Sptlc1 (serine palmitoyltransferase, long chain base subunit 1) - Rat Genome Database

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Gene: Sptlc1 (serine palmitoyltransferase, long chain base subunit 1) Mus musculus
Analyze
Symbol: Sptlc1
Name: serine palmitoyltransferase, long chain base subunit 1
RGD ID: 1315337
MGI Page MGI
Description: Enables serine C-palmitoyltransferase activity. Involved in regulation of fat cell apoptotic process and sphingomyelin biosynthetic process. Acts upstream of or within ceramide biosynthetic process; sphinganine biosynthetic process; and sphingosine biosynthetic process. Located in endoplasmic reticulum membrane. Is expressed in brain and liver. Human ortholog(s) of this gene implicated in hereditary sensory and autonomic neuropathy type 1A. Orthologous to human SPTLC1 (serine palmitoyltransferase long chain base subunit 1); PARTICIPATES IN Fabry disease pathway; Gaucher's disease pathway; Krabbe disease pathway; INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: AW552086; C77762; E030036H05; Lcb; LCB 1; Lcb1; long chain base biosynthesis protein 1; serine palmitoyltransferase 1; serine-palmitoyl-CoA transferase 1; Sp; SPT 1; SPT1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391353,486,784 - 53,531,453 (-)NCBIGRCm39mm39
GRCm39 Ensembl1353,486,784 - 53,531,433 (-)Ensembl
GRCm381353,332,748 - 53,377,417 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1353,332,748 - 53,377,397 (-)EnsemblGRCm38mm10GRCm38
MGSCv371353,428,117 - 53,472,730 (-)NCBIGRCm37mm9NCBIm37
MGSCv361353,340,282 - 53,384,895 (-)NCBImm8
Celera1354,411,645 - 54,456,357 (-)NCBICelera
Cytogenetic Map13B1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:1317856   PMID:9363775   PMID:9405408   PMID:10349636   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12477932   PMID:12782147   PMID:14610273   PMID:14681479  
PMID:15782199   PMID:16141072   PMID:16141073   PMID:16210380   PMID:16216550   PMID:16602821   PMID:16960033   PMID:17967808   PMID:18484747   PMID:18515784   PMID:18799693   PMID:19416652  
PMID:19923297   PMID:20211931   PMID:21267068   PMID:21873635   PMID:23096701   PMID:24293640   PMID:25269881   PMID:25332431   PMID:25602705   PMID:25691431   PMID:26301690   PMID:27113764  
PMID:28100772   PMID:28378742   PMID:30550785  


Genomics

Comparative Map Data
Sptlc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391353,486,784 - 53,531,453 (-)NCBIGRCm39mm39
GRCm39 Ensembl1353,486,784 - 53,531,433 (-)Ensembl
GRCm381353,332,748 - 53,377,417 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1353,332,748 - 53,377,397 (-)EnsemblGRCm38mm10GRCm38
MGSCv371353,428,117 - 53,472,730 (-)NCBIGRCm37mm9NCBIm37
MGSCv361353,340,282 - 53,384,895 (-)NCBImm8
Celera1354,411,645 - 54,456,357 (-)NCBICelera
Cytogenetic Map13B1NCBI
SPTLC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl992,000,087 - 92,115,413 (-)EnsemblGRCh38hg38GRCh38
GRCh38992,031,141 - 92,115,413 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37994,793,429 - 94,877,695 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36993,833,248 - 93,917,511 (-)NCBINCBI36hg18NCBI36
Build 34991,920,900 - 91,957,245NCBI
Celera965,229,735 - 65,313,999 (-)NCBI
Cytogenetic Map9q22.31NCBI
HuRef964,471,097 - 64,555,697 (-)NCBIHuRef
CHM1_1994,939,836 - 95,024,218 (-)NCBICHM1_1
Sptlc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21711,877,249 - 11,916,295 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1711,877,249 - 11,916,295 (+)Ensembl
Rnor_6.01711,856,525 - 11,895,566 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1711,856,525 - 11,895,566 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01713,956,140 - 13,995,224 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41717,576,401 - 17,615,246 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11717,599,561 - 17,613,645 (+)NCBI
Celera1711,642,596 - 11,681,492 (+)NCBICelera
Cytogenetic Map17p14NCBI
Sptlc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495551557,711 - 161,611 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495551557,711 - 161,012 (+)NCBIChiLan1.0ChiLan1.0
SPTLC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1991,185,574 - 91,213,003 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0963,087,798 - 63,174,977 (-)NCBIMhudiblu_PPA_v0panPan3
SPTLC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1194,997,240 - 95,062,424 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl194,997,290 - 95,064,468 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha195,445,084 - 95,510,150 (+)NCBI
ROS_Cfam_1.0195,597,902 - 95,649,028 (+)NCBI
UMICH_Zoey_3.1195,224,979 - 95,289,739 (+)NCBI
UNSW_CanFamBas_1.0194,951,482 - 95,016,318 (+)NCBI
UU_Cfam_GSD_1.0195,710,467 - 95,775,506 (+)NCBI
Sptlc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494413,566,496 - 13,627,827 (-)NCBI
SpeTri2.0NW_004936796886,946 - 948,254 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPTLC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl143,081,969 - 3,138,103 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1143,081,964 - 3,138,113 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2143,956,042 - 4,012,182 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SPTLC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.112102,475,437 - 102,551,401 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl12102,475,415 - 102,551,322 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603890,728,707 - 90,804,273 (-)NCBIVero_WHO_p1.0
Sptlc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624868317,992 - 393,776 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
AW552086  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381353,333,063 - 53,333,174UniSTSGRCm38
MGSCv371353,428,432 - 53,428,543UniSTSGRCm37
Celera1354,411,960 - 54,412,071UniSTS
Cytogenetic Map13B1UniSTS
Whitehead/MRC_RH13560.84UniSTS
RH126236  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381353,332,861 - 53,333,092UniSTSGRCm38
MGSCv371353,428,230 - 53,428,461UniSTSGRCm37
Celera1354,411,758 - 54,411,989UniSTS
Cytogenetic Map13B1UniSTS
Whitehead/MRC_RH13561.78UniSTS
Sptlc1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map13B1UniSTS
cM Map13 UniSTS
Sptlc1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map13B1UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
26884393Humsd7_mhumerus midshaft diameter 7, 16 week (mouse)13390000075900000Mouse
12880423V25Dq7_mvitamin D inactive form serum level QTL 7 (mouse)131940000053400000Mouse
1301015Sysbp2_msystolic blood pressure 2 (mouse)Not determined132029344259673791Mouse
4142147Mvwf4_mmodifier of von Willebrand factor 4 (mouse)Not determined20293442112761890Mouse
1357591Tesq1_mtestis weight QTL 1 (mouse)Not determined132043134255572704Mouse
4142009Pregq3_mpregnancy QTL 3 (mouse)Not determined132043134272237070Mouse
10045618Heal17_mwound healing/regeneration 17 (mouse)Not determined132056296354563080Mouse
1558844Lith15_mlithogenic gene 15 (mouse)Not determined132176326255763430Mouse
4142489Ath25_matherosclerosis 25 (mouse)Not determined2568305359683053Mouse
10401111Pgia40_mproteoglycan induced arthritis 40 (mouse)Not determined132776499361765084Mouse
1300710Pcd4ts2_mp-glycoprotein positive CD4 T cell subset 2 (mouse)Not determined132805696662057068Mouse
1357802Vtbt15_mvertebral trabecular bone trait 15 (mouse)Not determined132806390362064039Mouse
10045621Heal21_mwound healing/regeneration 21 (mouse)Not determined132806390362064039Mouse
10755517Chol15_mcholesterol 15 (mouse)133081599164815991Mouse
10755533Chol18_mcholesterol 18 (mouse)133081599164815991Mouse
12738439Twq4_mtestis weight QTL 4 (mouse)133097563464975634Mouse
14696729Kidlq2_mkidney weight, left QTL 2 (mouse)133119126065191260Mouse
1301299Sluc23_msusceptibility to lung cancer 23 (mouse)Not determined133476790768768045Mouse
10412235Scgq5_mspontaneous crescentic glomerulonephritis QTL 5 (mouse)Not determined133587692596102654Mouse
1301734Acsns2_mAngiostrongylus costaricensis nematode susceptibility 2 (mouse)Not determined133594749469947604Mouse
1357587Pfat3_mpredicted fat percentage 3 (mouse)Not determined133594749469947604Mouse
1300561Heal7_mwound healing/regeneration 7 (mouse)Not determined133599078469990868Mouse
1300862Cfbw5_mcystic fibrosis body weight 5 (mouse)Not determined133857254572572704Mouse
1301801Cpfd5_mcerebellum pattern fissures (mouse)Not determined133948143673481584Mouse
1302157Bwem2_mbody weight day 30 males 2 (mouse)Not determined133948143673481584Mouse
1300985Bmd13_mbone mineral density 13 (mouse)Not determined133948143673481584Mouse
15039353Nmrs35_mNAFLD-associated magnetic resonance shift 35 (mouse)134044044074440440Mouse
1300668Pas10_mpulmonary adenoma susceptibility 10 (mouse)Not determined134134122875341344Mouse
4142331Bxs6_mBXSB/MpJ autoimmune nephritis 6 (mouse)Not determined4505696683596627Mouse
10412109Bxs7_mBXSB/MpJ autoimmune nephritis 7 (mouse)Not determined134505696683596627Mouse
26884396Humsd4_mhumerus midshaft diameter 4, 10 week (mouse)134770000073000000Mouse
4142372Moo2_mmodifier of Odc2 (mouse)Not determinedX5017034784170495Mouse
1300916Mobe2_mmodifier of obesity 2 (mouse)Not determined135017034784170495Mouse
1301666Eae13_msusceptibility to experimental allergic encephalomyelitis 13 (mouse)Not determined135017034784170495Mouse
1300573Elsgp2_melevated serum gp70 2 (mouse)Not determined135046870984468908Mouse
14746975Manh74_mmandible shape 74 (mouse)135232915086329150Mouse
25671382Hrsq4_mhost response to SARS QTL 4, vascular cuffing (mouse)135272761554844925Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:337
Count of miRNA genes:288
Interacting mature miRNAs:301
Transcripts:ENSMUST00000021920
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_009269 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006516927 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_382233 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC159201 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF003823 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK028713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK043064 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK053207 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK079578 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK084391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK084445 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK089030 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK161140 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK161811 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK195391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK204734 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC046323 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466546 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X95641 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000021920   ⟹   ENSMUSP00000021920
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1353,486,784 - 53,531,433 (-)Ensembl
GRCm38.p6 Ensembl1353,332,748 - 53,377,397 (-)Ensembl
RefSeq Acc Id: ENSMUST00000221265
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1353,523,077 - 53,531,384 (-)Ensembl
GRCm38.p6 Ensembl1353,369,041 - 53,377,348 (-)Ensembl
RefSeq Acc Id: ENSMUST00000221709
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1353,530,732 - 53,531,401 (-)Ensembl
GRCm38.p6 Ensembl1353,376,696 - 53,377,365 (-)Ensembl
RefSeq Acc Id: NM_009269   ⟹   NP_033295
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391353,486,784 - 53,531,397 (-)NCBI
GRCm381353,332,748 - 53,377,361 (-)NCBI
MGSCv371353,428,117 - 53,472,730 (-)RGD
Celera1354,411,645 - 54,456,357 (-)RGD
cM Map13 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006516927   ⟹   XP_006516990
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391353,500,406 - 53,531,453 (-)NCBI
GRCm381353,346,370 - 53,377,417 (-)NCBI
Sequence:
RefSeq Acc Id: XR_382233
RefSeq Status:
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391353,486,784 - 53,531,453 (-)NCBI
GRCm381353,332,748 - 53,377,417 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_033295   ⟸   NM_009269
- UniProtKB: O35704 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006516990   ⟸   XM_006516927
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSMUSP00000021920   ⟸   ENSMUST00000021920
Protein Domains
Aminotran_1_2

Promoters
RGD ID:8680368
Promoter ID:EPDNEW_M18215
Type:multiple initiation site
Name:Sptlc1_1
Description:Mus musculus serine palmitoyltransferase, long chain base subunit1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381353,377,365 - 53,377,425EPDNEW
RGD ID:6824416
Promoter ID:MM_KWN:14157
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6
Transcripts:ENSMUST00000021920
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361353,472,511 - 53,473,011 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1099431 AgrOrtholog
Ensembl Genes ENSMUSG00000021468 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000021920 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000021920 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.640.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.90.1150.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Aminotransferase_I/II UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_dom1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_major UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:268656 UniProtKB/Swiss-Prot
MGD MGI:1099431 ENTREZGENE
NCBI Gene 268656 ENTREZGENE
Pfam Aminotran_1_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sptlc1 PhenoGen
Superfamily-SCOP SSF53383 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt O35704 ENTREZGENE
  Q3TST8_MOUSE UniProtKB/TrEMBL
  Q3TTW4_MOUSE UniProtKB/TrEMBL
  Q3V3A0_MOUSE UniProtKB/TrEMBL
  Q3V3Z5_MOUSE UniProtKB/TrEMBL
  Q8C295_MOUSE UniProtKB/TrEMBL
  SPTC1_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary O54813 UniProtKB/Swiss-Prot
  Q8BH11 UniProtKB/Swiss-Prot