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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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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

Gene LinkOut

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