Smpd1 (sphingomyelin phosphodiesterase 1) - Rat Genome Database

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Gene: Smpd1 (sphingomyelin phosphodiesterase 1) Rattus norvegicus
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
Previously known as: MGC94748; sphingomyelin phosphodiesterase; sphingomyelin phosphodiesterase 1, acid lysosomal
RGD Orthologs
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Rat AssemblyChrPosition (strand)SourceGenome Browsers
GRCr81169,304,772 - 169,308,615 (+)NCBIGRCr8
mRatBN7.21159,892,946 - 159,896,789 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1159,892,859 - 159,896,794 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1167,915,425 - 167,919,268 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01175,101,419 - 175,105,262 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01168,003,243 - 168,007,086 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01170,383,682 - 170,387,525 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1170,383,682 - 170,387,524 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01177,389,588 - 177,393,431 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41163,278,970 - 163,282,813 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1157,825,620 - 157,829,463 (+)NCBICelera
Cytogenetic Map1q32NCBI
JBrowse: View Region in Genome Browser (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)
benzo[a]pyrene  (ISO)
Benzo[k]fluoranthene  (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)
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)
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 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)


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  


Comparative Map Data
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
GRCr81169,304,772 - 169,308,615 (+)NCBIGRCr8
mRatBN7.21159,892,946 - 159,896,789 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1159,892,859 - 159,896,794 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1167,915,425 - 167,919,268 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01175,101,419 - 175,105,262 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01168,003,243 - 168,007,086 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01170,383,682 - 170,387,525 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1170,383,682 - 170,387,524 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01177,389,588 - 177,393,431 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41163,278,970 - 163,282,813 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1157,825,620 - 157,829,463 (+)NCBICelera
Cytogenetic Map1q32NCBI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh38116,390,474 - 6,394,996 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl116,390,440 - 6,394,998 (+)EnsemblGRCh38hg38GRCh38
GRCh37116,411,704 - 6,416,226 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36116,368,231 - 6,372,802 (+)NCBINCBI36Build 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
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm397105,203,567 - 105,207,596 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl7105,203,567 - 105,207,596 (+)EnsemblGRCm39 Ensembl
GRCm387105,554,360 - 105,558,389 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7105,554,360 - 105,558,389 (+)EnsemblGRCm38mm10GRCm38
MGSCv377112,702,874 - 112,706,903 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv367105,428,236 - 105,432,203 (+)NCBIMGSCv36mm8
Celera7105,825,502 - 105,829,531 (+)NCBICelera
Cytogenetic Map7E3NCBI
cM Map755.9NCBI
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
ChiLan1.0 EnsemblNW_00495541422,117,930 - 22,121,744 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541422,117,929 - 22,121,744 (+)NCBIChiLan1.0ChiLan1.0
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
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
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
CanFam3.12129,714,418 - 29,719,035 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2129,714,557 - 29,719,033 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2129,416,446 - 29,421,072 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02130,540,703 - 30,545,329 (+)NCBIROS_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_1.0
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
HiC_Itri_2NW_02440494756,222,931 - 56,227,200 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936842447,991 - 452,630 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936842448,315 - 452,557 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
Sscrofa11.1 Ensembl93,324,442 - 3,328,457 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.193,324,091 - 3,328,493 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.293,961,624 - 3,964,422 (+)NCBISscrofa10.2Sscrofa10.2susScr3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
ChlSab1.1158,431,677 - 58,436,233 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl158,432,068 - 58,436,236 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666038156,257,313 - 156,261,990 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
HetGla_female_1.0 EnsemblNW_0046248177,909,468 - 7,913,417 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248177,909,777 - 7,913,419 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Variants in Smpd1
12 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:244
Count of miRNA genes:155
Interacting mature miRNAs:181
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 (
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
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)181591954219808434Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)190508614173018436Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)190508614180359386Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)194494440172949803Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)194494440181830018Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)194494440198211706Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)194494440198324465Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)194642644214537671Rat
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)1100357752183970443Rat
1354591Cm36Cardiac mass QTL 364.1heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1102813953201278233Rat
1354615Cm32Cardiac mass QTL 325.2heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1102813953201278233Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1102813953218753816Rat
1300158Bp173Blood pressure QTL 1733.48arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1115540693185145286Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1115540693238914717Rat
631199Cm23Cardiac mass QTL 234.60.0004heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1115585465172949803Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118608292241799120Rat
2313060Bss71Bone structure and strength QTL 712.60.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)1118944747163944747Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118944897199050459Rat
1598850Bp297Blood pressure QTL 2972.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1121006655166006655Rat
1598866Bp287Blood pressure QTL 2875.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1121006655166006655Rat
61442Strs1Sensitivity to stroke QTL 17.4cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)1121767634166767634Rat
2293140Bp313Blood pressure QTL 313arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1121833674166833674Rat
631544Bp84Blood pressure QTL 845.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1123350408181759564Rat
1358189Cstrr1Cold stress response QTL 10.0001catecholamine amount (VT:0010543)urine norepinephrine level (CMO:0001629)1123350408182418476Rat
1641895Bp298Blood pressure QTL 298arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1123350408182418476Rat
1578770Stresp23Stress response QTL 23kidney sympathetic nerve activity (VT:0004050)stimulated renal sympathetic nerve activity to basal renal sympathetic nerve activity ratio (CMO:0001786)1123350408182418476Rat
631549Bp89Blood pressure QTL 895.7arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1123350581201284552Rat
634348Bp138Blood pressure QTL 138arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1125611501168883176Rat
9685799Bp375Blood pressure QTL 375arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1125611501170611501Rat
631654Bp107Blood pressure QTL 107arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1125611501170611501Rat
9685802Bp376Blood pressure QTL 376arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1126540680171540680Rat
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)1130636910175636910Rat
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)1130636910175636910Rat
6893347Bw98Body weight QTL 980.20.53body mass (VT:0001259)body weight (CMO:0000012)1133680936178680936Rat
6893361Bw104Body weight QTL 1040.590.27body mass (VT:0001259)body weight (CMO:0000012)1133680936178680936Rat
1558645Bw55Body weight QTL 553.20.004body mass (VT:0001259)body weight (CMO:0000012)1133680936178680936Rat
631206Niddm40Non-insulin dependent diabetes mellitus QTL 40blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1136745990163747690Rat
71118Thym1Thymus enlargement QTL 110.170.001thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1136829932181829932Rat
724550Thym3Thymus enlargement QTL 37.820.001thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1136829932181829932Rat
631519Pia11Pristane induced arthritis QTL 115.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1136830018181830018Rat
1598853Memor3Memory QTL 34.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)1143506580212458660Rat
61348Bp30Blood pressure QTL 302.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1144017057197814409Rat
70160Bw18Body weight QTL 185.7body mass (VT:0001259)body weight (CMO:0000012)1144267353196383668Rat
737828Hcas3Hepatocarcinoma susceptibility QTL 34.9liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)1144267353222987745Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1144267353251128347Rat
634315Niddm45Non-insulin dependent diabetes mellitus QTL 457.16blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1144267916172949660Rat
61379Bp44Blood pressure QTL 4419.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1144267916174133260Rat
7771612Cm80Cardiac mass QTL 808.4heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)1149448574221264292Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1150700142252085212Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1150700247252085048Rat
1578778Pur4Proteinuria QTL 43.30.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1150700247252085048Rat
1354602Bw35Body weight QTL 3512.2body mass (VT:0001259)body weight (CMO:0000012)1151162512201278233Rat
1354620Kidm19Kidney mass QTL 194kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512201278233Rat
1354634Kidm12Kidney mass QTL 123.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)1151162512201278233Rat
1354636Lmblg1Limb length QTL 16.4tibia length (VT:0004357)tibia length (CMO:0000450)1151162512201278233Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1358886Bp260Blood pressure QTL 2603.67arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1151162766225824951Rat
61343Bp28Blood pressure QTL 28arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1151646613196646613Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
2303622Vencon6Ventilatory control QTL 60.001respiration trait (VT:0001943)respiration rate (CMO:0000289)1154561505199561505Rat
1582204Livw1Liver weight QTL 13.60.0003liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)1155422851172949803Rat
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)1155866514200866514Rat
631548Bp88Blood pressure QTL 8850.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1156677124176484451Rat
1354618Kidm15Kidney mass QTL 155kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)1156677124201278233Rat
2312420Pur17Proteinuria QTL 177.10.0001urine protein amount (VT:0005160)urine total protein excretion rate (CMO:0000756)1156677124218753816Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
61347Bp197Blood pressure QTL 1974.2arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)1158633083203633083Rat

Markers in Region
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
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
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
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
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
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
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


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
Medium 3 43 57 41 19 41 8 11 74 35 39 11 8
Low 2
Below cutoff


RefSeq Acc Id: ENSRNOT00000024224   ⟹   ENSRNOP00000024224
Rat AssemblyChrPosition (strand)Source
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
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
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
RefSeq Acc Id: NP_001006998   ⟸   NM_001006997
- UniProtKB: Q5XIA6 (UniProtKB/TrEMBL),   F7ETC0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq 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


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

RGD ID:13690285
Promoter ID:EPDNEW_R810
Type:initiation region
Description:sphingomyelin phosphodiesterase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database,
Experiment Methods:Single-end sequencing.
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
  ENSRNOT00000024224.5 UniProtKB/TrEMBL
InterPro ASM_C 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
Pfam ASMase_C UniProtKB/TrEMBL
  Metallophos UniProtKB/TrEMBL
PhenoGen Smpd1 PhenoGen
PIRSF Sphingomy_PDE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000017977 RatGTEx
Superfamily-SCOP Saposin_like UniProtKB/TrEMBL
  SSF56300 UniProtKB/TrEMBL
UniProt A6I7I6_RAT 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