Smpd3 (sphingomyelin phosphodiesterase 3) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Smpd3 (sphingomyelin phosphodiesterase 3) Rattus norvegicus
Analyze
Symbol: Smpd3
Name: sphingomyelin phosphodiesterase 3
RGD ID: 619754
Description: Predicted to enable identical protein binding activity; neutral sphingomyelin phosphodiesterase activity; and phospholipid binding activity. Involved in several processes, including positive regulation of biosynthetic process; positive regulation of exosomal secretion; and positive regulation of non-canonical NF-kappaB signal transduction. Predicted to be located in Golgi cis cisterna and plasma membrane. Predicted to be active in cytoplasm. Used to study pulmonary hypertension and transient cerebral ischemia. Biomarker of chronic obstructive pulmonary disease. Orthologous to human SMPD3 (sphingomyelin phosphodiesterase 3); PARTICIPATES IN ceramide signaling pathway; sphingolipid metabolic pathway; INTERACTS WITH (+)-schisandrin B; 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cca1; confluent 3Y1 cell-associated 1; confluent 3Y1 cell-associated protein 1; neutral sphingomyelin phosphodiesterase 3; neutral sphingomyelinase 2; neutral sphingomyelinase II; nSMase-2; nSMase2; sphingomyelin phosphodiesterase 3, neutral; sphingomyelin phosphodiesterase 3, neutral membrane
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
GRCr81951,072,209 - 51,155,639 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1951,072,209 - 51,085,936 (-)EnsemblGRCr8
mRatBN7.21934,162,337 - 34,245,786 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1934,162,341 - 34,245,749 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1940,977,903 - 41,061,312 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01941,631,214 - 41,714,614 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01943,930,363 - 44,013,762 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01938,237,963 - 38,321,572 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1938,237,965 - 38,321,528 (-)Ensemblrn6Rnor6.0
Rnor_5.01949,107,658 - 49,191,221 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41936,112,166 - 36,195,564 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1933,589,416 - 33,672,639 (-)NCBICelera
RGSC_v3.11936,117,046 - 36,200,445 (-)NCBI
RH 3.4 Map19304.3RGD
Cytogenetic Map19q12NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(1->4)-beta-D-glucan  (ISO)
(S)-nicotine  (ISO)
1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (EXP)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4,4'-trichlorobiphenyl  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2,4-dinitrotoluene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (EXP)
2-hydroxypropanoic acid  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-dichloroaniline  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
aldehydo-D-glucosamine  (EXP)
all-trans-retinoic acid  (ISO)
alpha-Zearalanol  (EXP)
Ampullosporin  (EXP)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
Benzo[k]fluoranthene  (ISO)
beta-D-glucosamine  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
Butylbenzyl phthalate  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
camptothecin  (ISO)
carbon nanotube  (ISO)
cholesterol  (ISO)
choline  (ISO)
chrysene  (ISO)
clothianidin  (ISO)
copper(II) sulfate  (ISO)
cyproconazole  (ISO)
daunorubicin  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibutyl phthalate  (ISO)
dichloroacetic acid  (ISO)
dieldrin  (EXP)
diethyl phthalate  (ISO)
diisobutyl phthalate  (ISO)
diisononyl phthalate  (ISO)
diuron  (EXP)
endosulfan  (EXP)
epoxiconazole  (ISO)
ethanol  (ISO)
Evodiamine  (ISO)
fenamidone  (ISO)
fenofibrate  (ISO)
fipronil  (EXP)
flavonoids  (EXP)
folic acid  (ISO)
fumonisin B1  (ISO)
furan  (EXP)
GSK-J4  (ISO)
GW 4064  (ISO)
hydrogen peroxide  (ISO)
Indeno[1,2,3-cd]pyrene  (ISO)
ketamine  (EXP)
L-methionine  (ISO)
Lasiocarpine  (ISO)
lipopolysaccharide  (ISO)
lithocholic acid  (ISO)
magnesium dichloride  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-Nitrosopyrrolidine  (ISO)
nickel dichloride  (EXP)
nicotine  (ISO)
O-methyleugenol  (ISO)
Octicizer  (ISO)
okadaic acid  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
p-toluidine  (EXP)
paracetamol  (ISO)
paraquat  (EXP)
PCB138  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenethyl caffeate  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
propanal  (ISO)
propiconazole  (ISO)
rac-lactic acid  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sotorasib  (ISO)
tetrachloromethane  (EXP)
thapsigargin  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trametinib  (ISO)
triadimefon  (ISO)
tributyl phosphate  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triphenyl phosphate  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
tris(2-chloroethyl) phosphate  (ISO)
undecane  (EXP)
urethane  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
artery smooth muscle contraction  (IMP)
BMP signaling pathway  (ISO)
bone development  (ISO)
bone growth  (ISO)
bone mineralization  (ISO)
cartilage development  (ISO)
cellular response to hydrogen peroxide  (ISO)
cellular response to interleukin-1  (IEP)
cellular response to magnesium ion  (ISO)
cellular response to oxidised low-density lipoprotein particle stimulus  (ISO)
cellular response to peptide  (ISO)
cellular response to reactive oxygen species  (ISO)
cellular response to redox state  (ISO)
cellular response to tumor necrosis factor  (ISO)
ceramide metabolic process  (ISO)
chondrocyte development  (ISO)
chondrocyte development involved in endochondral bone morphogenesis  (ISO)
collagen metabolic process  (ISO)
dentinogenesis  (ISO)
DNA biosynthetic process  (ISO)
dopamine uptake  (IMP)
endochondral ossification  (ISO)
extracellular matrix assembly  (ISO)
G1 to G0 transition  (ISO)
hematopoietic progenitor cell differentiation  (ISO)
lipid metabolic process  (IEA)
lung alveolus development  (ISO)
lung development  (ISO)
mitotic nuclear division  (ISO)
multicellular organism growth  (ISO)
negative regulation of cytosolic calcium ion concentration  (IMP)
negative regulation of hyaluronan biosynthetic process  (ISO)
negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction  (ISO)
ossification  (ISO)
peptide hormone secretion  (ISO)
platelet-derived growth factor receptor signaling pathway  (ISO)
polysaccharide transport  (ISO)
positive regulation of ceramide biosynthetic process  (IMP)
positive regulation of exosomal secretion  (IMP)
positive regulation of mitotic nuclear division  (ISO)
positive regulation of nitric oxide biosynthetic process  (IMP)
positive regulation of non-canonical NF-kappaB signal transduction  (IMP)
positive regulation of smooth muscle cell proliferation  (ISO)
regulation of cartilage development  (ISO)
regulation of hyaluronan biosynthetic process  (ISO)
regulation of leukocyte migration  (ISO)
regulation of protein phosphorylation  (ISO)
respiratory system development  (ISO)
signal transduction  (ISO)
skeletal system development  (ISO)
sphingolipid mediated signaling pathway  (ISO)
sphingolipid metabolic process  (IEA,ISO)
sphingomyelin catabolic process  (IEA,ISO)
sphingomyelin metabolic process  (IBA,ISO,ISS)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Cardiac fibroblast-derived microRNA passenger strand-enriched exosomes mediate cardiomyocyte hypertrophy. Bang C, etal., J Clin Invest. 2014 May;124(5):2136-46. doi: 10.1172/JCI70577. Epub 2014 Apr 17.
2. Activation of neutral sphingomyelinase is involved in acute hypoxic pulmonary vasoconstriction. Cogolludo A, etal., Cardiovasc Res. 2009 May 1;82(2):296-302. doi: 10.1093/cvr/cvn349. Epub 2008 Dec 16.
3. Age-related changes in neutral sphingomyelin-specific phospholipase C activity in striatum, hippocampus, and frontal cortex: implication for sensitivity to stress and inflammation. Crivello NA, etal., Neurochem Int. 2005 Dec;47(8):573-9. Epub 2005 Sep 2.
4. Neutral sphingomyelinase 2: a novel target in cigarette smoke-induced apoptosis and lung injury. Filosto S, etal., Am J Respir Cell Mol Biol. 2011 Mar;44(3):350-60. doi: 10.1165/rcmb.2009-0422OC. Epub 2010 May 6.
5. Complementary nucleotide sequence for monitor peptide, a novel cholecystokinin-releasing peptide in the rat. Fukuoka SI and Scheele G, Nucleic Acids Res 1989 Dec 11;17(23):10111.
6. 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.
7. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
8. Early activation of nSMase2/ceramide pathway in astrocytes is involved in ischemia-associated neuronal damage via inflammation in rat hippocampi. Gu L, etal., J Neuroinflammation. 2013 Sep 3;10:109. doi: 10.1186/1742-2094-10-109.
9. cca1 is required for formation of growth-arrested confluent monolayer of rat 3Y1 cells. Hayashi Y, etal., J Biol Chem 1997 Jul 18;272(29):18082-6.
10. Neutral sphingomyelinase 2 induces dopamine uptake through regulation of intracellular calcium. Kim SK, etal., Cell Signal. 2010 May;22(5):865-70. doi: 10.1016/j.cellsig.2010.01.012. Epub 2010 Jan 21.
11. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
12. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
13. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
15. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
16. GOA pipeline RGD automated data pipeline
17. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
19. Regulation of neutral sphingomyelinase-2 by GSH: a new insight to the role of oxidative stress in aging-associated inflammation. Rutkute K, etal., J Lipid Res. 2007 Nov;48(11):2443-52. Epub 2007 Aug 10.
20. The role of neutral sphingomyelinase produced ceramide in lipopolysaccharide-mediated expression of inducible nitric oxide synthase. Won JS, etal., J Neurochem. 2004 Feb;88(3):583-93.
Additional References at PubMed
PMID:10823942   PMID:15059969   PMID:15764706   PMID:16025116   PMID:17561096   PMID:17591962   PMID:17626887   PMID:19476542   PMID:20352118   PMID:21708940   PMID:21788370   PMID:22383528  
PMID:22871113   PMID:22910579   PMID:22945695   PMID:23046545   PMID:23651497   PMID:23973266   PMID:24029230   PMID:24505141   PMID:24585429   PMID:25287744   PMID:27325675   PMID:28377412  
PMID:29043558   PMID:29867196   PMID:34089907  


Genomics

Comparative Map Data
Smpd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81951,072,209 - 51,155,639 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1951,072,209 - 51,085,936 (-)EnsemblGRCr8
mRatBN7.21934,162,337 - 34,245,786 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1934,162,341 - 34,245,749 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1940,977,903 - 41,061,312 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01941,631,214 - 41,714,614 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01943,930,363 - 44,013,762 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01938,237,963 - 38,321,572 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1938,237,965 - 38,321,528 (-)Ensemblrn6Rnor6.0
Rnor_5.01949,107,658 - 49,191,221 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41936,112,166 - 36,195,564 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1933,589,416 - 33,672,639 (-)NCBICelera
RGSC_v3.11936,117,046 - 36,200,445 (-)NCBI
RH 3.4 Map19304.3RGD
Cytogenetic Map19q12NCBI
SMPD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381668,358,327 - 68,448,508 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1668,358,327 - 68,448,508 (-)Ensemblhg38GRCh38
GRCh371668,392,230 - 68,482,411 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361666,949,731 - 67,039,905 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341666,949,732 - 67,039,905NCBI
Celera1652,900,779 - 52,990,952 (-)NCBICelera
Cytogenetic Map16q22.1NCBI
HuRef1654,265,453 - 54,355,875 (-)NCBIHuRef
CHM1_11669,800,294 - 69,890,458 (-)NCBICHM1_1
T2T-CHM13v2.01674,154,167 - 74,244,330 (-)NCBIT2T-CHM13v2.0
Smpd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398106,979,180 - 107,064,597 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8106,979,180 - 107,064,620 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm388106,252,548 - 106,337,965 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8106,252,548 - 106,337,988 (-)Ensemblmm10GRCm38
MGSCv378108,776,448 - 108,861,888 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv368109,141,677 - 109,227,117 (-)NCBIMGSCv36mm8
Celera8110,480,448 - 110,565,952 (-)NCBICelera
Cytogenetic Map8D3NCBI
cM Map853.12NCBI
Smpd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554848,272,572 - 8,298,144 (+)Ensembl
ChiLan1.0NW_0049554848,207,686 - 8,298,164 (+)NCBIChiLan1.0ChiLan1.0
SMPD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21877,905,024 - 77,995,458 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11683,816,346 - 83,906,775 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01648,734,664 - 48,825,241 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11668,129,034 - 68,219,625 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1668,131,905 - 68,142,871 (-)EnsemblpanPan2panpan1.1
SMPD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1581,089,657 - 81,172,173 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl581,142,888 - 81,172,189 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha581,080,156 - 81,162,625 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0581,524,565 - 81,607,194 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl581,553,588 - 81,606,670 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1581,351,425 - 81,433,990 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0581,034,510 - 81,116,929 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0581,675,446 - 81,757,898 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Smpd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934940,833,996 - 40,920,586 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647518,671,428 - 18,755,208 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647518,667,563 - 18,755,132 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMPD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl628,938,290 - 29,025,357 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1628,938,287 - 29,025,397 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2626,117,915 - 26,204,889 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMPD3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1558,965,965 - 59,057,823 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl559,029,093 - 59,059,577 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604721,702,920 - 21,795,181 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smpd3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474617,920,835 - 17,948,468 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474617,857,779 - 17,948,469 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Smpd3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11725,998,607 - 26,079,684 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Smpd3
518 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:1298
Count of miRNA genes:288
Interacting mature miRNAs:348
Transcripts:ENSRNOT00000000274, ENSRNOT00000031977
Prediction methods:Microtar, Miranda, Rnahybrid
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
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19799775052997750Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)191922068964220689Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19799775052997750Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)194622677874246245Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194438513474246245Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)193128753251431640Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19799775052997750Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19799775052997750Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)192010930665109306Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)194072709254856850Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)194072709254856850Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)194172254674246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)194072709254856850Rat

Markers in Region
D19Got24  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21934,205,359 - 34,205,608 (+)MAPPERmRatBN7.2
Rnor_6.01938,280,979 - 38,281,227NCBIRnor6.0
Rnor_5.01949,150,672 - 49,150,920UniSTSRnor5.0
RGSC_v3.41936,155,177 - 36,155,425UniSTSRGSC3.4
RGSC_v3.41936,155,176 - 36,155,425RGDRGSC3.4
Celera1933,632,282 - 33,632,530UniSTS
RGSC_v3.11936,160,058 - 36,160,306RGD
RH 3.4 Map19322.2UniSTS
RH 3.4 Map19322.2RGD
RH 2.0 Map19433.5RGD
Cytogenetic Map19q12UniSTS
D19Got57  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21934,205,436 - 34,205,661 (+)MAPPERmRatBN7.2
Rnor_6.01938,281,056 - 38,281,280NCBIRnor6.0
Rnor_5.01949,150,749 - 49,150,973UniSTSRnor5.0
RGSC_v3.41936,155,254 - 36,155,478UniSTSRGSC3.4
RGSC_v3.41936,155,253 - 36,155,478RGDRGSC3.4
Celera1933,632,359 - 33,632,583UniSTS
RGSC_v3.11936,160,135 - 36,160,359RGD
RH 3.4 Map19316.9UniSTS
RH 3.4 Map19316.9RGD
RH 2.0 Map19438.3RGD
Cytogenetic Map19q12UniSTS
RH141370  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21934,162,184 - 34,162,381 (+)MAPPERmRatBN7.2
Rnor_6.01938,237,809 - 38,238,005NCBIRnor6.0
Rnor_5.01949,107,502 - 49,107,698UniSTSRnor5.0
RGSC_v3.41936,112,010 - 36,112,206UniSTSRGSC3.4
Celera1933,589,260 - 33,589,456UniSTS
RH 3.4 Map19304.6UniSTS
Cytogenetic Map19q12UniSTS
Smpd3  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81951,074,987 - 51,075,312 (+)Marker Load Pipeline
mRatBN7.21934,165,117 - 34,165,442 (+)MAPPERmRatBN7.2
Rnor_6.01938,240,742 - 38,241,066NCBIRnor6.0
Rnor_5.01949,110,435 - 49,110,759UniSTSRnor5.0
RGSC_v3.41936,114,943 - 36,115,267UniSTSRGSC3.4
Celera1933,592,193 - 33,592,517UniSTS
RH 3.4 Map19304.3UniSTS
Cytogenetic Map19q12UniSTS
UniSTS:498356  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21934,164,511 - 34,165,050 (+)MAPPERmRatBN7.2
Rnor_6.01938,240,136 - 38,240,674NCBIRnor6.0
Rnor_5.01949,109,829 - 49,110,367UniSTSRnor5.0
RGSC_v3.41936,114,337 - 36,114,875UniSTSRGSC3.4
Celera1933,591,587 - 33,592,125UniSTS
Cytogenetic Map19q12UniSTS
Smpd3  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81951,073,829 - 51,074,096 (+)Marker Load Pipeline
RH 3.4 Map19304.3UniSTS
Cytogenetic Map19q12UniSTS


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 57 164 91 90 59 81 59 6 332 171 11 143 78 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000031977   ⟹   ENSRNOP00000030458
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1951,072,209 - 51,085,936 (-)Ensembl
mRatBN7.2 Ensembl1934,162,341 - 34,245,749 (-)Ensembl
Rnor_6.0 Ensembl1938,237,965 - 38,321,528 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000097806   ⟹   ENSRNOP00000096473
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1951,072,209 - 51,085,732 (-)Ensembl
mRatBN7.2 Ensembl1934,162,341 - 34,175,864 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000125553   ⟹   ENSRNOP00000099691
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1951,072,209 - 51,085,732 (-)Ensembl
RefSeq Acc Id: NM_053605   ⟹   NP_446057
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81951,072,209 - 51,155,610 (-)NCBI
mRatBN7.21934,162,339 - 34,245,749 (-)NCBI
Rnor_6.01938,237,965 - 38,321,528 (-)NCBI
Rnor_5.01949,107,658 - 49,191,221 (-)NCBI
RGSC_v3.41936,112,166 - 36,195,564 (-)RGD
Celera1933,589,416 - 33,672,639 (-)RGD
Sequence:
RefSeq Acc Id: XM_006255543   ⟹   XP_006255605
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81951,072,209 - 51,155,639 (-)NCBI
mRatBN7.21934,162,337 - 34,245,786 (-)NCBI
Rnor_6.01938,237,963 - 38,321,572 (-)NCBI
Rnor_5.01949,107,658 - 49,191,221 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601396   ⟹   XP_017456885
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81951,072,209 - 51,099,939 (-)NCBI
mRatBN7.21934,162,337 - 34,188,352 (-)NCBI
Rnor_6.01938,237,963 - 38,265,752 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063278336   ⟹   XP_063134406
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81951,072,209 - 51,108,561 (-)NCBI
RefSeq Acc Id: XM_063278337   ⟹   XP_063134407
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81951,072,209 - 51,108,561 (-)NCBI
RefSeq Acc Id: NP_446057   ⟸   NM_053605
- UniProtKB: O35049 (UniProtKB/Swiss-Prot),   D4A8L3 (UniProtKB/TrEMBL),   A6IYW6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255605   ⟸   XM_006255543
- Peptide Label: isoform X1
- UniProtKB: O35049 (UniProtKB/Swiss-Prot),   D4A8L3 (UniProtKB/TrEMBL),   A6IYW6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456885   ⟸   XM_017601396
- Peptide Label: isoform X1
- UniProtKB: O35049 (UniProtKB/Swiss-Prot),   D4A8L3 (UniProtKB/TrEMBL),   A6IYW6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000030458   ⟸   ENSRNOT00000031977
Ensembl Acc Id: ENSRNOP00000096473   ⟸   ENSRNOT00000097806
RefSeq Acc Id: XP_063134407   ⟸   XM_063278337
- Peptide Label: isoform X1
- UniProtKB: O35049 (UniProtKB/Swiss-Prot),   A6IYW6 (UniProtKB/TrEMBL),   D4A8L3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063134406   ⟸   XM_063278336
- Peptide Label: isoform X1
- UniProtKB: O35049 (UniProtKB/Swiss-Prot),   A6IYW6 (UniProtKB/TrEMBL),   D4A8L3 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000099691   ⟸   ENSRNOT00000125553
Protein Domains
Endonuclease/exonuclease/phosphatase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O35049-F1-model_v2 AlphaFold O35049 1-655 view protein structure

Transcriptome

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

Promoters
RGD ID:13701108
Promoter ID:EPDNEW_R11631
Type:multiple initiation site
Name:Smpd3_1
Description:sphingomyelin phosphodiesterase 3
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_6.01938,321,524 - 38,321,584EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619754 AgrOrtholog
BioCyc Gene G2FUF-5782 BioCyc
BioCyc Pathway PWY3DJ-11281 [sphingomyelin metabolism] BioCyc
BioCyc Pathway Image PWY3DJ-11281 BioCyc
Ensembl Genes ENSRNOG00000000257 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000031977 ENTREZGENE
Gene3D-CATH 3.60.10.10 UniProtKB/Swiss-Prot
InterPro Endo/exonu/phosph_ase_sf UniProtKB/Swiss-Prot
  Endo/exonuclease/phosphatase UniProtKB/Swiss-Prot
  Sph/SMPD2-like UniProtKB/Swiss-Prot
  Sphingomyelinase/PLipase_C UniProtKB/Swiss-Prot
KEGG Report rno:94338 UniProtKB/Swiss-Prot
NCBI Gene 94338 ENTREZGENE
PANTHER SPHINGOMYELIN PHOSPHODIESTERASE 3 UniProtKB/Swiss-Prot
  SPHINGOMYELINASE FAMILY MEMBER UniProtKB/Swiss-Prot
Pfam Exo_endo_phos UniProtKB/Swiss-Prot
PhenoGen Smpd3 PhenoGen
RatGTEx ENSRNOG00000000257 RatGTEx
Superfamily-SCOP SSF56219 UniProtKB/Swiss-Prot
UniProt A0A8I6ALV5_RAT UniProtKB/TrEMBL
  A0ABK0L9Q2_RAT UniProtKB/TrEMBL
  A6IYW6 ENTREZGENE, UniProtKB/TrEMBL
  D4A8L3 ENTREZGENE, UniProtKB/TrEMBL
  NSMA2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-16 Smpd3  sphingomyelin phosphodiesterase 3  Smpd3  sphingomyelin phosphodiesterase 3, neutral membrane  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-01-19 Smpd3  sphingomyelin phosphodiesterase 3, neutral membrane  Smpd3  sphingomyelin phosphodiesterase 3, neutral  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Smpd3  sphingomyelin phosphodiesterase 3, neutral      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Smpd3  sphingomyelin phosphodiesterase 3, neutral      Symbol and Name status set to provisional 70820 PROVISIONAL