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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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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