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 have serine C-palmitoyltransferase activity. Predicted to be involved in positive regulation of lipophagy; regulation of fat cell apoptotic process; and sphingolipid biosynthetic process. Predicted to localize to SPOTS complex. 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 2,4-dinitrotoluene; 2,6-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21711,877,249 - 11,916,295 (+)NCBI
Rnor_6.0 Ensembl1711,856,525 - 11,895,566 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01711,856,525 - 11,895,566 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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

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 (+)NCBI
Rnor_6.0 Ensembl1711,856,525 - 11,895,566 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01711,856,525 - 11,895,566 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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
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
(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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.112102,475,437 - 102,551,401 (-)NCBI
ChlSab1.1 Ensembl12102,475,415 - 102,551,322 (-)Ensembl
Sptlc1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624868317,992 - 393,776 (+)NCBI

Position Markers
AI235989  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21711,890,037 - 11,890,254 (+)MAPPER
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 (+)MAPPER
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 (+)MAPPER
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 (Rnor_6.0)
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)17124787908Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17132230361Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17133303755Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17138243814Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17163676140Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17173413148Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17173413148Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)1751977023422380Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1751977036283402Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)17333697224030841Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17333697224030841Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17333697237790462Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17333697263676140Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17333697273413148Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17333697273413148Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17333697273413148Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17341403928073589Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17471606727691136Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17471606727691136Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17519104750191047Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17519104750191047Rat
1581553Pur14Proteinuria QTL 145.30.0001total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)17842446716620067Rat
1582224Epfw4Epididymal fat weight QTL 43.50.0058epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)17973026321491085Rat
1582225Bw67Body weight QTL 676.20.0001body mass (VT:0001259)body weight (CMO:0000012)17973026321491085Rat
1582226Bw64Body weight QTL 644.20.0017body mass (VT:0001259)body weight (CMO:0000012)17973026321491085Rat
1582241Bw70Body weight QTL 704.60.0003body mass (VT:0001259)body weight (CMO:0000012)17973026321491085Rat
1582245Bw73Body weight QTL 734.60.0004body mass (VT:0001259)body weight (CMO:0000012)17973026321491085Rat
1582258Bw76Body weight QTL 764.60.0005body mass (VT:0001259)body weight (CMO:0000012)17973026321491085Rat
1582199Insul5Insulin level QTL 53.40.0119blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)17973026321491085Rat
1582208Kidm32Kidney mass QTL 323.90.0018kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17973026321491085Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17982730454827304Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)171052970942542027Rat

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
Rnor_6.0 Ensembl1711,856,525 - 11,895,566 (+)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

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 (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307140 AgrOrtholog
Ensembl Genes ENSRNOG00000010882 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000014546 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000014546 ENTREZGENE, UniProtKB/Swiss-Prot
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 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