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

    Gene ID: 268656, updated on 9-Dec-2024

    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; epidermis; and liver. Human ortholog(s) of this gene implicated in hereditary sensory and autonomic neuropathy type 1A and juvenile amyotrophic lateral sclerosis type 27. Orthologous to human SPTLC1 (serine palmitoyltransferase long chain base subunit 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in bladder adult (RPKM 10.7), placenta adult (RPKM 10.3) and 28 other tissues See more
    Orthologs
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    Genomic context

    See Sptlc1 in Genome Data Viewer
    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_000079.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 33574 Neighboring gene predicted gene, 33631 Neighboring gene STARR-seq mESC enhancer starr_34568 Neighboring gene STARR-positive B cell enhancer mm9_chr13:53472671-53472972 Neighboring gene predicted gene 2762 Neighboring gene predicted gene, 38564 Neighboring gene STARR-seq mESC enhancer starr_34569 Neighboring gene predicted gene, 33763 Neighboring gene msh homeobox 2

    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)

    Pathways from PubChem

    Interactions

    General gene information

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    involved_in ceramide biosynthetic process  
    acts_upstream_of_or_within ceramide biosynthetic process PubMed 
    acts_upstream_of_or_within ceramide biosynthetic process PubMed 
    acts_upstream_of lipophagy  
    acts_upstream_of_or_within positive regulation of lipophagy  
    involved_in regulation of fat cell apoptotic process PubMed 
    acts_upstream_of_or_within sphinganine biosynthetic process PubMed 
    acts_upstream_of_or_within sphingolipid biosynthetic process  
    involved_in sphingolipid metabolic process PubMed 
    involved_in sphingomyelin biosynthetic process PubMed 
    acts_upstream_of_or_within sphingomyelin biosynthetic process PubMed 
    acts_upstream_of_or_within sphingomyelin biosynthetic process PubMed 
    involved_in sphingosine biosynthetic process  
    acts_upstream_of_or_within sphingosine biosynthetic process PubMed 
    involved_in sphingosine biosynthetic process  
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum  
    located_in endoplasmic reticulum  
    located_in endoplasmic reticulum membrane PubMed 
    part_of serine palmitoyltransferase complex PubMed 
    part_of serine palmitoyltransferase complex PubMed 
    part_of serine palmitoyltransferase complex  

    General protein information

    Preferred Names
    serine palmitoyltransferase 1
    Names
    long chain base biosynthesis protein 1
    serine-palmitoyl-CoA transferase 1
    NP_001413392.1
    NP_001413393.1
    NP_001413395.1
    NP_001413396.1
    NP_001413397.1
    NP_033295.2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001426463.1NP_001413392.1  serine palmitoyltransferase 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC159201
      UniProtKB/TrEMBL
      Q3TTW4, Q3V3Z5, Q8C295
    2. NM_001426464.1NP_001413393.1  serine palmitoyltransferase 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC159201
      UniProtKB/TrEMBL
      Q3TTW4, Q3V3Z5, Q8C295
    3. NM_001426466.1NP_001413395.1  serine palmitoyltransferase 1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC159201
      UniProtKB/TrEMBL
      Q3V3Z5
    4. NM_001426467.1NP_001413396.1  serine palmitoyltransferase 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC159201
      UniProtKB/TrEMBL
      Q3TST8, Q3V3A0
    5. NM_001426468.1NP_001413397.1  serine palmitoyltransferase 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC159201
    6. NM_009269.3NP_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:81467
      BioF; 7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]
      cl18945
      Location:11472
      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 ...

    RNA

    1. NR_189736.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC159201
    2. NR_189737.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC159201

    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_000079.7 Reference GRCm39 C57BL/6J

      Range
      53486784..53531401 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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