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SPTLC2 serine palmitoyltransferase long chain base subunit 2 [ Homo sapiens (human) ]

Gene ID: 9517, updated on 5-Aug-2018

Summary

Official Symbol
SPTLC2provided by HGNC
Official Full Name
serine palmitoyltransferase long chain base subunit 2provided by HGNC
Primary source
HGNC:HGNC:11278
See related
Ensembl:ENSG00000100596 MIM:605713; Vega:OTTHUMG00000171540
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LCB2; SPT2; HSN1C; LCB2A; NSAN1C; hLCB2a
Summary
This gene encodes a long chain base subunit of serine palmitoyltransferase. Serine palmitoyltransferase, which consists of two different subunits, is the key enzyme in sphingolipid biosynthesis. It catalyzes the pyridoxal-5-prime-phosphate-dependent condensation of L-serine and palmitoyl-CoA to 3-oxosphinganine. Mutations in this gene were identified in patients with hereditary sensory neuropathy type I. [provided by RefSeq, Mar 2011]
Expression
Ubiquitous expression in esophagus (RPKM 11.7), colon (RPKM 11.4) and 25 other tissues See more
Orthologs

Genomic context

See SPTLC2 in Genome Data Viewer
Location:
14q24.3
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 14 NC_000014.9 (77505997..77616767, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (77972340..78083110, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene activator of HSP90 ATPase activity 1 Neighboring gene isthmin 2 Neighboring gene RNA, 7SL, cytoplasmic 587, pseudogene Neighboring gene cytochrome c oxidase subunit 6C pseudogene 11 Neighboring gene alkB homolog 1, histone H2A dioxygenase Neighboring gene ribosomal protein L21 pseudogene 10

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat upregulates serine palmitoyltransferase, long chain base subunit 2 (SPTLC2, SPT2) expression in Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0526

Gene Ontology Provided by GOA

Function Evidence Code Pubs
pyridoxal phosphate binding IEA
Inferred from Electronic Annotation
more info
 
serine C-palmitoyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to serine C-palmitoyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
serine C-palmitoyltransferase activity TAS
Traceable Author Statement
more info
 
Process Evidence Code Pubs
ceramide biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of lipophagy IDA
Inferred from Direct Assay
more info
PubMed 
sphinganine biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
sphingolipid biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
sphingolipid biosynthetic process TAS
Traceable Author Statement
more info
PubMed 
sphingomyelin biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
sphingosine biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
serine C-palmitoyltransferase complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
serine palmitoyltransferase 2
Names
LCB 2
SPT 2
long chain base biosynthesis protein 2a
serine palmitoyltransferase, subunit II
serine-palmitoyl-CoA transferase 2
NP_004854.1
XP_011535686.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_028282.1 RefSeqGene

    Range
    5001..115771
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_371

mRNA and Protein(s)

  1. NM_004863.3NP_004854.1  serine palmitoyltransferase 2

    See identical proteins and their annotated locations for NP_004854.1

    Status: REVIEWED

    Source sequence(s)
    AB011098, AF111168, BQ338973
    Consensus CDS
    CCDS9865.1
    UniProtKB/Swiss-Prot
    O15270
    UniProtKB/TrEMBL
    A0A024R6H1
    Related
    ENSP00000216484.2, OTTHUMP00000246380, ENST00000216484.6, OTTHUMT00000414030
    Conserved Domains (1) summary
    PLN02483
    Location:67542
    PLN02483; serine palmitoyltransferase

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p12 Primary Assembly

    Range
    77505997..77616767 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011537384.2XP_011535686.1  serine palmitoyltransferase 2 isoform X1

    See identical proteins and their annotated locations for XP_011535686.1

    Related
    ENSP00000452189.1, OTTHUMP00000246382, ENST00000554901.1, OTTHUMT00000414032
    Conserved Domains (2) summary
    PLN02483
    Location:67435
    PLN02483; serine palmitoyltransferase
    COG0156
    Location:117426
    BioF; 7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]
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