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

SPTSSA Gene

protein-coding   GIFtS: 40
GCID: GC14M034902

Serine Palmitoyltransferase, Small Subunit A

(Previous name: chromosome 14 open reading frame 147)
(Previous symbol: C14orf147)
  Search for SPTSSA
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Serine Palmitoyltransferase, Small Subunit A1 2     Chromosome 14 Open Reading Frame 1471
C14orf1471 2 3 5     Serine Palmitoyltransferase Small Subunit A2
Small Subunit Of Serine Palmitoyltransferase A1 2 3     ssSPTa3
SSSPTA2 3 5     

External Ids:    HGNC: 203611   Entrez Gene: 1715462   Ensembl: ENSG000001653897   OMIM: 6135405   UniProtKB: Q969W03   

Export aliases for SPTSSA gene to outside databases


(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 SPTSSA Gene:
Serine palmitoyltransferase (SPT; EC 2.3.1.50) catalyzes the first committed and rate-limiting step in
sphingolipid biosynthesis. SSSPTA 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)

GeneCards Summary for SPTSSA Gene: 
SPTSSA (serine palmitoyltransferase, small subunit A) is a protein-coding gene. GO annotations related to this gene include protein binding and serine C-palmitoyltransferase activity. An important paralog of this gene is SPTSSB.

UniProtKB/Swiss-Prot: SPTSA_HUMAN, Q969W0
Function: Stimulates the activity of serine palmitoyltransferase (SPT). The composition of the serine
palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC2-SPTSSA complex shows a
strong preference for C16-CoA substrate, while the SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as
substrates, with a slight preference for C14-CoA




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000014.8  NC_018925.2  NT_026437.12  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for SPTSSA
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSPTSSA promoter sequence
   Search SABiosciences Chromatin IP Primers for SPTSSA

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


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

Entrez Gene cytogenetic band: 14q13.1   Ensembl cytogenetic band:  14q13.1   HGNC cytogenetic band: 14q13.1

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

GeneLoc information about chromosome 14         GeneLoc Exon Structure

GeneLoc location for GC14M034902:  view genomic region     (about GC identifiers)

Start:
34,901,995 bp from pter      End:
34,931,562 bp from pter
Size:
29,568 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SPTSA_HUMAN, Q969W0 (See protein sequence)
Recommended Name: Serine palmitoyltransferase small subunit A  
Size: 71 amino acids; 8466 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)
Caution: It is uncertain whether Met-1 or Met-4 is the initiator
Sequence caution: Sequence=AAH16805.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=AAH16808.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAH21701.1;
Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAH68480.1; Type=Erroneous
initiation; Note=Translation N-terminally extended; Sequence=BAG37801.1; Type=Erroneous initiation;
Note=Translation N-terminally extended;
Secondary accessions: B2RD54 D3DS93 Q8WTZ7

Explore the universe of human proteins at neXtProt for SPTSSA: NX_Q969W0

Explore proteomics data for SPTSSA at MOPED 

SPTSSA Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

SPTSSA Protein Expression

REFSEQ proteins: NP_612145.2  
ENSEMBL proteins: 
 ENSP00000298130  

Human Recombinant Protein Products for SPTSSA: 
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Browse Proteins at Cloud-Clone Corp. 

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

SPTSSA for ontologies           About GeneDecksing



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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
1 InterPro protein domain:
 IPR024512 Ser_palmitoyltrfase_ssu-like

Graphical View of Domain Structure for InterPro Entry Q969W0

ProtoNet protein and cluster: Q969W0

UniProtKB/Swiss-Prot: SPTSA_HUMAN, Q969W0
Similarity: Belongs to the SPTSS family. SPTSSA subfamily


SPTSSA for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Molecular Function:

     UniProtKB/Swiss-Prot Summary: SPTSA_HUMAN, Q969W0
Function: Stimulates the activity of serine palmitoyltransferase (SPT). The composition of the serine
palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC2-SPTSSA complex shows a
strong preference for C16-CoA substrate, while the SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as
substrates, with a slight preference for C14-CoA

     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
     
SPTSSA for ontologies           About GeneDecksing


Phenotypes:
     1 MGI phenotypic allele for Sptssa (no phenotypes)

SPTSSA for phenotypes           About GeneDecksing

Animal Models:
   inGenious Targeting Laboratory - Custom generated mouse model solutions for SPTSSA 
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miRNA
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SwitchGear 3'UTR luciferase reporter plasmidSPTSSA 3' UTR sequence
Inhib. RNA
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In Situ Assay
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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, 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 Oct 2013 via Entrez Gene).
About This Section

SuperPaths for SPTSSA About                                                                                                See pathways by source

SuperPathContained pathways About
1ceramide de novo biosynthesis
ceramide de novo biosynthesis


1 BioSystems Pathway for SPTSSA
    ceramide de novo biosynthesis


UniProtKB/Swiss-Prot: SPTSA_HUMAN, Q969W0
Pathway: Lipid metabolism; sphingolipid metabolism

Interactions:

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

STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

5/11 Interacting proteins for SPTSSA (Q969W02, 3 ENSP000002981304) via UniProtKB, MINT, STRING, and/or I2D (see all 11)

InteractantInteraction Details
GeneCardExternal ID(s)
ENSG00000258947Q135093I2D: score=2 
TUBB3Q135093I2D: score=2 
TUBB4AP043503, ENSP000002640714I2D: score=1 STRING: ENSP00000264071
SPTLC1ENSP000002625544STRING: ENSP00000262554
SPTLC2ENSP000002164844STRING: ENSP00000216484
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

SPTSSA for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 SPTSSA (SPTSA)

Search CenterWatch for drugs/clinical trials and news about SPTSSA / SPTSA

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, 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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for SPTSSA gene: 
NM_138288.3  

Unigene Cluster for SPTSSA:

Serine palmitoyltransferase, small subunit A
Hs.740577  [show with all ESTs]
Unigene Representative Sequence: BC068480
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000298130(uc001wsc.3)
miRNA
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Inhib. RNA
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                     Customized lentivirus expression plasmids for stable overexpression of SPTSSA 
Primer
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Additional mRNA sequence: 

AK001993.1 AK315409.1 AL080066.1 BC016805.1 BC016808.1 BC021701.1 BC068480.1 

7 DOTS entries:

DT.448692  DT.95159464  DT.95183621  DT.91774571  DT.120782648  DT.95183615  DT.91756209 

24/299 AceView cDNA sequences (see all 299):

BP337986 BM785499 CA389318 AI655587 AI589705 BM773469 CB139633 BI821640 
BE042393 BX379451 AW612857 AA365350 BI917628 AW079261 BC068480 AV682125 
BE468034 AI916735 CA454682 H93575 BU687716 AI308821 BM126944 AA838745 

GeneLoc Exon Structure


(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

SPTSSA expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TGTTGTGTTC
SPTSSA Expression
About this image


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

SOURCE GeneReport for Unigene cluster: Hs.740577
    SABiosciences Custom PCR Arrays for SPTSSA
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SPTSSA

(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 SPTSSA gene from 5/13 species (see all 13)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Sptssa1 , 5 RIKEN cDNA 1110002B05 gene5
serine palmitoyltransferase, small subunit A1
91.08(n)1
98.59(a)1
  12 (23.46 cM)5
1047251  NM_134054.21  NP_598815.21 
 546453745 
chicken
(Gallus gallus)
Aves SPTSSA1 serine palmitoyltransferase, small subunit A 87.75(n)
95.59(a)
  423318  XM_421234.3  XP_421234.2 
lizard
(Anolis carolinensis)
Reptilia SPTSSA6
Uncharacterized protein
94(a)
1 ↔ 1
2(54806441-54811985)
African clawed frog
(Xenopus laevis)
Amphibia BQ385602.12   -- 83.87(n)    BQ385602.1 
zebrafish
(Danio rerio)
Actinopterygii wufb60h112 wufb60h11 74.68(n)   322432  BM776360.1 


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

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for SPTSSA gene
SPTSSB2  
1 SIMAP similar gene for SPTSSA using alignment to 1 protein entry:     SPTSA_HUMAN:
SPTSSB

SPTSSA for paralogs           About GeneDecksing


1 Pseudogenes.org Pseudogene for SPTSSA
PGOHUM00000244865


(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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

10/741 SNPs in SPTSSA are shown (see all 741)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 14 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1864125641,2
--34901676(+) AATTAC/GAATGA 1 -- ds50010--------
rs1443215531,2
C--34901855(+) TTGTTA/GTCTTA 1 -- ds50010--------
rs1487670771,2
--34901862(+) CTTATC/TTTTAA 1 -- ds50010--------
rs1125839141,2
C,F--34901928(+) CATCAC/ACATCA 1 -- ds50011Minor allele frequency- A:0.50CSA 2
rs287221311,2
C,F--34901977(+) GAAGGC/GTCAAA 1 -- ds50015Minor allele frequency- G:0.27NA CSA WA 126
rs284486601,2
C,F,H--34902033(+) AGGTAA/C/TATTGG 1 -- ds50019NS NA CSA WA 1014
rs1154118921,2
C,F--34902088(+) CTACAG/AGATGG 1 -- ds50011Minor allele frequency- A:0.05WA 118
rs1920849821,2
--34902116(+) TATGCA/CGGGGA 1 -- ds50010--------
rs286875041,2
C,F--34902378(+) AAGACC/TAAACT 1 -- ut315Minor allele frequency- T:0.29NA CSA WA 125
rs1471661891,2
C--34902497(+) GCCAGA/GATAGG 1 -- ut310--------

HapMap Linkage Disequilibrium report for SPTSSA (34901995 - 34931562 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for SPTSSA:    About this table     
Variant IDTypeSubtypePubMed ID
nsv901600CNV Gain21882294
nsv528989CNV Gain19592680

SABiosciences Cancer Mutation PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

SPTSSA for disorders           About MalaCards
OMIM gene information: 613540    OMIM disorders: --


SPTSSA for disorders           About GeneDecksing


Export disorders for SPTSSA gene to outside databases

(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 SPTSSA gene integrated from 9 sources:
(articles sorted by number of sources associating them with SPTSSA)
    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. 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)
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
  4. Identification of VKORC1 interaction partners by spli t-ubiquitin system and coimmunoprecipitation. (PubMed id 21103663)1 Schaafhausen A....MA1ller C.R. (2011)
  5. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (2009)
  6. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)
  7. A human protein-protein interaction network: a resource for annotating the proteome. (PubMed id 16169070)1 Stelzl U.... Wanker E.E. (2005)
  8. 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)

(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)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 171546 HGNC: 20361 AceView: C14orf147 Ensembl:ENSG00000165389 euGenes: HUgn171546
ECgene: SPTSSA H-InvDB: SPTSSA

(According to HUGE)
About This Section
  --

(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 SPTSSA Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for SPTSSA gene:
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GeneCards and IP:
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(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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