Smpd3 (sphingomyelin phosphodiesterase 3) - Rat Genome Database

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Gene: Smpd3 (sphingomyelin phosphodiesterase 3) Rattus norvegicus
Analyze
Symbol: Smpd3
Name: sphingomyelin phosphodiesterase 3
RGD ID: 619754
Description: Predicted to have identical protein binding activity; neutral sphingomyelin phosphodiesterase activity; and phospholipid binding activity. Involved in several processes, including positive regulation of NIK/NF-kappaB signaling; positive regulation of cellular biosynthetic process; and positive regulation of exosomal secretion. Localizes to cytoplasm and membrane. 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
Also 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
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21934,162,337 - 34,245,786 (-)NCBI
Rnor_6.0 Ensembl1938,237,965 - 38,321,528 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01938,237,963 - 38,321,572 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01949,107,658 - 49,191,221 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41936,112,166 - 36,195,564 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11936,117,046 - 36,200,445 (-)NCBI
Celera1933,589,416 - 33,672,639 (-)NCBICelera
RH 3.4 Map19304.3RGD
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(S)-nicotine  (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)
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)
2,4-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-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
aldehydo-D-glucosamine  (EXP)
all-trans-retinoic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
Benzo[k]fluoranthene  (ISO)
beta-D-glucosamine  (EXP)
bisphenol A  (EXP)
caffeine  (ISO)
camptothecin  (ISO)
carbon nanotube  (ISO)
cholesterol  (ISO)
choline  (ISO)
chrysene  (ISO)
copper(II) sulfate  (ISO)
cyproconazole  (ISO)
daunorubicin  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dichloroacetic acid  (ISO)
dieldrin  (EXP)
diuron  (EXP)
endosulfan  (EXP)
epoxiconazole  (ISO)
ethanol  (ISO)
fenamidone  (ISO)
fenofibrate  (ISO)
fipronil  (EXP)
flavonoids  (EXP)
folic acid  (ISO)
fumonisin B1  (ISO)
furan  (EXP)
GW 4064  (ISO)
hydrogen peroxide  (ISO)
Indeno[1,2,3-cd]pyrene  (ISO)
L-methionine  (ISO)
Lasiocarpine  (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)
oxaliplatin  (EXP)
p-toluidine  (EXP)
paracetamol  (ISO)
PCB138  (ISO)
phenethyl caffeate  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
propanal  (ISO)
propiconazole  (ISO)
rac-lactic acid  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
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
aging  (IEP)
artery smooth muscle contraction  (IMP)
BMP signaling pathway  (IEA,ISO)
bone development  (ISO)
bone growth  (IEA,ISO)
bone mineralization  (IEA,ISO)
cartilage development  (ISO)
cellular response to hydrogen peroxide  (IEA,ISO)
cellular response to interleukin-1  (IEP)
cellular response to magnesium ion  (IEA,ISO)
cellular response to oxidised low-density lipoprotein particle stimulus  (IEA,ISO)
cellular response to peptide  (IEA,ISO)
cellular response to reactive oxygen species  (ISO)
cellular response to redox state  (IEA,ISO)
cellular response to tumor necrosis factor  (IEA,ISO)
ceramide metabolic process  (IEA,ISO)
chondrocyte development  (ISO)
chondrocyte development involved in endochondral bone morphogenesis  (IEA,ISO)
collagen metabolic process  (IEA,ISO)
dentinogenesis  (IEA,ISO)
DNA biosynthetic process  (IEA,ISO)
dopamine uptake  (IMP)
endochondral ossification  (IEA,ISO)
extracellular matrix assembly  (IEA,ISO)
G1 to G0 transition  (IEA,ISO)
hematopoietic progenitor cell differentiation  (IEA,ISO)
lung alveolus development  (IEA,ISO)
lung development  (ISO)
mitotic nuclear division  (IEA,ISO)
multicellular organism growth  (IEA,ISO)
negative regulation of cytosolic calcium ion concentration  (IMP)
negative regulation of hyaluronan biosynthetic process  (IEA,ISO)
ossification  (ISO)
peptide hormone secretion  (IEA,ISO)
platelet-derived growth factor receptor signaling pathway  (IEA,ISO)
polysaccharide transport  (IEA,ISO)
positive regulation of ceramide biosynthetic process  (IMP)
positive regulation of exosomal secretion  (IMP)
positive regulation of mitotic nuclear division  (IEA,ISO)
positive regulation of NIK/NF-kappaB signaling  (IMP)
positive regulation of nitric oxide biosynthetic process  (IMP)
positive regulation of smooth muscle cell proliferation  (IEA,ISO)
protein kinase B signaling  (IEA,ISO)
regulation of cartilage development  (IEA,ISO)
regulation of hyaluronan biosynthetic process  (ISO)
regulation of leukocyte migration  (IEA,ISO)
regulation of protein phosphorylation  (IEA,ISO)
respiratory system development  (ISO)
signal transduction  (ISO)
skeletal system development  (ISO)
sphingolipid mediated signaling pathway  (IEA,ISO)
sphingolipid metabolic process  (ISO)
sphingomyelin catabolic process  (IEA,ISO)
sphingomyelin metabolic process  (IBA,ISO,ISS)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Bang C, etal., J Clin Invest. 2014 May;124(5):2136-46. doi: 10.1172/JCI70577. Epub 2014 Apr 17.
2. Cogolludo A, etal., Cardiovasc Res. 2009 May 1;82(2):296-302. doi: 10.1093/cvr/cvn349. Epub 2008 Dec 16.
3. Crivello NA, etal., Neurochem Int. 2005 Dec;47(8):573-9. Epub 2005 Sep 2.
4. 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. Fukuoka SI and Scheele G, Nucleic Acids Res 1989 Dec 11;17(23):10111.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. GOA data from the GO Consortium
8. Gu L, etal., J Neuroinflammation. 2013 Sep 3;10:109. doi: 10.1186/1742-2094-10-109.
9. Hayashi Y, etal., J Biol Chem 1997 Jul 18;272(29):18082-6.
10. Kim SK, etal., Cell Signal. 2010 May;22(5):865-70. doi: 10.1016/j.cellsig.2010.01.012. Epub 2010 Jan 21.
11. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
12. MGD data from the GO Consortium
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. Pipeline to import KEGG annotations from KEGG into RGD
15. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
16. RGD automated data pipeline
17. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. RGD automated import pipeline for gene-chemical interactions
19. Rutkute K, etal., J Lipid Res. 2007 Nov;48(11):2443-52. Epub 2007 Aug 10.
20. 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  


Genomics

Comparative Map Data
Smpd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21934,162,337 - 34,245,786 (-)NCBI
Rnor_6.0 Ensembl1938,237,965 - 38,321,528 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01938,237,963 - 38,321,572 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01949,107,658 - 49,191,221 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41936,112,166 - 36,195,564 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11936,117,046 - 36,200,445 (-)NCBI
Celera1933,589,416 - 33,672,639 (-)NCBICelera
RH 3.4 Map19304.3RGD
Cytogenetic Map19q12NCBI
SMPD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1668,358,327 - 68,448,508 (-)EnsemblGRCh38hg38GRCh38
GRCh381668,358,327 - 68,448,703 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371668,392,230 - 68,482,411 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361666,949,731 - 67,039,905 (-)NCBINCBI36hg18NCBI36
Build 341666,949,732 - 67,039,905NCBI
Celera1652,900,779 - 52,990,952 (-)NCBI
Cytogenetic Map16q22.1NCBI
HuRef1654,265,453 - 54,355,875 (-)NCBIHuRef
CHM1_11669,800,294 - 69,890,458 (-)NCBICHM1_1
Smpd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398106,979,180 - 107,064,597 (-)NCBIGRCm39mm39
GRCm39 Ensembl8106,979,180 - 107,064,620 (-)Ensembl
GRCm388106,252,548 - 106,337,965 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8106,252,548 - 106,337,988 (-)EnsemblGRCm38mm10GRCm38
MGSCv378108,776,448 - 108,861,888 (-)NCBIGRCm37mm9NCBIm37
MGSCv368109,141,677 - 109,227,117 (-)NCBImm8
Celera8110,480,448 - 110,565,952 (-)NCBICelera
Cytogenetic Map8D3NCBI
Smpd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554848,272,572 - 8,298,144 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554848,207,686 - 8,298,164 (+)NCBIChiLan1.0ChiLan1.0
SMPD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11668,129,034 - 68,219,625 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1668,131,905 - 68,142,871 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01648,734,664 - 48,825,241 (-)NCBIMhudiblu_PPA_v0panPan3
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha581,080,156 - 81,162,625 (+)NCBI
ROS_Cfam_1.0581,524,565 - 81,607,194 (+)NCBI
UMICH_Zoey_3.1581,351,425 - 81,433,990 (+)NCBI
UNSW_CanFamBas_1.0581,034,510 - 81,116,929 (+)NCBI
UU_Cfam_GSD_1.0581,675,446 - 81,757,898 (+)NCBI
Smpd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934940,833,996 - 40,920,586 (+)NCBI
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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1628,938,287 - 29,025,397 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2626,117,915 - 26,204,889 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMPD3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1558,965,965 - 59,057,823 (+)NCBI
ChlSab1.1 Ensembl559,029,093 - 59,059,577 (+)Ensembl
Vero_WHO_p1.0NW_02366604721,702,920 - 21,795,181 (+)NCBI
Smpd3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474617,857,779 - 17,948,469 (+)NCBI

Position Markers
D19Got24  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21934,205,359 - 34,205,608 (+)MAPPER
Rnor_6.01938,280,979 - 38,281,227NCBIRnor6.0
Rnor_5.01949,150,672 - 49,150,920UniSTSRnor5.0
RGSC_v3.41936,155,176 - 36,155,425RGDRGSC3.4
RGSC_v3.41936,155,177 - 36,155,425UniSTSRGSC3.4
RGSC_v3.11936,160,058 - 36,160,306RGD
Celera1933,632,282 - 33,632,530UniSTS
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 (+)MAPPER
Rnor_6.01938,281,056 - 38,281,280NCBIRnor6.0
Rnor_5.01949,150,749 - 49,150,973UniSTSRnor5.0
RGSC_v3.41936,155,253 - 36,155,478RGDRGSC3.4
RGSC_v3.41936,155,254 - 36,155,478UniSTSRGSC3.4
RGSC_v3.11936,160,135 - 36,160,359RGD
Celera1933,632,359 - 33,632,583UniSTS
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 (+)MAPPER
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
mRatBN7.21934,165,117 - 34,165,442 (+)MAPPER
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 (+)MAPPER
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
RH 3.4 Map19304.3UniSTS
Cytogenetic Map19q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19104464846044648Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19195770746957707Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19243296347217667Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)19370183548701835Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)19370183548701835Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19500757143907843Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19807254547318201Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191130392747879277Rat
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)191593952838798459Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191702800352538299Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192445572643907843Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)193119430141686140Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)193119430141686140Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)193119430141686140Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193791679960220451Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193791679960220451Rat

miRNA Target Status

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.


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 68 2
Low 21 37 21 19 21 8 11 6 17 35 11 8
Below cutoff 12 20 20 20 18 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000031977   ⟹   ENSRNOP00000030458
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1938,237,965 - 38,321,528 (-)Ensembl
RefSeq Acc Id: NM_053605   ⟹   NP_446057
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_008772541   ⟹   XP_008770763
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01938,237,963 - 38,321,572 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601396   ⟹   XP_017456885
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21934,162,337 - 34,188,352 (-)NCBI
Rnor_6.01938,237,963 - 38,265,752 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_446057 (Get FASTA)   NCBI Sequence Viewer  
  XP_006255605 (Get FASTA)   NCBI Sequence Viewer  
  XP_017456885 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAA22932 (Get FASTA)   NCBI Sequence Viewer  
  EDL92444 (Get FASTA)   NCBI Sequence Viewer  
  O35049 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446057   ⟸   NM_053605
- Sequence:
RefSeq Acc Id: XP_006255605   ⟸   XM_006255543
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008770763   ⟸   XM_008772541
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017456885   ⟸   XM_017601396
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000030458   ⟸   ENSRNOT00000031977

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

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619754 AgrOrtholog
Ensembl Genes ENSRNOG00000000257 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000030458 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000031977 ENTREZGENE, UniProtKB/TrEMBL
InterPro Endo/exonu/phosph_ase_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sphingomyelinase/PLipase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:94338 UniProtKB/Swiss-Prot
NCBI Gene 94338 ENTREZGENE
PhenoGen Smpd3 PhenoGen
Superfamily-SCOP SSF56219 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt D4A8L3_RAT 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