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    Sptssb serine palmitoyltransferase, small subunit B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 100362555, updated on 3-Apr-2024

    Summary

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    Official Symbol
    Sptssbprovided by RGD
    Official Full Name
    serine palmitoyltransferase, small subunit Bprovided by RGD
    Primary source
    RGD:2324614
    See related
    Ensembl:ENSRNOG00000009388 AllianceGenome:RGD:2324614
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to contribute to serine C-palmitoyltransferase activity. Predicted to be involved in ceramide biosynthetic process; endoplasmic reticulum organization; and regulation of serine C-palmitoyltransferase activity. Predicted to act upstream of or within sphingolipid biosynthetic process. Predicted to be integral component of membrane. Predicted to be part of serine C-palmitoyltransferase complex. Orthologous to human SPTSSB (serine palmitoyltransferase small subunit B). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Adrenal (RPKM 37.3), Brain (RPKM 34.8) and 3 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Sptssb in Genome Data Viewer
    Location:
    2q32
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (156432509..156461936, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (154133728..154162127, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (166654036..166682325, complement)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene NMD3 ribosome export adaptor Neighboring gene NSA2 ribosome biogenesis factor, pseudogene 13 Neighboring gene otolin 1 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene small nucleolar RNA SNORA17

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Elevation of 20-carbon long chain bases due to a mutation in serine palmitoyltransferase small subunit b results in neurodegeneration. Zhao L, et al. Proc Natl Acad Sci U S A, 2015 Oct 20. PMID 26438849, Free PMC Article
    2. Identification of small subunits of mammalian serine palmitoyltransferase that confer distinct acyl-CoA substrate specificities. Han G, et al. Proc Natl Acad Sci U S A, 2009 May 19. PMID 19416851, Free PMC Article
    3. 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
    4. 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 RGD

    Function Evidence Code Pubs
    contributes_to serine C-palmitoyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    contributes_to serine C-palmitoyltransferase activity ISO
    Inferred from Sequence Orthology
    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 ceramide biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endoplasmic reticulum organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within endoplasmic reticulum organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of serine C-palmitoyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within sphingolipid biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in sphingosine biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of serine C-palmitoyltransferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of serine C-palmitoyltransferase complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    serine palmitoyltransferase small subunit B
    Names
    androgen down regulated in mouse prostate

    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_001271299.1 → NP_001258228.1  serine palmitoyltransferase small subunit B

      See identical proteins and their annotated locations for NP_001258228.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      BC087706, FM125939
      UniProtKB/TrEMBL
      A6J5N9
      Related
      ENSRNOT00000091198.2
      Conserved Domains (1) summary
      pfam11779
      Location:7 → 60
      SPT_ssu-like; Small subunit of serine palmitoyltransferase-like

    2. NM_001271301.1 → NP_001258230.1  serine palmitoyltransferase small subunit B

      See identical proteins and their annotated locations for NP_001258230.1

      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)
      BC087706
      UniProtKB/TrEMBL
      A6J5N9
      Related
      ENSRNOT00000012422.6
      Conserved Domains (1) summary
      pfam11779
      Location:7 → 60
      SPT_ssu-like; Small subunit of serine palmitoyltransferase-like

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086020.1 Reference GRCr8

      Range
      156432509..156461936 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063281087.1 → XP_063137157.1  serine palmitoyltransferase small subunit B isoform X1

      UniProtKB/TrEMBL
      A6J5N9

    2. XM_063281086.1 → XP_063137156.1  serine palmitoyltransferase small subunit B isoform X1

      UniProtKB/TrEMBL
      A6J5N9
    Nucleotide Protein Strain
    Heading Accession and Version

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