Smpd1 (sphingomyelin phosphodiesterase 1) - Rat Genome Database

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Gene: Smpd1 (sphingomyelin phosphodiesterase 1) Rattus norvegicus
Analyze
Symbol: Smpd1
Name: sphingomyelin phosphodiesterase 1
RGD ID: 1549719
Description: Predicted to enable acid sphingomyelin phosphodiesterase activity and zinc ion binding activity. Involved in several processes, including ceramide biosynthetic process; positive regulation of apoptotic process; and response to cocaine. Located in extracellular space and lamellar body. Used to study Wilson disease. Human ortholog(s) of this gene implicated in Niemann-Pick disease; Niemann-Pick disease type A; and Niemann-Pick disease type B. Orthologous to human SMPD1 (sphingomyelin phosphodiesterase 1); PARTICIPATES IN ceramide signaling pathway; FasL mediated signaling pathway; Trail mediated signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MGC94748; sphingomyelin phosphodiesterase; sphingomyelin phosphodiesterase 1, acid lysosomal
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81169,304,772 - 169,308,615 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1169,304,708 - 169,308,614 (+)EnsemblGRCr8
mRatBN7.21159,892,946 - 159,896,789 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1159,892,859 - 159,896,794 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1167,915,425 - 167,919,268 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01175,101,419 - 175,105,262 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01168,003,243 - 168,007,086 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01170,383,682 - 170,387,525 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1170,383,682 - 170,387,524 (+)Ensemblrn6Rnor6.0
Rnor_5.01177,389,588 - 177,393,431 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41163,278,970 - 163,282,813 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1157,825,620 - 157,829,463 (+)NCBICelera
Cytogenetic Map1q32NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2-hydroxypropanoic acid  (ISO)
3',4',5-trihydroxy-3,7-dimethoxyflavone  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3-diphenyl-N-(1-phenylethyl)-1-propanamine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
7-ketocholesterol  (ISO)
actinomycin D  (ISO)
afimoxifene  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
amitriptyline  (ISO)
aristolochic acid A  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
Benzo[k]fluoranthene  (ISO)
beta-lapachone  (ISO)
bezafibrate  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
cholesterol  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
clotrimazole  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
daunorubicin  (ISO)
DDE  (ISO)
desipramine  (ISO)
dexamethasone  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (EXP)
diethyl maleate  (ISO)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (ISO)
ethylparaben  (ISO)
fluoxetine  (ISO)
flutamide  (EXP)
folic acid  (ISO)
gentamycin  (EXP)
glucose  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
lead diacetate  (ISO)
lead(0)  (ISO)
morphine  (ISO)
N-nitrosodiethylamine  (EXP)
naloxone  (ISO)
nitrates  (ISO)
oxaliplatin  (EXP)
paracetamol  (EXP,ISO)
paraquat  (ISO)
peroxynitrous acid  (ISO)
phenethyl isothiocyanate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
quercetin  (ISO)
quercitrin  (ISO)
rac-lactic acid  (ISO)
S-allylcysteine  (ISO)
SB 431542  (ISO)
sevoflurane  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sorafenib  (ISO)
streptozocin  (ISO)
superoxide  (ISO)
tamibarotene  (ISO)
temozolomide  (ISO)
thiram  (ISO)
topotecan  (EXP)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
Yessotoxin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
endolysosome  (IEA,ISO)
endosome  (IEA,ISO)
extracellular region  (IEA)
extracellular space  (IBA,IDA,IEA,ISO)
lamellar body  (IDA)
lipid droplet  (IEA)
lysosome  (IBA,IEA,ISO)
plasma membrane  (IEA,ISO)

References

References - curated
# Reference Title Reference Citation
1. Pioglitazone induces de novo ceramide synthesis in the rat heart. Baranowski M, etal., Prostaglandins Other Lipid Mediat. 2007 Feb;83(1-2):99-111. Epub 2006 Nov 16.
2. Hydrophobic bile salts trigger ceramide formation through endosomal acidification. Becker S, etal., Biol Chem. 2007 Feb;388(2):185-96.
3. 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.
4. Effect of streptozotocin-diabetes on the functioning of the sphingomyelin-signalling pathway in skeletal muscles of the rat. Gorska M, etal., Horm Metab Res. 2004 Jan;36(1):14-21.
5. Liver cell death and anemia in Wilson disease involve acid sphingomyelinase and ceramide. Lang PA, etal., Nat Med. 2007 Feb;13(2):164-70. Epub 2007 Jan 28.
6. Oxidized phospholipids in minimally modified low density lipoprotein induce apoptotic signaling via activation of acid sphingomyelinase in arterial smooth muscle cells. Loidl A, etal., J Biol Chem. 2003 Aug 29;278(35):32921-8. Epub 2003 Jun 19.
7. Cocaine induces a mixed lysosomal lipidosis in cultured fibroblasts, by inactivation of acid sphingomyelinase and inhibition of phospholipase A1. Nassogne MC, etal., Toxicol Appl Pharmacol. 2004 Jan 15;194(2):101-10.
8. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
10. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
11. GOA pipeline RGD automated data pipeline
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Comprehensive gene review and curation RGD comprehensive gene curation
15. Seven novel acid sphingomyelinase gene mutations in Niemann-Pick type A and B patients. Sikora J, etal., Ann Hum Genet. 2003 Jan;67(Pt 1):63-70.
16. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:8702487   PMID:16025116   PMID:18815062   PMID:19279008   PMID:19279011   PMID:20956541   PMID:22383528   PMID:23046545   PMID:23376485   PMID:23533145   PMID:23973266   PMID:26830134  
PMID:27659707  


Genomics

Comparative Map Data
Smpd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81169,304,772 - 169,308,615 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1169,304,708 - 169,308,614 (+)EnsemblGRCr8
mRatBN7.21159,892,946 - 159,896,789 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1159,892,859 - 159,896,794 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1167,915,425 - 167,919,268 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01175,101,419 - 175,105,262 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01168,003,243 - 168,007,086 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01170,383,682 - 170,387,525 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1170,383,682 - 170,387,524 (+)Ensemblrn6Rnor6.0
Rnor_5.01177,389,588 - 177,393,431 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41163,278,970 - 163,282,813 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1157,825,620 - 157,829,463 (+)NCBICelera
Cytogenetic Map1q32NCBI
SMPD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38116,390,474 - 6,394,996 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl116,390,414 - 6,394,998 (+)Ensemblhg38GRCh38
GRCh37116,411,704 - 6,416,226 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36116,368,231 - 6,372,802 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34116,368,230 - 6,372,801NCBI
Celera116,530,711 - 6,535,296 (+)NCBICelera
Cytogenetic Map11p15.4NCBI
HuRef116,070,739 - 6,075,337 (+)NCBIHuRef
CHM1_1116,410,778 - 6,415,363 (+)NCBICHM1_1
T2T-CHM13v2.0116,448,931 - 6,453,455 (+)NCBIT2T-CHM13v2.0
Smpd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397105,203,567 - 105,207,596 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl7105,203,567 - 105,207,596 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm387105,554,360 - 105,558,389 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7105,554,360 - 105,558,389 (+)Ensemblmm10GRCm38
MGSCv377112,702,874 - 112,706,903 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv367105,428,236 - 105,432,203 (+)NCBIMGSCv36mm8
Celera7105,825,502 - 105,829,531 (+)NCBICelera
Cytogenetic Map7E3NCBI
cM Map755.9NCBI
Smpd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541422,117,930 - 22,121,744 (+)Ensembl
ChiLan1.0NW_00495541422,117,929 - 22,121,744 (+)NCBIChiLan1.0ChiLan1.0
SMPD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v298,826,802 - 8,831,484 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1118,790,673 - 8,795,342 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0116,521,812 - 6,526,349 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1116,205,278 - 6,209,950 (+)NCBIPanPan1.1PanPan1.1panPan2
SMPD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12129,714,418 - 29,719,035 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2129,714,557 - 29,719,033 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2129,416,446 - 29,421,072 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02130,540,703 - 30,545,329 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2130,540,764 - 30,545,592 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12129,861,608 - 29,866,232 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02130,027,386 - 30,032,012 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02130,222,733 - 30,227,359 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Smpd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494756,222,931 - 56,227,200 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936842447,991 - 452,630 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936842448,315 - 452,557 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMPD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl93,324,442 - 3,328,457 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.193,324,091 - 3,328,493 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.293,961,624 - 3,964,422 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SMPD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1158,431,677 - 58,436,233 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl158,432,068 - 58,436,236 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666038156,257,313 - 156,261,990 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smpd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248177,909,468 - 7,913,417 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248177,909,777 - 7,913,419 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Smpd1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12104,390,759 - 104,394,682 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Smpd1
20 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:244
Count of miRNA genes:155
Interacting mature miRNAs:181
Transcripts:ENSRNOT00000024224
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61442Strs1Sensitivity to stroke QTL 17.4cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)1131179947176179947Rat
1578778Pur4Proteinuria QTL 43.30.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1160111531262090437Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1160573753266453731Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)1137611478182611478Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1153679879198679879Rat
1598866Bp287Blood pressure QTL 2875.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130419227175419227Rat
1578770Stresp23Stress response QTL 23kidney sympathetic nerve activity (VT:0004050)stimulated renal sympathetic nerve activity to basal renal sympathetic nerve activity ratio (CMO:0001786)1132760429191848948Rat
70160Bw18Body weight QTL 185.7body mass (VT:0001259)body weight (CMO:0000012)1153679879205813246Rat
8694166Bw147Body weight QTL 1476.830.001body mass (VT:0001259)body weight gain (CMO:0000420)1153788989198788989Rat
631199Cm23Cardiac mass QTL 234.60.0004heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1142582336182383862Rat
1354636Lmblg1Limb length QTL 16.4tibia length (VT:0004357)tibia length (CMO:0000450)1160573753210707719Rat
1598850Bp297Blood pressure QTL 2972.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130419227175419227Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1162548015270518180Rat
152025235Bw194Body weight QTL 1944.86body mass (VT:0001259)1132966869252856240Rat
61341Bp26Blood pressure QTL 26arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1139442053223964440Rat
1598853Memor3Memory QTL 34.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)1152919152268496042Rat
1354634Kidm12Kidney mass QTL 123.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)1160573753210707719Rat
4889428Stresp24Stress response QTL 240.05heart pumping trait (VT:2000009)absolute change in electrocardiographic low frequency R-R spectral component to high frequency R-R spectral component ratio (CMO:0002162)1165278545210278545Rat
152025232Bw192Body weight QTL 1923.93body mass (VT:0001259)1127329268206393015Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1160111531262090437Rat
61343Bp28Blood pressure QTL 28arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1161077990206077990Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)199645382182701046Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)199645382221502378Rat
61347Bp197Blood pressure QTL 1974.2arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)1168063662213063662Rat
61348Bp30Blood pressure QTL 302.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1159894717207261263Rat
8655649Arrd1Age-related retinal degeneration QTL 14.89retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1109493780193400781Rat
2303622Vencon6Ventilatory control QTL 60.001respiration trait (VT:0001943)respiration rate (CMO:0000289)1163992710208992710Rat
7771612Cm80Cardiac mass QTL 808.4heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)1146080545243492863Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1103779152223964440Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)198879955208479939Rat
1300158Bp173Blood pressure QTL 1733.48arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1155359438194575574Rat
631206Niddm40Non-insulin dependent diabetes mellitus QTL 40blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1140833106185833106Rat
737828Hcas3Hepatocarcinoma susceptibility QTL 34.9liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)1153679879232414077Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1160573753266453731Rat
1358886Bp260Blood pressure QTL 2603.67arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1160574007235238518Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1116099376191260518Rat
2293140Bp313Blood pressure QTL 313arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1131243790176243790Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1160111426262090599Rat
737974Bp161Blood pressure QTL 1610.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1129182274174182274Rat
1641895Bp298Blood pressure QTL 298arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1132760429191848948Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1154961463266453731Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1162753891207753891Rat
631496Bp97Blood pressure QTL 973.08arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1115183611176289080Rat
634315Niddm45Non-insulin dependent diabetes mellitus QTL 457.16blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1153680016182383862Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151941022208479811Rat
61379Bp44Blood pressure QTL 4419.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1153680016183564652Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1102780511182384005Rat
6893347Bw98Body weight QTL 980.20.53body mass (VT:0001259)body weight (CMO:0000012)1143092939188092939Rat
1354591Cm36Cardiac mass QTL 364.1heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1111949780210707719Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1128019551173019551Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134184556172281316Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134565911208798288Rat
631519Pia11Pristane induced arthritis QTL 115.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)193903998191260518Rat
6893361Bw104Body weight QTL 1040.590.27body mass (VT:0001259)body weight (CMO:0000012)1143092939188092939Rat
724562Rends1Renal damage susceptibility QTL 10.05kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)1139442053223964440Rat
738006Anxrr14Anxiety related response QTL 1440.00035locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1140048073185048073Rat
1558645Bw55Body weight QTL 553.20.004body mass (VT:0001259)body weight (CMO:0000012)1143092939188092939Rat
1354615Cm32Cardiac mass QTL 325.2heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1111949780210707719Rat
634348Bp138Blood pressure QTL 138arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1135021436178317588Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1160573753266453731Rat
738028Anxrr12Anxiety related response QTL 124.90.00001locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1140048073185048073Rat
1354620Kidm19Kidney mass QTL 194kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1160573753210707719Rat
8693608Alc24Alcohol consumption QTL 242.30.74drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)1159863716177663210Rat
1576310Schws2Schwannoma susceptibility QTL 20.029nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1153788989198788989Rat
1354618Kidm15Kidney mass QTL 155kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)1165707719210707719Rat
631654Bp107Blood pressure QTL 107arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1135021436180021436Rat
631544Bp84Blood pressure QTL 845.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1132760429191190115Rat
152025212Bw190Body weight QTL 1905.7body mass (VT:0001259)1132966869206393015Rat
631548Bp88Blood pressure QTL 8850.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1140915717185915717Rat
1358189Cstrr1Cold stress response QTL 10.0001catecholamine amount (VT:0010543)urine norepinephrine level (CMO:0001629)1132760429191848948Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1111949780228180370Rat
7411599Foco11Food consumption QTL 1118.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1153788989198788989Rat
1354602Bw35Body weight QTL 3512.2body mass (VT:0001259)body weight (CMO:0000012)1160573753210707719Rat

Markers in Region
AF206720  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21159,897,088 - 159,897,230 (+)MAPPERmRatBN7.2
Rnor_6.01170,387,825 - 170,387,966NCBIRnor6.0
Rnor_5.01177,393,731 - 177,393,872UniSTSRnor5.0
RGSC_v3.41163,283,113 - 163,283,254UniSTSRGSC3.4
Celera1157,829,763 - 157,829,904UniSTS
Cytogenetic Map1q33UniSTS
RH130448  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21159,896,553 - 159,896,734 (+)MAPPERmRatBN7.2
Rnor_6.01170,387,290 - 170,387,470NCBIRnor6.0
Rnor_5.01177,393,196 - 177,393,376UniSTSRnor5.0
RGSC_v3.41163,282,578 - 163,282,758UniSTSRGSC3.4
Celera1157,829,228 - 157,829,408UniSTS
RH 3.4 Map11295.8UniSTS
Cytogenetic Map1q33UniSTS
Smpd1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21159,893,020 - 159,894,288 (+)MAPPERmRatBN7.2
Rnor_6.01170,383,757 - 170,385,024NCBIRnor6.0
Rnor_5.01177,389,663 - 177,390,930UniSTSRnor5.0
RGSC_v3.41163,279,045 - 163,280,312UniSTSRGSC3.4
Celera1157,825,695 - 157,826,962UniSTS
Cytogenetic Map1q33UniSTS
RH134756  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21159,897,030 - 159,897,222 (+)MAPPERmRatBN7.2
Rnor_6.01170,387,767 - 170,387,958NCBIRnor6.0
Rnor_5.01177,393,673 - 177,393,864UniSTSRnor5.0
RGSC_v3.41163,283,055 - 163,283,246UniSTSRGSC3.4
Celera1157,829,705 - 157,829,896UniSTS
RH 3.4 Map11297.5UniSTS
Cytogenetic Map1q33UniSTS
UniSTS:235734  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21159,892,930 - 159,893,039 (+)MAPPERmRatBN7.2
Rnor_6.01170,383,667 - 170,383,775NCBIRnor6.0
Rnor_5.01177,389,573 - 177,389,681UniSTSRnor5.0
RGSC_v3.41163,278,955 - 163,279,063UniSTSRGSC3.4
Celera1157,825,605 - 157,825,713UniSTS
Cytogenetic Map1q33UniSTS
SMPD1_855  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21159,896,107 - 159,896,914 (+)MAPPERmRatBN7.2
Rnor_6.01170,386,844 - 170,387,650NCBIRnor6.0
Rnor_5.01177,392,750 - 177,393,556UniSTSRnor5.0
RGSC_v3.41163,282,132 - 163,282,938UniSTSRGSC3.4
Celera1157,828,782 - 157,829,588UniSTS
Cytogenetic Map1q33UniSTS
Smpd1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21159,895,451 - 159,896,203 (+)MAPPERmRatBN7.2
Rnor_6.01170,386,188 - 170,386,939NCBIRnor6.0
Rnor_5.01177,392,094 - 177,392,845UniSTSRnor5.0
RGSC_v3.41163,281,476 - 163,282,227UniSTSRGSC3.4
Celera1157,828,126 - 157,828,877UniSTS
Cytogenetic Map1q33UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000024224   ⟹   ENSRNOP00000024224
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1169,304,708 - 169,308,614 (+)Ensembl
mRatBN7.2 Ensembl1159,892,859 - 159,896,794 (+)Ensembl
Rnor_6.0 Ensembl1170,383,682 - 170,387,524 (+)Ensembl
RefSeq Acc Id: NM_001006997   ⟹   NP_001006998
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81169,304,772 - 169,308,615 (+)NCBI
mRatBN7.21159,892,946 - 159,896,789 (+)NCBI
Rnor_6.01170,383,682 - 170,387,525 (+)NCBI
Rnor_5.01177,389,588 - 177,393,431 (+)NCBI
RGSC_v3.41163,278,970 - 163,282,813 (+)RGD
Celera1157,825,620 - 157,829,463 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001006998 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH83780 (Get FASTA)   NCBI Sequence Viewer  
  EDM18044 (Get FASTA)   NCBI Sequence Viewer  
  EDM18045 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000024224
  ENSRNOP00000024224.4
RefSeq Acc Id: NP_001006998   ⟸   NM_001006997
- UniProtKB: Q5XIA6 (UniProtKB/TrEMBL),   F7ETC0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000024224   ⟸   ENSRNOT00000024224
Protein Domains
Saposin B-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XIA6-F1-model_v2 AlphaFold Q5XIA6 1-627 view protein structure

Transcriptome

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

Promoters
RGD ID:13690285
Promoter ID:EPDNEW_R810
Type:initiation region
Name:Smpd1_1
Description:sphingomyelin phosphodiesterase 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_6.01170,383,634 - 170,383,694EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1549719 AgrOrtholog
BioCyc Gene G2FUF-58017 BioCyc
BioCyc Pathway PWY3DJ-11281 [sphingomyelin metabolism] BioCyc
BioCyc Pathway Image PWY3DJ-11281 BioCyc
Ensembl Genes ENSRNOG00000017977 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024224 ENTREZGENE
  ENSRNOT00000024224.6 UniProtKB/TrEMBL
Gene3D-CATH 3.60.21.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7096039 IMAGE-MGC_LOAD
InterPro ASM_C UniProtKB/TrEMBL
  ASMase/PPN1_MPP UniProtKB/TrEMBL
  M-pesterase UniProtKB/TrEMBL
  Metallo-depent_PP-like UniProtKB/TrEMBL
  Saposin-like UniProtKB/TrEMBL
  SaposinB UniProtKB/TrEMBL
  Sphingomy_PDE UniProtKB/TrEMBL
KEGG Report rno:308909 UniProtKB/TrEMBL
MGC_CLONE MGC:94748 IMAGE-MGC_LOAD
NCBI Gene 308909 ENTREZGENE
PANTHER SPHINGOMYELIN PHOSPHODIESTERASE UniProtKB/TrEMBL
  SPHINGOMYELIN PHOSPHODIESTERASE UniProtKB/TrEMBL
Pfam ASMase_C UniProtKB/TrEMBL
  Metallophos UniProtKB/TrEMBL
PharmGKB SMPD1 RGD
PhenoGen Smpd1 PhenoGen
PIRSF Sphingomy_PDE UniProtKB/TrEMBL
PROSITE SAP_B UniProtKB/TrEMBL
RatGTEx ENSRNOG00000017977 RatGTEx
SMART SapB UniProtKB/TrEMBL
Superfamily-SCOP Saposin_like UniProtKB/TrEMBL
  SSF56300 UniProtKB/TrEMBL
UniProt A6I7I6_RAT UniProtKB/TrEMBL
  F7ETC0 ENTREZGENE, UniProtKB/TrEMBL
  Q5XIA6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-16 Smpd1  sphingomyelin phosphodiesterase 1  Smpd1  sphingomyelin phosphodiesterase 1, acid lysosomal  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Smpd1  sphingomyelin phosphodiesterase 1, acid lysosomal      Symbol and Name status set to approved 1299863 APPROVED
2005-09-15 Smpd1  sphingomyelin phosphodiesterase 1, acid lysosomal      Symbol and Name status set to provisional 70820 PROVISIONAL