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

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Gene: Sptlc1 (serine palmitoyltransferase, long chain base subunit 1) Rattus norvegicus
Analyze
Symbol: Sptlc1
Name: serine palmitoyltransferase, long chain base subunit 1
RGD ID: 1307140
Description: Predicted to enable serine C-palmitoyltransferase activity. Predicted to be involved in ceramide biosynthetic process; regulation of fat cell apoptotic process; and sphingosine biosynthetic process. Predicted to act upstream of or within positive regulation of lipophagy; sphinganine biosynthetic process; and sphingomyelin biosynthetic process. Predicted to be located in endoplasmic reticulum membrane. Predicted to be part of SPOTS complex. Predicted to be active in endoplasmic reticulum. 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 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LCB 1; Lcb1; LOC361213; long chain base biosynthesis protein 1; RGD1306617; serine palmitoyltransferase 1; serine palmitoyltransferase subunit 1; serine-palmitoyl-CoA transferase 1; similar to Serine palmitoyltransferase 1; SPT 1; Spt1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
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
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
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9363775   PMID:11816724   PMID:16216550   PMID:18922131   PMID:19416652   PMID:19416851   PMID:20182505   PMID:25332431   PMID:25691431   PMID:25771159   PMID:26301690   PMID:28100772  


Genomics

Comparative Map Data
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38992,031,147 - 92,115,413 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl992,000,087 - 92,115,413 (-)EnsemblGRCh38hg38GRCh38
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
T2T-CHM13v2.09104,197,620 - 104,281,900 (-)NCBI
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
(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_female_1.0 EnsemblNW_004624868318,059 - 393,773 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_004624868317,992 - 393,776 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
AI235989  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21711,890,037 - 11,890,254 (+)MAPPERmRatBN7.2
Rnor_6.01711,869,311 - 11,869,527NCBIRnor6.0
Rnor_5.01713,968,969 - 13,969,185UniSTSRnor5.0
RGSC_v3.41717,588,991 - 17,589,207UniSTSRGSC3.4
Celera1711,655,239 - 11,655,455UniSTS
RH 3.4 Map17110.7UniSTS
Cytogenetic Map17p14UniSTS
RH131111  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21711,915,387 - 11,915,570 (+)MAPPERmRatBN7.2
Rnor_6.01711,894,659 - 11,894,841NCBIRnor6.0
Rnor_5.01713,994,317 - 13,994,499UniSTSRnor5.0
RGSC_v3.41717,614,339 - 17,614,521UniSTSRGSC3.4
Celera1711,680,585 - 11,680,767UniSTS
RH 3.4 Map17112.4UniSTS
Cytogenetic Map17p14UniSTS
RH141238  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21711,915,005 - 11,915,225 (+)MAPPERmRatBN7.2
Rnor_6.01711,894,277 - 11,894,496NCBIRnor6.0
Rnor_5.01713,993,935 - 13,994,154UniSTSRnor5.0
RGSC_v3.41717,613,957 - 17,614,176UniSTSRGSC3.4
Celera1711,680,203 - 11,680,422UniSTS
Cytogenetic Map17p14UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122871563Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)17211514921881669Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)17429913021293263Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17429913021293263Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17435448727028127Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17435448727028127Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
1581553Pur14Proteinuria QTL 145.30.0001total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)17797996816317111Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
1582199Insul5Insulin level QTL 53.40.0119blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)17920136523653323Rat
1582208Kidm32Kidney mass QTL 323.90.0018kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17920136523653323Rat
1582224Epfw4Epididymal fat weight QTL 43.50.0058epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)17920136523653323Rat
1582225Bw67Body weight QTL 676.20.0001body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582226Bw64Body weight QTL 644.20.0017body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582241Bw70Body weight QTL 704.60.0003body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582245Bw73Body weight QTL 734.60.0004body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582258Bw76Body weight QTL 764.60.0005body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)17999128640540197Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:169
Count of miRNA genes:133
Interacting mature miRNAs:144
Transcripts:ENSRNOT00000014546
Prediction methods:Miranda, Pita
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


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 28 49 33 19 33 1 1 74 35 41 11 1
Low 15 8 8 8 7 10 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000014546   ⟹   ENSRNOP00000014546
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1711,877,249 - 11,916,295 (+)Ensembl
Rnor_6.0 Ensembl1711,856,525 - 11,895,566 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000103100   ⟹   ENSRNOP00000082531
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1711,879,861 - 11,916,295 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113906   ⟹   ENSRNOP00000085605
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1711,879,896 - 11,916,295 (+)Ensembl
RefSeq Acc Id: NM_001108406   ⟹   NP_001101876
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21711,877,249 - 11,916,295 (+)NCBI
Rnor_6.01711,856,525 - 11,895,566 (+)NCBI
Rnor_5.01713,956,140 - 13,995,224 (+)NCBI
RGSC_v3.41717,576,401 - 17,615,246 (+)RGD
Celera1711,642,596 - 11,681,492 (+)RGD
Sequence:
RefSeq Acc Id: XM_017600596   ⟹   XP_017456085
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21711,883,883 - 11,915,785 (+)NCBI
Rnor_6.01711,861,708 - 11,895,056 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039095851   ⟹   XP_038951779
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21711,877,332 - 11,915,785 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001101876   ⟸   NM_001108406
- UniProtKB: D4A2H2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456085   ⟸   XM_017600596
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000014546   ⟸   ENSRNOT00000014546
RefSeq Acc Id: XP_038951779   ⟸   XM_039095851
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000082531   ⟸   ENSRNOT00000103100
RefSeq Acc Id: ENSRNOP00000085605   ⟸   ENSRNOT00000113906

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A2H2-F1-model_v2 AlphaFold D4A2H2 1-473 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13700330
Promoter ID:EPDNEW_R10854
Type:multiple initiation site
Name:Sptlc1_1
Description:serine palmitoyltransferase, long chain base subunit 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01711,856,520 - 11,856,580EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307140 AgrOrtholog
BioCyc Gene G2FUF-10122 BioCyc
Ensembl Genes ENSRNOG00000010882 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000014546 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000082531.1 UniProtKB/TrEMBL
  ENSRNOP00000085605.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014546 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000103100.1 UniProtKB/TrEMBL
  ENSRNOT00000113906.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.640.10 UniProtKB/Swiss-Prot
  3.90.1150.10 UniProtKB/Swiss-Prot
InterPro Aminotransferase_I/II UniProtKB/Swiss-Prot
  PyrdxlP-dep_Trfase UniProtKB/Swiss-Prot
  PyrdxlP-dep_Trfase_dom1 UniProtKB/Swiss-Prot
  PyrdxlP-dep_Trfase_major UniProtKB/Swiss-Prot
KEGG Report rno:361213 UniProtKB/Swiss-Prot
NCBI Gene 361213 ENTREZGENE
Pfam Aminotran_1_2 UniProtKB/Swiss-Prot
PhenoGen Sptlc1 PhenoGen
Superfamily-SCOP SSF53383 UniProtKB/Swiss-Prot
UniProt A0A8I5ZUP8_RAT UniProtKB/TrEMBL
  A0A8I6A3Q5_RAT UniProtKB/TrEMBL
  D4A2H2 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Sptlc1  serine palmitoyltransferase, long chain base subunit 1   Sptlc1_predicted  serine palmitoyltransferase, long chain base subunit 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-04-05 Sptlc1_predicted  serine palmitoyltransferase, long chain base subunit 1 (predicted)  RGD1306617_predicted  similar to Serine palmitoyltransferase 1 (predicted)  Data Merged 737654 APPROVED
2005-01-20 RGD1306617_predicted  similar to Serine palmitoyltransferase 1 (predicted)  LOC361213_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 Sptlc1_predicted  serine palmitoyltransferase, long chain base subunit 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED
2005-01-12 LOC361213_predicted  similar to Serine palmitoyltransferase 1 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL