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Sptlc2 serine palmitoyltransferase, long chain base subunit 2 [ Mus musculus (house mouse) ]

Gene ID: 20773, updated on 9-May-2024

Summary

Official Symbol
Sptlc2provided by MGI
Official Full Name
serine palmitoyltransferase, long chain base subunit 2provided by MGI
Primary source
MGI:MGI:108074
See related
Ensembl:ENSMUSG00000021036 AllianceGenome:MGI:108074
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
LCB2; Spt2; LCB2a
Summary
This gene encodes a long chain base subunit of serine palmitoyltransferase. The enzyme, serine palmitoyltransferase, consists of two different subunits, and is the key enzyme in sphingolipid biosynthesis. It catalyzes the pyridoxal-5-prime-phosphate-dependent condensation of L-serine and palmitoyl-CoA to 3-oxosphinganine. A mutant allele of this gene in mice is used as a model for the human disease 'Susceptibilty to Psoriasis 1'. Mutations in the human gene are associated with hereditary sensory neuropathy type I. [provided by RefSeq, Sep 2015]
Expression
Ubiquitous expression in placenta adult (RPKM 14.0), large intestine adult (RPKM 10.5) and 28 other tissues See more
Orthologs
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Genomic context

See Sptlc2 in Genome Data Viewer
Location:
12 D2; 12 41.52 cM
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (87351832..87435129, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (87305058..87388355, complement)

Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 53736 Neighboring gene STARR-seq mESC enhancer starr_32874 Neighboring gene isthmin 2 Neighboring gene predicted gene, 51956 Neighboring gene STARR-seq mESC enhancer starr_32879 Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:88729340-88729523 Neighboring gene predicted gene, 33444 Neighboring gene STARR-seq mESC enhancer starr_32884 Neighboring gene STARR-seq mESC enhancer starr_32886 Neighboring gene 60S ribosomal protein L21-like Neighboring gene STARR-seq mESC enhancer starr_32888 Neighboring gene alkB homolog 1, histone H2A dioxygenase Neighboring gene microRNA 3068

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (4) 
  • Gene trapped (1) 
  • Targeted (4)  1 citation

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • mKIAA0526

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables acyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables pyridoxal phosphate binding IEA
Inferred from Electronic Annotation
more info
 
contributes_to serine C-palmitoyltransferase activity IDA
Inferred from Direct Assay
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 adipose tissue development IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
 
acts_upstream_of_or_within sphinganine biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
involved_in sphingolipid 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
 
acts_upstream_of_or_within sphingolipid metabolic process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within sphingomyelin biosynthetic process IMP
Inferred from Mutant Phenotype
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
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 
located_in mitochondrion HDA PubMed 
part_of serine C-palmitoyltransferase complex IBA
Inferred from Biological aspect of Ancestor
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

Preferred Names
serine palmitoyltransferase 2
Names
LCB 2
SPT 2
long chain base biosynthesis protein 2
long chain base biosynthesis protein 2a
serine-palmitoyl-CoA transferase 2
NP_035609.1

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_011479.4NP_035609.1  serine palmitoyltransferase 2

    See identical proteins and their annotated locations for NP_035609.1

    Status: REVIEWED

    Source sequence(s)
    AK037908, AK044917, BY789607, CF747116, CT030249
    Consensus CDS
    CCDS26076.1
    UniProtKB/Swiss-Prot
    P97356, P97363
    UniProtKB/TrEMBL
    Q542D6
    Related
    ENSMUSP00000021424.5, ENSMUST00000021424.5
    Conserved Domains (2) summary
    PLN02483
    Location:65540
    PLN02483; serine palmitoyltransferase
    COG0156
    Location:115530
    BioF; 7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000078.7 Reference GRCm39 C57BL/6J

    Range
    87351832..87435129 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)