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Sptlc2 Gene Detail
Summary
  • Symbol
    Sptlc2
  • Name
    serine palmitoyltransferase, long chain base subunit 2
  • Synonyms
    LCB2, Spt2
  • Feature Type
    protein coding gene
  • IDs
    MGI:108074
    NCBI Gene: 20773
  • Alliance
    gene page
  • Transcription Start Sites
    5 TSS
Location &
Maps
more
  • Sequence Map
    Chr12:87351832-87435129 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 12, 41.52 cM, cytoband E
  • Mapping Data
    3 experiments
Strain
Comparison
more
  • SNPs within 2kb
    1941 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_108074
 protein coding gene Chr12:87351832-87435129 (-)
129S1/SvImJ MGP_129S1SvImJ_G0019986
 protein coding gene Chr12:88208344-88295571 (-)
A/J MGP_AJ_G0019944
 protein coding gene Chr12:84857053-84941107 (-)
AKR/J MGP_AKRJ_G0019919
 protein coding gene Chr12:87163806-87243070 (-)
BALB/cJ MGP_BALBcJ_G0019923
 protein coding gene Chr12:85188803-85272224 (-)
C3H/HeJ MGP_C3HHeJ_G0019729
 protein coding gene Chr12:87651920-87736523 (-)
C57BL/6NJ MGP_C57BL6NJ_G0020375
 protein coding gene Chr12:90750780-90838783 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0017993
 protein coding gene Chr12:81737004-81820672 (-)
CAST/EiJ MGP_CASTEiJ_G0019279
 protein coding gene Chr12:82684364-82772097 (-)
CBA/J MGP_CBAJ_G0019701
 protein coding gene Chr12:94218466-94301017 (-)
DBA/2J MGP_DBA2J_G0019814
 protein coding gene Chr12:84352236-84436798 (-)
FVB/NJ MGP_FVBNJ_G0019801
 protein coding gene Chr12:83346232-83429760 (-)
LP/J MGP_LPJ_G0019888
 protein coding gene Chr12:88085580-88171504 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0019840
 protein coding gene Chr12:96985583-97071008 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0020407
 protein coding gene Chr12:86787075-86872400 (-)
PWK/PhJ MGP_PWKPhJ_G0019043
 protein coding gene Chr12:78908808-78996323 (-)
SPRET/EiJ MGP_SPRETEiJ_G0018838
 protein coding gene Chr12:81300620-81381264 (-)
WSB/EiJ MGP_WSBEiJ_G0019332
 protein coding gene Chr12:87564623-87650632 (-)



Homology
more
  • Human Ortholog
    SPTLC2, serine palmitoyltransferase long chain base subunit 2
  • Vertebrate Orthologs
    4
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    SPTLC2, serine palmitoyltransferase long chain base subunit 2
  • Synonyms
    hLCB2a, HSN1C, LCB2, LCB2A, NSAN1C, SPT2
  • Links
    NCBI Gene ID: 9517
    neXtProt AC: NX_O15270
    UniProt: O15270

  • Chr Location
    14q24.3; chr14:77505997-77616637 (-)  GRCh38
Human Diseases
more
  • Diseases
    1 with Sptlc2 mouse models; 1 with human SPTLC2 associations

Human Disease Mouse Models
      
IDs
 View 1 model
      
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    1 with disease annotations
  • References
    1 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    62 phenotypes from 4 alleles in 5 genetic backgrounds
    35 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Mice homozygous for a knock-out allele exhibit embryonic lethality. Mice heterozygous for this allele exhibit abnormal liver and circulating shingolipid levels.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    22
  • GO References
    12
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    807
  • Tissues
    98
  • cDNA Data
    20
  • Literature Summary
    4
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 20773 NCBI Gene Model | MGI Sequence Detail 83298 C57BL/6J ±  kb
    transcript NM_011479 RefSeq | MGI Sequence Detail 6725 C57BL/6  
    polypeptide P97363 UniProt | EBI | MGI Sequence Detail 560 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      6 Sequences
    • Protein Ontology
      PR:000015597 serine palmitoyltransferase 2
      (term hierarchy)
    • EC
      2.3.1.50
    • InterPro Domains
      IPR050087 8-amino-7-oxononanoate synthase class-II
      IPR004839 Aminotransferase, class I/classII
      IPR001917 Aminotransferase, class-II, pyridoxal-phosphate binding site
      IPR015424 Pyridoxal phosphate-dependent transferase
      IPR015421 Pyridoxal phosphate-dependent transferase, major domain
      IPR015422 Pyridoxal phosphate-dependent transferase, small domain
    • GlyGen
      P97363 2 sites, 1 N-linked glycan (1 site), 1 O-linked glycan (1 site)
    Molecular
    Reagents
    less
    • All nucleic 25
      Genomic 1
      cDNA 22
      Primer pair 2

      Microarray probesets 6
    Other
    Accession IDs
    less
    MGD-MRK-37111, MGI:2144769
    References
    more
    • Summaries
      All 74
      Developmental Gene Expression 4
      Diseases 1
      Gene Ontology 12
      Phenotypes 35
    • Earliest
      J:20131 Kerr SM, et al., Analysis of cDNA sequences from mouse testis. Mamm Genome. 1994 Sep;5(9):557-65
    • Latest
      J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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    Funding Information
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    Send questions and comments to User Support.     		last database update
    11/12/2024
    MGI 6.24     		The Jackson Laboratory