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    SPTSSB serine palmitoyltransferase small subunit B [ Homo sapiens (human) ]

    Gene ID: 165679, updated on 5-Mar-2024

    Summary

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    Official Symbol
    SPTSSBprovided by HGNC
    Official Full Name
    serine palmitoyltransferase small subunit Bprovided by HGNC
    Primary source
    HGNC:HGNC:24045
    See related
    Ensembl:ENSG00000196542 MIM:610412; AllianceGenome:HGNC:24045
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ADMP; SSSPTB; C3orf57
    Summary
    Serine palmitoyltransferase (SPT; EC 2.3.1.50) catalyzes the first committed and rate-limiting step in sphingolipid biosynthesis. SSSPTB is a small SPT subunit that stimulates SPT activity and confers acyl-CoA preference to the SPT catalytic heterodimer of SPTLC1 (MIM 605712) and either SPTLC2 (MIM 605713) or SPTLC3 (MIM 611120) (Han et al., 2009 [PubMed 19416851]).[supplied by OMIM, Nov 2010]
    Expression
    Biased expression in stomach (RPKM 17.1), skin (RPKM 13.9) and 5 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    3q26.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (161344798..161371517, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (164119563..164146294, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (161062586..161089305, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene eukaryotic translation elongation factor 1 gamma pseudogene 4 Neighboring gene proteasome 26S subunit, ATPase 1 pseudogene 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:161088778-161089332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:161089333-161089887 Neighboring gene uncharacterized LOC107986150 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:161138438-161139086 Neighboring gene long intergenic non-protein coding RNA 2067 Neighboring gene ribosomal protein L23a pseudogene 42

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Molecular cloning and characterization of a novel androgen repressible gene expressed in the prostate epithelium. Singh J, et al. Gene, 2005 Mar 28. PMID 15777716
    2. Structural insights into the regulation of human serine palmitoyltransferase complexes. Wang Y, et al. Nat Struct Mol Biol, 2021 Mar. PMID 33558761, Free PMC Article
    3. 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
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article
    5. 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

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ADMP expression was seen predominantly in the prostate epithelium with weaker expression in the fibroblasts and endothelial cells.
      Title: Molecular cloning and characterization of a novel androgen repressible gene expressed in the prostate epithelium.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC104229

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    contributes_to serine C-palmitoyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    contributes_to serine C-palmitoyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in endoplasmic reticulum organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within endoplasmic reticulum organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of serine C-palmitoyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of serine C-palmitoyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within sphingolipid biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in sphingolipid biosynthetic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in sphingosine biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    part_of serine C-palmitoyltransferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of serine C-palmitoyltransferase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of serine C-palmitoyltransferase complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    serine palmitoyltransferase small subunit B
    Names
    androgen down regulated in mouse prostate
    likely ortholog of androgen down regulated gene expressed in mouse prostate
    small subunit of serine palmitoyltransferase B

    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_001040100.2 → NP_001035189.1  serine palmitoyltransferase small subunit B

      See identical proteins and their annotated locations for NP_001035189.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC112491
      Consensus CDS
      CCDS33887.1
      UniProtKB/Swiss-Prot
      B2R5D3, D3DNM8, Q0P5S6, Q8NFR3
      Related
      ENSP00000480827.1, ENST00000620149.2
      Conserved Domains (1) summary
      pfam11779
      Location:7 → 60
      SPT_ssu-like; Small subunit of serine palmitoyltransferase-like

    2. NM_001320679.2 → NP_001307608.1  serine palmitoyltransferase small subunit B

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC112491
      Consensus CDS
      CCDS33887.1
      UniProtKB/Swiss-Prot
      B2R5D3, D3DNM8, Q0P5S6, Q8NFR3
      Related
      ENSP00000420115.1, ENST00000497137.1
      Conserved Domains (1) summary
      pfam11779
      Location:7 → 60
      SPT_ssu-like; Small subunit of serine palmitoyltransferase-like

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      161344798..161371517 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024453380.2 → XP_024309148.1  serine palmitoyltransferase small subunit B isoform X1

      UniProtKB/Swiss-Prot
      B2R5D3, D3DNM8, Q0P5S6, Q8NFR3
      Conserved Domains (1) summary
      pfam11779
      Location:7 → 60
      SPT_ssu-like; Small subunit of serine palmitoyltransferase-like

    2. XM_024453379.2 → XP_024309147.1  serine palmitoyltransferase small subunit B isoform X1

      UniProtKB/Swiss-Prot
      B2R5D3, D3DNM8, Q0P5S6, Q8NFR3
      Conserved Domains (1) summary
      pfam11779
      Location:7 → 60
      SPT_ssu-like; Small subunit of serine palmitoyltransferase-like

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      164119563..164146294 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054345480.1 → XP_054201455.1  serine palmitoyltransferase small subunit B isoform X1

      UniProtKB/Swiss-Prot
      B2R5D3, D3DNM8, Q0P5S6, Q8NFR3

    2. XM_054345479.1 → XP_054201454.1  serine palmitoyltransferase small subunit B isoform X1

      UniProtKB/Swiss-Prot
      B2R5D3, D3DNM8, Q0P5S6, Q8NFR3

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_145035.2: Suppressed sequence

      Description
      NM_145035.2: This RefSeq was permanently suppressed because it contains the wrong CDS and is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NFR3.1 GenPept UniProtKB/Swiss-Prot:Q8NFR3

    Gene LinkOut

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

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