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    sptlc3 serine palmitoyltransferase, long chain base subunit 3 [ Danio rerio (zebrafish) ]

    Gene ID: 445168, updated on 2-Nov-2024

    Summary

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    Official Symbol
    sptlc3provided by ZNC
    Official Full Name
    serine palmitoyltransferase, long chain base subunit 3provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-041210-281
    See related
    Ensembl:ENSDARG00000030743 AllianceGenome:ZFIN:ZDB-GENE-041210-281
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    zgc:101107; si:dkey-246k9.1
    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 biosynthetic process. Predicted to be located in membrane. Predicted to be part of serine palmitoyltransferase complex. Is expressed in EVL; gut; periderm; and pronephric duct. Orthologous to human SPTLC3 (serine palmitoyltransferase long chain base subunit 3). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See sptlc3 in Genome Data Viewer
    Location:
    chromosome: 13
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 13 NC_007124.7 (34799766..34858516, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 13 NC_007124.6 (34678234..34736330, complement)

    Chromosome 13 - NC_007124.7Genomic Context describing neighboring genes Neighboring gene taspase, threonine aspartase, 1 Neighboring gene isthmin 1 Neighboring gene U6atac minor spliceosomal RNA Neighboring gene BTB (POZ) domain containing 3b

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Exome Sequence Analysis Suggests that Genetic Burden Contributes to Phenotypic Variability and Complex Neuropathy. Gonzaga-Jauregui C, et al. Cell Rep, 2015 Aug 18. PMID 26257172, Free PMC Article
    2. Parallel Reaction Monitoring reveals structure-specific ceramide alterations in the zebrafish. Zhang T, et al. Sci Rep, 2019 Dec 27. PMID 31882772, Free PMC Article
    3. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    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
    		  
    enables serine C-palmitoyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables serine C-palmitoyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ceramide biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sphingosine biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of serine palmitoyltransferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    serine palmitoyltransferase 3
    NP_001003562.2
    XP_021336238.1
    XP_021336239.1

    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_001003562.3 → NP_001003562.2  serine palmitoyltransferase 3

      Status: VALIDATED

      Source sequence(s)
      CR376850, CU640432
      UniProtKB/TrEMBL
      A0A8M9Q9N3, Q6DC52
      Related
      ENSDARP00000146370.1, ENSDART00000184843.1
      Conserved Domains (1) summary
      PLN02483
      Location:58 → 535
      PLN02483; serine palmitoyltransferase

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007124.7 Reference GRCz11 Primary Assembly

      Range
      34799766..34858516 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021480563.2 → XP_021336238.1  serine palmitoyltransferase 3 isoform X1

      UniProtKB/TrEMBL
      A0A8M9Q9N3, Q6DC52
      Conserved Domains (1) summary
      PLN02483
      Location:58 → 535
      PLN02483; serine palmitoyltransferase

    2. XM_021480564.2 → XP_021336239.1  serine palmitoyltransferase 3 isoform X1

      UniProtKB/TrEMBL
      A0A8M9Q9N3, Q6DC52
      Related
      ENSDARP00000047551.5, ENSDART00000047552.8
      Conserved Domains (1) summary
      PLN02483
      Location:58 → 535
      PLN02483; serine palmitoyltransferase
    Nucleotide Protein Strain
    Heading Accession and Version

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