

NP_001413392.1

EC 2.3.1.50

NP_001413393.1

EC 2.3.1.50

NP_001413395.1

EC 2.3.1.50

NP_001413396.1

EC 2.3.1.50

NP_001413397.1

EC 2.3.1.50

NP_033295.2

EC 2.3.1.50

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_001426463.1 → NP_001413392.1 serine palmitoyltransferase 1 isoform 2

Status: VALIDATED

Source sequence(s)

AC159201
NM_001426464.1 → NP_001413393.1 serine palmitoyltransferase 1 isoform 3

Status: VALIDATED

Source sequence(s)

AC159201
NM_001426466.1 → NP_001413395.1 serine palmitoyltransferase 1 isoform 4

Status: VALIDATED

Source sequence(s)

AC159201
NM_001426467.1 → NP_001413396.1 serine palmitoyltransferase 1 isoform 5

Status: VALIDATED

Source sequence(s)

AC159201

UniProtKB/TrEMBL

Q3TST8
NM_001426468.1 → NP_001413397.1 serine palmitoyltransferase 1 isoform 6

Status: VALIDATED

Source sequence(s)

AC159201
NM_009269.3 → NP_033295.2 serine palmitoyltransferase 1 isoform 1

See identical proteins and their annotated locations for NP_033295.2

Status: VALIDATED

Source sequence(s)

AC159201

Consensus CDS

CCDS26521.1

UniProtKB/Swiss-Prot

O35704, O54813, Q8BH11

UniProtKB/TrEMBL

Q3TTW4, Q3V3Z5, Q8C295

Related

ENSMUSP00000021920.7, ENSMUST00000021920.8

Conserved Domains (2) summary

COG0156
Location:81 → 467

BioF; 7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]

cl18945
Location:11 → 472

AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...