Sgpl1 (sphingosine-1-phosphate lyase 1) - Rat Genome Database

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Gene: Sgpl1 (sphingosine-1-phosphate lyase 1) Rattus norvegicus
Analyze
Symbol: Sgpl1
Name: sphingosine-1-phosphate lyase 1
RGD ID: 628599
Description: Predicted to enable sphinganine-1-phosphate aldolase activity. Predicted to be involved in apoptotic signaling pathway; fatty acid metabolic process; and sphingolipid metabolic process. Predicted to act upstream of or within several processes, including face morphogenesis; gonad development; and vasculogenesis. Predicted to be located in endoplasmic reticulum membrane. Predicted to be active in endoplasmic reticulum. Human ortholog(s) of this gene implicated in nephrotic syndrome type 14. Orthologous to human SGPL1 (sphingosine-1-phosphate lyase 1); PARTICIPATES IN Fabry disease pathway; Gaucher's disease pathway; Krabbe disease pathway; INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: S1PL; SP-lyase 1; Spgl1; sphingosine phosphate lyase 1; sphingosine-1-phosphate aldolase; spl; SPL 1
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
mRatBN7.22029,047,793 - 29,094,209 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2029,047,796 - 29,094,084 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2030,065,894 - 30,110,041 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02029,452,195 - 29,496,346 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02030,194,650 - 30,238,806 (-)NCBIRnor_WKY
Rnor_6.02030,699,936 - 30,769,178 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2030,699,872 - 30,749,940 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02032,497,280 - 32,543,188 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42028,459,734 - 28,505,017 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12028,473,533 - 28,518,817 (-)NCBI
Celera2030,483,317 - 30,527,561 (-)NCBICelera
Cytogenetic Map20q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease 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 MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
5. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Subcellular localization and membrane topology of sphingosine-1-phosphate lyase in rat liver. Van Veldhoven PP and Mannaerts GP, J Biol Chem 1991 Jul 5;266(19):12502-7.
Additional References at PubMed
PMID:14570870   PMID:17143286   PMID:19056881   PMID:24809814   PMID:25630683   PMID:28165339   PMID:29070677   PMID:33450132  


Genomics

Comparative Map Data
Sgpl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22029,047,793 - 29,094,209 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2029,047,796 - 29,094,084 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2030,065,894 - 30,110,041 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02029,452,195 - 29,496,346 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02030,194,650 - 30,238,806 (-)NCBIRnor_WKY
Rnor_6.02030,699,936 - 30,769,178 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2030,699,872 - 30,749,940 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02032,497,280 - 32,543,188 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42028,459,734 - 28,505,017 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12028,473,533 - 28,518,817 (-)NCBI
Celera2030,483,317 - 30,527,561 (-)NCBICelera
Cytogenetic Map20q11NCBI
SGPL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381070,815,948 - 70,881,184 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1070,815,905 - 70,895,816 (+)EnsemblGRCh38hg38GRCh38
GRCh371072,575,704 - 72,640,941 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361072,245,722 - 72,309,873 (+)NCBINCBI36Build 36hg18NCBI36
Build 341072,245,721 - 72,309,871NCBI
Celera1065,857,672 - 65,923,231 (+)NCBICelera
Cytogenetic Map10q22.1NCBI
HuRef1066,569,390 - 66,634,948 (+)NCBIHuRef
CHM1_11072,858,499 - 72,923,730 (+)NCBICHM1_1
T2T-CHM13v2.01071,685,760 - 71,750,988 (+)NCBIT2T-CHM13v2.0
Sgpl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391060,934,421 - 60,983,463 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1060,934,421 - 60,983,482 (-)EnsemblGRCm39 Ensembl
GRCm381061,098,642 - 61,147,684 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1061,098,642 - 61,147,703 (-)EnsemblGRCm38mm10GRCm38
MGSCv371060,561,390 - 60,610,413 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361060,493,999 - 60,542,956 (-)NCBIMGSCv36mm8
Celera1062,199,269 - 62,248,215 (-)NCBICelera
Cytogenetic Map10B4NCBI
cM Map1032.14NCBI
Sgpl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543720,488,330 - 20,547,171 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543720,489,641 - 20,547,105 (-)NCBIChiLan1.0ChiLan1.0
SGPL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11069,812,082 - 69,876,444 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1069,812,092 - 69,876,438 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01067,286,349 - 67,351,574 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SGPL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1421,666,264 - 21,717,476 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl421,660,939 - 21,715,155 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha421,795,341 - 21,851,669 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0421,939,185 - 21,995,525 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl421,944,334 - 21,995,521 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1421,834,799 - 21,891,148 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0422,040,063 - 22,096,345 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0422,392,266 - 22,448,632 (+)NCBIUU_Cfam_GSD_1.0
Sgpl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721359,357,640 - 59,407,321 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365217,848,972 - 7,900,041 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365217,850,370 - 7,899,998 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SGPL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1473,724,100 - 73,781,800 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11473,696,902 - 73,781,830 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21479,572,301 - 79,628,480 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SGPL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1960,425,703 - 60,487,196 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl960,424,305 - 60,487,146 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604821,148,927 - 21,211,740 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sgpl1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247544,844,552 - 4,886,709 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247544,844,472 - 4,889,006 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sgpl1
56 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:34
Count of miRNA genes:32
Interacting mature miRNAs:34
Transcripts:ENSRNOT00000065127
Prediction methods:Miranda, Rnahybrid, Targetscan
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat


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 30 45 29 19 29 1 1 74 35 36 11 1
Low 13 12 12 12 7 10 5 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065127   ⟹   ENSRNOP00000059089
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2030,702,005 - 30,749,940 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084391   ⟹   ENSRNOP00000070983
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2029,047,796 - 29,094,084 (-)Ensembl
Rnor_6.0 Ensembl2030,699,872 - 30,748,784 (-)Ensembl
RefSeq Acc Id: NM_173116   ⟹   NP_775139
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,049,862 - 29,094,023 (-)NCBI
Rnor_6.02030,702,005 - 30,749,940 (-)NCBI
Rnor_5.02032,497,280 - 32,543,188 (-)NCBI
RGSC_v3.42028,459,734 - 28,505,017 (-)RGD
Celera2030,483,317 - 30,527,561 (-)RGD
Sequence:
RefSeq Acc Id: XM_008772871   ⟹   XP_008771093
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,047,793 - 29,094,209 (-)NCBI
Rnor_6.02030,699,936 - 30,749,948 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008772872   ⟹   XP_008771094
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,047,793 - 29,094,022 (-)NCBI
Rnor_6.02030,699,936 - 30,749,839 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039098466   ⟹   XP_038954394
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,047,793 - 29,094,119 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_775139   ⟸   NM_173116
- UniProtKB: Q8CHN6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008771093   ⟸   XM_008772871
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008771094   ⟸   XM_008772872
- Peptide Label: isoform X2
- UniProtKB: Q8CHN6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000059089   ⟸   ENSRNOT00000065127
RefSeq Acc Id: ENSRNOP00000070983   ⟸   ENSRNOT00000084391
RefSeq Acc Id: XP_038954394   ⟸   XM_039098466
- Peptide Label: isoform X2
- UniProtKB: Q8CHN6 (UniProtKB/Swiss-Prot)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8CHN6-F1-model_v2 AlphaFold Q8CHN6 1-568 view protein structure

Transcriptome

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

Promoters
RGD ID:13701600
Promoter ID:EPDNEW_R12123
Type:multiple initiation site
Name:Sgpl1_1
Description:sphingosine-1-phosphate lyase 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_6.02030,749,961 - 30,750,021EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628599 AgrOrtholog
BioCyc Gene G2FUF-3729 BioCyc
Ensembl Genes ENSRNOG00000000565 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000070983 ENTREZGENE
  ENSRNOP00000070983.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000084391 ENTREZGENE
  ENSRNOT00000084391.2 UniProtKB/TrEMBL
Gene3D-CATH 3.40.640.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.90.1150.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro PyrdxlP-dep_de-COase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_dom1 UniProtKB/Swiss-Prot
  PyrdxlP-dep_Trfase_major UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_small UniProtKB/TrEMBL
KEGG Report rno:286896 UniProtKB/Swiss-Prot
NCBI Gene 286896 ENTREZGENE
Pfam Pyridoxal_deC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sgpl1 PhenoGen
Superfamily-SCOP SSF53383 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2R514_RAT UniProtKB/TrEMBL
  Q8CHN6 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-11-17 Sgpl1  sphingosine-1-phosphate lyase 1  Sgpl1  sphingosine phosphate lyase 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-12-17 Sgpl1  sphingosine phosphate lyase 1  Spgl1  sphingosine-1-phosphate lyase 1  Symbol and Name updated 1303942 APPROVED
2003-02-27 Spgl1  sphingosine-1-phosphate lyase 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to the microsomal fraction 727205