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Sptlc3 serine palmitoyltransferase, long chain base subunit 3 [ Mus musculus (house mouse) ]

Gene ID: 228677, updated on 2-Nov-2024

Summary

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Official Symbol
Sptlc3provided by MGI
Official Full Name
serine palmitoyltransferase, long chain base subunit 3provided by MGI
Primary source
MGI:MGI:2444678
See related
Ensembl:ENSMUSG00000039092 AllianceGenome:MGI:2444678
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
C130053K05Rik
Summary
Predicted to enable serine C-palmitoyltransferase activity. Predicted to be involved in ceramide biosynthetic process and sphingosine biosynthetic process. Predicted to act upstream of or within sphingoid biosynthetic process. Predicted to be located in endoplasmic reticulum membrane. Predicted to be part of serine palmitoyltransferase complex. Is expressed in several structures, including alimentary system; genitourinary system; integumental system; respiratory system; and sensory organ. Orthologous to human SPTLC3 (serine palmitoyltransferase long chain base subunit 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in bladder adult (RPKM 11.3) and limb E14.5 (RPKM 0.7) See more
Orthologs
human all
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Genomic context

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See Sptlc3 in Genome Data Viewer
Location:
2 F3; 2 68.52 cM
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (139335833..139478981)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (139493913..139637061)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_05832 Neighboring gene predicted gene 14066 Neighboring gene ADP/ATP translocase 2 pseudogene Neighboring gene STARR-seq mESC enhancer starr_05833 Neighboring gene STARR-seq mESC enhancer starr_05835 Neighboring gene STARR-seq mESC enhancer starr_05836 Neighboring gene STARR-seq mESC enhancer starr_05837 Neighboring gene isthmin 1, angiogenesis inhibitor Neighboring gene STARR-seq mESC enhancer starr_05838 Neighboring gene STARR-seq mESC enhancer starr_05839 Neighboring gene taspase, threonine aspartase 1 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:139750776-139750959 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:139760469-139760763 Neighboring gene STARR-positive B cell enhancer mm9_chr2:139792158-139792459 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:139867947-139868134 Neighboring gene STARR-positive B cell enhancer ABC_E4503

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data 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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Related articles in PubMed

  1. SPTLC3 Is Essential for Complex I Activity and Contributes to Ischemic Cardiomyopathy. Kovilakath A, et al. Circulation, 2024 Aug 20. PMID 38660786,
  2. Hepatic expression of the Sptlc3 subunit of serine palmitoyltransferase is associated with the development of hepatocellular carcinoma in a mouse model of nonalcoholic steatohepatitis. Yoshimine Y, et al. Oncol Rep, 2015 Apr. PMID 25607821
  3. The RIPK4-IRF6 signalling axis safeguards epidermal differentiation and barrier function. Oberbeck N, et al. Nature, 2019 Oct. PMID 31578523
  4. Transcription factor Ctip2 controls epidermal lipid metabolism and regulates expression of genes involved in sphingolipid biosynthesis during skin development. Wang Z, et al. J Invest Dermatol, 2013 Mar. PMID 23096701, Free PMC Article
  5. Morphology-based mammalian stem cell tests reveal potential developmental toxicity of donepezil. Lau CG, et al. Mol Reprod Dev, 2014 Nov. PMID 25269881

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SPTLC3 Is Essential for Complex I Activity and Contributes to Ischemic Cardiomyopathy.
    Title: SPTLC3 Is Essential for Complex I Activity and Contributes to Ischemic Cardiomyopathy.
  2. hepatic expression of Sptlc3 mRNA may be closely associated with NASH-associated hepatocarcinogenesis.
    Title: Hepatic expression of the Sptlc3 subunit of serine palmitoyltransferase is associated with the development of hepatocellular carcinoma in a mouse model of nonalcoholic steatohepatitis.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
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
  
enables serine C-palmitoyltransferase activity ISO
Inferred from Sequence Orthology
more info
  
enables serine C-palmitoyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in ceramide biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within sphingoid biosynthetic process ISO
Inferred from Sequence Orthology
more info
  
involved_in sphingosine biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sphingosine biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in sphingosine biosynthetic process ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  
part_of serine palmitoyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of serine palmitoyltransferase complex ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
serine palmitoyltransferase 3
Names
LCB 3
LCB2b
SPT 3
long chain base biosynthesis protein 2b
long chain base biosynthesis protein 3
serine-palmitoyl-CoA transferase 3
serine-palmityl-CoA transferase 3
NP_001343436.1
NP_780676.1

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_001356507.1 → NP_001343436.1  serine palmitoyltransferase 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    AK078679, AL928899
    Consensus CDS
    CCDS16800.1
    UniProtKB/Swiss-Prot
    Q505L2, Q8BG54
    Related
    ENSMUSP00000105710.2, ENSMUST00000110083.8
    Conserved Domains (1) summary
    PLN02483
    Location:56 → 535
    PLN02483; serine palmitoyltransferase

  2. NM_175467.4 → NP_780676.1  serine palmitoyltransferase 3

    See identical proteins and their annotated locations for NP_780676.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    AK048374, AK078686, AL928899
    Consensus CDS
    CCDS16800.1
    UniProtKB/Swiss-Prot
    Q505L2, Q8BG54
    Related
    ENSMUSP00000048313.3, ENSMUST00000047370.3
    Conserved Domains (1) summary
    PLN02483
    Location:56 → 535
    PLN02483; serine palmitoyltransferase

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_000068.8 Reference GRCm39 C57BL/6J

    Range
    139335833..139478981
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8BG54.1 GenPept UniProtKB/Swiss-Prot:Q8BG54

Gene LinkOut

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