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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SPTSSB Gene

protein-coding   GIFtS: 39
GCID: GC03M161063

serine palmitoyltransferase, small subunit B

(Previous name: chromosome 3 open reading frame 57 )
(Previous symbol: C3orf57)
 Explore 1 disease affiliated with
SPTSSB via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for SPTSSB    

Aliases
for SPTSSB gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Serine Palmitoyltransferase, Small Subunit B1 2     Chromosome 3 Open Reading Frame 571
ADMP1 2 3     Androgen Down Regulated In Mouse Prostate2
C3orf571 2 3     Likely Ortholog Of Androgen Down Regulated Gene Expressed In Mouse Prostate2
SsSPTb1     Serine Palmitoyltransferase Small Subunit B2
Small Subunit Of Serine Palmitoyltransferase B2 3     Protein ADMP3
SSSPTB2 3     

External Ids:    HGNC: 240451   Entrez Gene: 1656792   Ensembl: ENSG000001965427   OMIM: 6104125   UniProtKB: Q8NFR33   

Export aliases for SPTSSB gene to outside databases


Summaries
for SPTSSB gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for SPTSSB:
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)

UniProtKB/Swiss-Prot: SPTSB_HUMAN, Q8NFR3
Function: Stimulates the activity of serine palmitoyltransferase (SPT). The composition of the serine
palmitoyltransferase (SPT) complex determines the substrate preference, complexes with this subunit showing a clear
preference for longer acyl-CoAs. The SPTLC1-SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate,
while the SPTLC1-SPTLC3-SPTSSB isozyme displays an ability to use a broader range of acyl-CoAs, without apparent
preference. May play a role in signal transduction




Genomic Views
for SPTSSB gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000003.11  NC_018914.1  NT_005612.16  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for SPTSSB
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for SPTSSB

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SPTSSB


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3q26.1   Ensembl cytogenetic band:  3q26.1   HGNC cytogenetic band: 3q26.1

SPTSSB Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SPTSSB gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M161063:  view genomic region     (about GC identifiers)

Start:
 161,062,580 bp from pter      End:
 161,090,668 bp from pter
Size:
 28,089 bases      Orientation:
 minus strand

Proteins
for SPTSSB gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: SPTSB_HUMAN, Q8NFR3 (See protein sequence)
Recommended Name: Serine palmitoyltransferase small subunit B  
Size: 76 amino acids; 9198 Da
Subunit: Interacts with SPTLC1; the interaction is direct. Component of the serine palmitoyltransferase (SPT) complex,
composed of SPTLC1, either SPTLC2 or SPTLC3, and either SPTSSA or SPTSSB
Subcellular location: Endoplasmic reticulum membrane; Multi-pass membrane protein (Potential)
Secondary accessions: B2R5D3 D3DNM8 Q0P5S6

Explore the universe of human proteins at neXtProt for SPTSSB: NX_Q8NFR3

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8NFR3

    • SPTSSB Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_001035189.1  
    ENSEMBL proteins: 
     ENSP00000352097   ENSP00000420115  

    Human Recombinant Protein Products: 
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    Novus Biologicals SPTSSB Lysate
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    Uscn Proteins for SPTSSB

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral to membrane IEA--
    GO:0017059serine C-palmitoyltransferase complex IDA19416851


    SPTSSB for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for SPTSSB

    Protein Domains /
    Families
    for SPTSSB gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    SPTSSB for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR024512 Ser_palmitoyltrfase_ssu-like

    Graphical View of Domain Structure for InterPro Entry Q8NFR3

    ProtoNet protein and cluster: Q8NFR3

    UniProtKB/Swiss-Prot: SPTSB_HUMAN, Q8NFR3
    Similarity: Belongs to the SPTSS family. SPTSSB subfamily


    Function
    for SPTSSB gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: SPTSB_HUMAN, Q8NFR3
    Function: Stimulates the activity of serine palmitoyltransferase (SPT). The composition of the serine
    palmitoyltransferase (SPT) complex determines the substrate preference, complexes with this subunit showing a clear
    preference for longer acyl-CoAs. The SPTLC1-SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate,
    while the SPTLC1-SPTLC3-SPTSSB isozyme displays an ability to use a broader range of acyl-CoAs, without apparent
    preference. May play a role in signal transduction
    Induction: Expression is suppressed by androgens in the androgen-sensitive LNCaP cell line

    miRNA
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    Inhib. RNA
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    Gene Editing
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    Clone
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    Cell Line
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    Search LifeMap BioReagents cell lines for SPTSSB

    In Situ Assay
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004758contributes to serine C-palmitoyltransferase activity IDA19416851
    GO:0005515protein binding IPI19416851


    SPTSSB for ontologies           About GeneDecksing



    Pathways & Interactions
    for SPTSSB gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    UniProtKB/Swiss-Prot: SPTSB_HUMAN, Q8NFR3
    Pathway: Lipid metabolism; sphingolipid metabolism

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SPTSSB

    STRING Interaction Network Preview (showing 5 interactants - click image to see more details)

    5 Interacting proteins for SPTSSB (ENSP000003520974) via UniProtKB, MINT, STRING, and/or I2D

    InteractantInteraction Details
    GeneCardExternal ID(s)
    SPTLC1ENSP000002625544STRING: ENSP00000262554
    SPTLC2ENSP000002164844STRING: ENSP00000216484
    SPTLC3ENSP000003819684STRING: ENSP00000381968
    SPTSSAENSP000002981304STRING: ENSP00000298130
    ORMDL3ENSP000003048584STRING: ENSP00000304858
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030148sphingolipid biosynthetic process TAS19416851


    SPTSSB for ontologies           About GeneDecksing



    Drugs & Compounds
    for SPTSSB gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SPTSSB
    Search CenterWatch for drugs/clinical trials and news about SPTSSB / SPTSB 

    Transcripts
    for SPTSSB gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for SPTSSB gene (2 alternative transcripts): 
    NM_145035.2  NM_001040100.1  

    Unigene Cluster for SPTSSB:

    Serine palmitoyltransferase, small subunit B
    Hs.369104  [show with all ESTs]
    Unigene Representative Sequence: AK123348
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000359175(uc003fee.3) ENST00000497137 ENST00000497374

    miRNA
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    Inhib. RNA
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    Clone
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    Primer
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    Additional cDNA sequence: 

    AF458592.1 AK123348.1 BC037817.2 BC065208.1 BC071875.1 BC107756.1 BC126236.1 BC130565.1 

    1 DOTS entry:

    DT.100645029 

    24/46 AceView cDNA sequences (see all 46):

    CA487194 AI921685 AK123348 NM_145035 BV193848 BU959155 BG289890 BC037817 
    AF458592 BC065208 BP374673 BC071875 CA455115 BG286222 BX509773 BU858267 
    BF365359 BG403886 AI559486 BU950276 BI766630 BQ778568 BG287503 BG402906 

    GeneLoc Exon Structure


    Expression
    for SPTSSB gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SPTSSB expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    SPTSSB expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    2 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    KidneyRenal Collecting Duct SystemKidney
    LimbLimb BudLimb
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See SPTSSB Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SPTSSB

    SOURCE GeneReport for Unigene cluster: Hs.369104

    UniProtKB/Swiss-Prot: SPTSB_HUMAN, Q8NFR3
    Tissue specificity: Expression is seen predominantly in the prostate epithelium with weaker expression in the
    fibroblasts and endothelial cells

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    In Situ
    Assay Products:     
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    Orthologs
    for SPTSSB gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of chordates.

    Orthologs for SPTSSB gene from 3/10 species (see all 10)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves SPTSSB1 serine palmitoyltransferase, small subunit B 71.11(n)
    66.67(a)    		   425008  XM_003641780.1  XP_003641828.1 
    lizard
    (Anolis carolinensis)    		 Reptilia SPTSSB6
    		 --
    		 59(a)
    		 1 ↔ 1
    		 3(12570125-12570364)
    zebrafish
    (Danio rerio)    		 Actinopterygii sptssb1 serine palmitoyltransferase, small subunit B 63.29(n)
    60.87(a)    		   678546  NM_001159833.1  NP_001153305.1 


    ENSEMBL Gene Tree for SPTSSB (if available)
    TreeFam Gene Tree for SPTSSB (if available) 

    Paralogs
    for SPTSSB gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SPTSSB gene
    SPTSSA2  
    1 SIMAP similar gene for SPTSSB using alignment to 1 protein entry:     SPTSB_HUMAN:
    SPTSSA

    SPTSSB for paralogs           About GeneDecksing



    Genomic Variants
    for SPTSSB gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/528 NCBI SNPs in SPTSSB are shown (see all 528)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 3 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1444184101,2
    		--161062271(+) GCCCGA/GTGTGG 1 -- ds50010--------
    rs76524471,2
    		C,F,H,--161062331(+) CTAATC/TGACCT 1 -- ds500117Minor allele frequency- T:0.18EA NS NA WA CSA 1995
    rs1857811241,2
    		--161062347(+) AAGAAA/CTGTAA 1 -- ds50010--------
    rs801132361,2
    		F,--161062426(+) TGTCCA/CGCATG 1 -- ds50011Minor allele frequency- C:0.03WA 118
    rs76301921,2
    		C,--161062429(+) CCAGCA/CTGGAG 1 -- ds50012Minor allele frequency- C:0.06CSA WA 120
    rs1413139181,2
    		--161062467(+) GTTACC/TGTTTT 1 -- ds50010--------
    rs76106781,2
    		C,F,A,H,--161062468(+) TTACCG/ATTTTA 1 -- ds50015Minor allele frequency- A:0.04EA NS CSA WA 418
    rs130593401,2
    		C,F,H,--161062631(+) ATACAT/CGTTCA 1 -- ut3115Minor allele frequency- C:0.36NA EA NS WA CSA 810
    rs1633271,2
    		C,F,H,--161062724(-) CAAGGC/TGAGCT 1 -- ut3129Minor allele frequency- T:0.27MN NA EA NS WA CSA 2868
    rs76108871,2
    		C,F,H,--161062757(+) AACAAG/AGGTGC 1 -- ut3110Minor allele frequency- A:0.08EA NS NA CSA WA 1094

    HapMap Linkage Disequilibrium report for SPTSSB (161062580 - 161090668 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for SPTSSB: --

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    Disorders / Diseases
    for SPTSSB gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    SPTSSB for disorders           About GeneDecksing

    OMIM gene information: 610412    OMIM disorders: --

    1 disease for SPTSSB:    About MalaCards
    prostatitis


    Export disorders for SPTSSB gene to outside databases

    Publications
    for SPTSSB gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for SPTSSB gene integrated from 9 sources:
    (articles sorted by number of sources associating them with SPTSSB)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of small subunits of mammalian serine palmitoyltransferase that confer distinct acyl-CoA substrate specificities. (PubMed id 19416851)1, 2, 3 Han G.... Dunn T.M. (2009)
    2. Molecular cloning and characterization of a novel androgen repressible gene expressed in the prostate epithelium. (PubMed id 15777716)1, 2, 3 Singh J.... Dong Q. (2005)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    6. Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )2 Aoki H.... Hino O. (2000)

    External Searches for SPTSSB gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing SPTSSB gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 165679 HGNC: 24045 AceView: ADMP Ensembl:ENSG00000196542 euGenes: HUgn165679
    ECgene: SPTSSB H-InvDB: SPTSSB

    Other Databases showing SPTSSB gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing SPTSSB gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SPTSSB Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for SPTSSB gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for SPTSSB gene:
    Search GeneIP for patents involving SPTSSB

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    In Situ Hybridization Assays from
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