Smpd1 (sphingomyelin phosphodiesterase 1)

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Gene: Smpd1 (sphingomyelin phosphodiesterase 1) Rattus norvegicus

Analyze

Symbol:

Smpd1

Name:

sphingomyelin phosphodiesterase 1

RGD ID:

1549719

Description:

Predicted to have acid sphingomyelin phosphodiesterase activity and zinc ion binding activity. Involved in several processes, including ceramide biosynthetic process; response to cocaine; and response to drug. Localizes to 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; 3,3',4,4',5-pentachlorobiphenyl; bezafibrate.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

MGC94748; sphingomyelin phosphodiesterase; sphingomyelin phosphodiesterase 1, acid lysosomal

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	SMPD1 (sphingomyelin phosphodiesterase 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Smpd1 (sphingomyelin phosphodiesterase 1, acid lysosomal)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Smpd1 (sphingomyelin phosphodiesterase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SMPD1 (sphingomyelin phosphodiesterase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SMPD1 (sphingomyelin phosphodiesterase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Smpd1 (sphingomyelin phosphodiesterase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SMPD1 (sphingomyelin phosphodiesterase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	SMPD1 (sphingomyelin phosphodiesterase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Smpd1 (sphingomyelin phosphodiesterase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	SMPD1 (sphingomyelin phosphodiesterase 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Smpd1 (sphingomyelin phosphodiesterase 1, acid lysosomal)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	CG15533	Alliance	DIOPT (Ensembl Compara\|OMA\|PANTHER)
Caenorhabditis elegans (roundworm):	asm-1	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	asm-3	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	CG15534	Alliance	DIOPT (Ensembl Compara\|OMA\|PANTHER)
Saccharomyces cerevisiae (baker's yeast):	PPN1	Alliance	DIOPT (Ensembl Compara\|OrthoInspector\|PANTHER\|TreeFam)
Drosophila melanogaster (fruit fly):	CG3376	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	asm-2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	159,892,946 - 159,896,789 (+)	NCBI
Rnor_6.0 Ensembl	1	170,383,682 - 170,387,524 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	170,383,682 - 170,387,525 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	177,389,588 - 177,393,431 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	163,278,970 - 163,282,813 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	1	157,825,620 - 157,829,463 (+)	NCBI		Celera
Cytogenetic Map	1	q32	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Experimental Diabetes Mellitus (IDA)

Gaucher's disease (ISO)

kidney disease (ISO)

Neoplasm Invasiveness (ISO)

neuronal ceroid lipofuscinosis (ISO)

neuronal ceroid lipofuscinosis 6 (ISO)

Niemann-Pick disease (ISO)

Niemann-Pick disease type A (ISO)

Niemann-Pick disease type B (ISO)

Niemann-Pick Disease, Intermediate, Protracted Neurovisceral (ISO)

Wilson disease (IDA)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (EXP)

2,3,7,8-tetrachlorodibenzodioxine (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)

7-ketocholesterol (ISO)

afimoxifene (ISO)

all-trans-retinoic acid (ISO)

amitriptyline (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)

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)

daunorubicin (ISO)

desipramine (ISO)

dexamethasone (ISO)

dibutyl phthalate (EXP)

dioxygen (ISO)

diuron (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

entinostat (ISO)

ethanol (ISO)

fluoxetine (ISO)

flutamide (EXP)

folic acid (ISO)

gentamycin (EXP)

hydrogen peroxide (ISO)

indometacin (ISO)

lead diacetate (ISO)

lead(0) (ISO)

lead(2+) (ISO)

morphine (ISO)

N-nitrosodiethylamine (EXP)

naloxone (ISO)

oxaliplatin (EXP)

paracetamol (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)

sorafenib (ISO)

superoxide (ISO)

tamibarotene (ISO)

topotecan (EXP)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

vorinostat (ISO)

Yessotoxin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cellular response to calcium ion (ISO)

cellular response to UV (IEA,ISO)

ceramide biosynthetic process (IBA,IMP,ISO)

ceramide metabolic process (ISO)

cholesterol metabolic process (ISO)

negative regulation of MAP kinase activity (ISO)

plasma membrane repair (ISO)

positive regulation of apoptotic process (IMP,ISO)

positive regulation of endocytosis (ISO)

positive regulation of protein dephosphorylation (ISO)

response to cocaine (IDA)

response to drug (IEP)

response to interleukin-1 (IEA,ISO)

response to ionizing radiation (ISO)

response to tumor necrosis factor (IEA,ISO)

response to type I interferon (IEA,ISO)

response to virus (ISO)

sphingomyelin catabolic process (IBA,ISO)

termination of signal transduction (ISO)

viral entry into host cell (ISO)

wound healing (ISO)

Cellular Component

endolysosome (IEA,ISO)

endosome (ISO)

extracellular space (IBA,IDA,ISO)

integral component of membrane (IEA)

lamellar body (IDA)

lysosome (IBA,ISO)

plasma membrane (ISO)

Molecular Function

acid sphingomyelin phosphodiesterase activity (IBA,ISO)

hydrolase activity, acting on glycosyl bonds (IEA)

molecular_function (ND)

phosphoric diester hydrolase activity (IBA)

protein binding (ISO)

sphingomyelin phosphodiesterase activity (ISO)

zinc ion binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

ceramide signaling pathway (ISO)

FasL mediated signaling pathway (ISO)

sphingolipid metabolic pathway (IEA)

Trail mediated signaling pathway (ISO)

tumor necrosis factor mediated signaling pathway (ISO)

References

References - curated


1.	Baranowski M, etal., Prostaglandins Other Lipid Mediat. 2007 Feb;83(1-2):99-111. Epub 2006 Nov 16.
2.	Becker S, etal., Biol Chem. 2007 Feb;388(2):185-96.
3.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4.	Gorska M, etal., Horm Metab Res. 2004 Jan;36(1):14-21.
5.	Lang PA, etal., Nat Med. 2007 Feb;13(2):164-70. Epub 2007 Jan 28.
6.	Loidl A, etal., J Biol Chem. 2003 Aug 29;278(35):32921-8. Epub 2003 Jun 19.
7.	Nassogne MC, etal., Toxicol Appl Pharmacol. 2004 Jan 15;194(2):101-10.
8.	OMIM Disease Annotation Pipeline
9.	Pipeline to import KEGG annotations from KEGG into RGD
10.	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
11.	RGD automated data pipeline
12.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13.	RGD automated import pipeline for gene-chemical interactions
14.	RGD comprehensive gene curation
15.	Sikora J, etal., Ann Hum Genet. 2003 Jan;67(Pt 1):63-70.
16.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Additional References at PubMed

PMID:8702487	PMID:16025116	PMID:18815062	PMID:19279008	PMID:19279011	PMID:20956541	PMID:22383528	PMID:23046545	PMID:23376485	PMID:23533145	PMID:23973266	PMID:26830134
PMID:27659707

Genomics

Comparative Map Data

Smpd1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	159,892,946 - 159,896,789 (+)	NCBI
Rnor_6.0 Ensembl	1	170,383,682 - 170,387,524 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	170,383,682 - 170,387,525 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	177,389,588 - 177,393,431 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	163,278,970 - 163,282,813 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	1	157,825,620 - 157,829,463 (+)	NCBI		Celera
Cytogenetic Map	1	q32	NCBI

SMPD1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	11	6,390,440 - 6,394,998 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	11	6,390,474 - 6,394,998 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	11	6,411,704 - 6,416,226 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
GRCh37	11	6,411,644 - 6,416,228 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	6,368,231 - 6,372,802 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	11	6,368,230 - 6,372,801	NCBI
Celera	11	6,530,711 - 6,535,296 (+)	NCBI
Cytogenetic Map	11	p15.4	NCBI
HuRef	11	6,070,739 - 6,075,337 (+)	NCBI		HuRef
CHM1_1	11	6,410,778 - 6,415,363 (+)	NCBI		CHM1_1

Smpd1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	105,203,567 - 105,207,596 (+)	NCBI	GRCm39		mm39
GRCm38	7	105,554,360 - 105,558,389 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	105,554,360 - 105,558,389 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	112,702,874 - 112,706,903 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	7	105,428,236 - 105,432,203 (+)	NCBI			mm8
Celera	7	105,825,502 - 105,829,531 (+)	NCBI		Celera
Cytogenetic Map	7	E3	NCBI
cM Map	7	55.9	NCBI

Smpd1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955414	22,117,930 - 22,121,744 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955414	22,117,929 - 22,121,744 (+)	NCBI	ChiLan1.0	ChiLan1.0

SMPD1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	11	6,205,278 - 6,209,950 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
Mhudiblu_PPA_v0	11	6,521,812 - 6,526,349 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

SMPD1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	21	29,714,557 - 29,719,033 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	21	29,714,418 - 29,719,035 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Smpd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936842	448,315 - 452,557 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SMPD1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	9	3,324,091 - 3,328,373 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	9	3,324,091 - 3,328,493 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	9	3,961,624 - 3,964,422 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SMPD1
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	1	58,431,677 - 58,436,233 (-)	NCBI
ChlSab1.1 Ensembl	1	58,432,068 - 58,436,236 (-)	Ensembl

Smpd1
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624817	7,909,777 - 7,913,419 (+)	NCBI

Position Markers

AF206720

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	170,387,825 - 170,387,966	NCBI	Rnor6.0
Rnor_5.0	1	177,393,731 - 177,393,872	UniSTS	Rnor5.0
RGSC_v3.4	1	163,283,113 - 163,283,254	UniSTS	RGSC3.4
Celera	1	157,829,763 - 157,829,904	UniSTS
Cytogenetic Map	1	q33	UniSTS

RH130448

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	170,387,290 - 170,387,470	NCBI	Rnor6.0
Rnor_5.0	1	177,393,196 - 177,393,376	UniSTS	Rnor5.0
RGSC_v3.4	1	163,282,578 - 163,282,758	UniSTS	RGSC3.4
Celera	1	157,829,228 - 157,829,408	UniSTS
RH 3.4 Map	1	1295.8	UniSTS
Cytogenetic Map	1	q33	UniSTS

Smpd1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	170,383,757 - 170,385,024	NCBI	Rnor6.0
Rnor_5.0	1	177,389,663 - 177,390,930	UniSTS	Rnor5.0
RGSC_v3.4	1	163,279,045 - 163,280,312	UniSTS	RGSC3.4
Celera	1	157,825,695 - 157,826,962	UniSTS
Cytogenetic Map	1	q33	UniSTS

RH134756

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	170,387,767 - 170,387,958	NCBI	Rnor6.0
Rnor_5.0	1	177,393,673 - 177,393,864	UniSTS	Rnor5.0
RGSC_v3.4	1	163,283,055 - 163,283,246	UniSTS	RGSC3.4
Celera	1	157,829,705 - 157,829,896	UniSTS
RH 3.4 Map	1	1297.5	UniSTS
Cytogenetic Map	1	q33	UniSTS

UniSTS:235734

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	170,383,667 - 170,383,775	NCBI	Rnor6.0
Rnor_5.0	1	177,389,573 - 177,389,681	UniSTS	Rnor5.0
RGSC_v3.4	1	163,278,955 - 163,279,063	UniSTS	RGSC3.4
Celera	1	157,825,605 - 157,825,713	UniSTS
Cytogenetic Map	1	q33	UniSTS

SMPD1_855

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	170,386,844 - 170,387,650	NCBI	Rnor6.0
Rnor_5.0	1	177,392,750 - 177,393,556	UniSTS	Rnor5.0
RGSC_v3.4	1	163,282,132 - 163,282,938	UniSTS	RGSC3.4
Celera	1	157,828,782 - 157,829,588	UniSTS
Cytogenetic Map	1	q33	UniSTS

Smpd1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	170,386,188 - 170,386,939	NCBI	Rnor6.0
Rnor_5.0	1	177,392,094 - 177,392,845	UniSTS	Rnor5.0
RGSC_v3.4	1	163,281,476 - 163,282,227	UniSTS	RGSC3.4
Celera	1	157,828,126 - 157,828,877	UniSTS
Cytogenetic Map	1	q33	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34993530	173445086	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	35377692	217372257	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49578693	217054291	Rat
1578780	Cm52	Cardiac mass QTL 52	3.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	1	82788437	239853971	Rat
724521	Uae1	Urinary albumin excretion QTL 1	3.8	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	94201400	184846632	Rat
1358902	Bw47	Body weight QTL 47	1.67		body mass (VT:0001259)	body weight (CMO:0000012)	1	94201400	197187904	Rat
1331793	Bp200	Blood pressure QTL 200	3.71601		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	99983293	188289386	Rat
1331751	Bp199	Blood pressure QTL 199	3.60022		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	99983293	198656062	Rat
1331749	Hrtrt11	Heart rate QTL 11	2.973		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	99983293	216213510	Rat
70209	Niddm23	Non-insulin dependent diabetes mellitus QTL 23	2.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	99983293	216325819	Rat
731168	Bp154	Blood pressure QTL 154	3.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	100131562	236763528	Rat
8655649	Arrd1	Age-related retinal degeneration QTL 1	4.89		retinal layer morphology trait (VT:0003727)	percentage of study population developing retinopathy during a period of time (CMO:0002453)	1	106002252	202571904	Rat
1354591	Cm36	Cardiac mass QTL 36	4.1		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	108986301	219232156	Rat
1354615	Cm32	Cardiac mass QTL 32	5.2		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	1	108986301	219232156	Rat
1354606	Bp246	Blood pressure QTL 246	3.6		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	108986301	238830534	Rat
1300158	Bp173	Blood pressure QTL 173	3.48		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	1	122614824	201146953	Rat
7794788	Mcs32	Mammary carcinoma susceptibility QTL 32	2.61		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	1	122614824	262664716	Rat
631199	Cm23	Cardiac mass QTL 23	4.6	0.0004	heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	1	124603592	188289386	Rat
7421630	Bp362	Blood pressure QTL 362		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	125875758	262433692	Rat
631205	Bp196	Blood pressure QTL 196	4	0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	126240667	217054291	Rat
2293140	Bp313	Blood pressure QTL 313			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	129208943	174208943	Rat
631544	Bp84	Blood pressure QTL 84	5.6		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	130779148	198585664	Rat
1358189	Cstrr1	Cold stress response QTL 1		0.0001	catecholamine amount (VT:0010543)	urine norepinephrine level (CMO:0001629)	1	130779148	199254774	Rat
1578770	Stresp23	Stress response QTL 23			kidney sympathetic nerve activity (VT:0004050)	stimulated renal sympathetic nerve activity to basal renal sympathetic nerve activity ratio (CMO:0001786)	1	130779148	199254774	Rat
1641895	Bp298	Blood pressure QTL 298			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	130779148	199254774	Rat
631549	Bp89	Blood pressure QTL 89	5.7		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	130779320	219238476	Rat
1598850	Bp297	Blood pressure QTL 297	2.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	131334152	176334152	Rat
1598866	Bp287	Blood pressure QTL 287	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	131334152	176334152	Rat
631654	Bp107	Blood pressure QTL 107			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	133076978	178076978	Rat
9685799	Bp375	Blood pressure QTL 375			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	133076978	178076978	Rat
634348	Bp138	Blood pressure QTL 138			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	133076978	184188922	Rat
61442	Strs1	Sensitivity to stroke QTL 1	7.4		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	1	133946489	178946489	Rat
9685802	Bp376	Blood pressure QTL 376			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	134089429	179089429	Rat
724562	Rends1	Renal damage susceptibility QTL 1		0.05	kidney glomerulus integrity trait (VT:0010546)	index of glomerular damage (CMO:0001135)	1	137787261	236763528	Rat
61341	Bp26	Blood pressure QTL 26			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	137787261	236763528	Rat
738006	Anxrr14	Anxiety related response QTL 14	4	0.00035	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	1	141296374	186296374	Rat
738028	Anxrr12	Anxiety related response QTL 12	4.9	0.00001	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	1	141296374	186296374	Rat
1558645	Bw55	Body weight QTL 55	3.2	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	1	144395993	189395993	Rat
6893347	Bw98	Body weight QTL 98	0.2	0.53	body mass (VT:0001259)	body weight (CMO:0000012)	1	144395993	189395993	Rat
6893361	Bw104	Body weight QTL 104	0.59	0.27	body mass (VT:0001259)	body weight (CMO:0000012)	1	144395993	189395993	Rat
7771612	Cm80	Cardiac mass QTL 80	8.4		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	1	144634295	241482368	Rat
631206	Niddm40	Non-insulin dependent diabetes mellitus QTL 40			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	144723107	174343537	Rat
71118	Thym1	Thymus enlargement QTL 1	10.17	0.001	thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	153655976	198655976	Rat
724550	Thym3	Thymus enlargement QTL 3	7.82	0.001	thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	153655976	198655976	Rat
631519	Pia11	Pristane induced arthritis QTL 11	5.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	153656062	198656062	Rat
1598853	Memor3	Memory QTL 3	4.5		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	1	153834077	232297227	Rat
61348	Bp30	Blood pressure QTL 30	2.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	154337847	215828102	Rat
70160	Bw18	Body weight QTL 18	5.7		body mass (VT:0001259)	body weight (CMO:0000012)	1	156446196	214277437	Rat
737828	Hcas3	Hepatocarcinoma susceptibility QTL 3	4.9		liver integrity trait (VT:0010547)	liver tumorous lesion volume to total liver volume ratio (CMO:0001082)	1	156446196	243311614	Rat
2302378	Insul11	Insulin level QTL 11	3.25		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	156446196	274977688	Rat
634315	Niddm45	Non-insulin dependent diabetes mellitus QTL 45	7.16		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	156446783	188289244	Rat
61379	Bp44	Blood pressure QTL 44	19.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	156446783	189514504	Rat
8693608	Alc24	Alcohol consumption QTL 24	2.3	0.74	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	1	161072673	178935582	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	161321152	273792054	Rat
1578759	Uae30	Urinary albumin excretion QTL 30	3.3	0.003	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	161321256	273791893	Rat
1578778	Pur4	Proteinuria QTL 4	3.3	0.003	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	1	161321256	273791893	Rat
1354634	Kidm12	Kidney mass QTL 12	3.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	1	161784169	219232156	Rat
1354636	Lmblg1	Limb length QTL 1	6.4		tibia length (VT:0004357)	tibia length (CMO:0000450)	1	161784169	219232156	Rat
1354602	Bw35	Body weight QTL 35	12.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	219232156	Rat
1354620	Kidm19	Kidney mass QTL 19	4		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	161784169	219232156	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	161784169	278228889	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1358886	Bp260	Blood pressure QTL 260	3.67		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	161784422	246226103	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	163796316	282763074	Rat
1582204	Livw1	Liver weight QTL 1	3.6	0.0003	liver mass (VT:0003402)	liver weight as percentage of body weight (CMO:0000141)	1	166100317	188289386	Rat
4889428	Stresp24	Stress response QTL 24		0.05	heart pumping trait (VT:2000009)	absolute change in electrocardiographic low frequency R-R spectral component to high frequency R-R spectral component ratio (CMO:0002162)	1	166577232	211577232	Rat
61343	Bp28	Blood pressure QTL 28			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	167027868	212027868	Rat
631548	Bp88	Blood pressure QTL 88	5	0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	167394665	191883991	Rat
1354618	Kidm15	Kidney mass QTL 15	5		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	1	167394665	219232156	Rat
2312420	Pur17	Proteinuria QTL 17	7.1	0.0001	urine protein amount (VT:0005160)	urine total protein excretion rate (CMO:0000756)	1	167394665	238830534	Rat
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	167394665	278228889	Rat
2303622	Vencon6	Ventilatory control QTL 6		0.001	respiration trait (VT:0001943)	respiration rate (CMO:0000289)	1	169971964	214971964	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	244
Count of miRNA genes:	155
Interacting mature miRNAs:	181
Transcripts:	ENSRNOT00000024224
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

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

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001006997	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC097992	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC083780	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473956	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000042	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000024224 ⟹ ENSRNOP00000024224

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	170,383,682 - 170,387,524 (+)	Ensembl

RefSeq Acc Id:

NM_001006997 ⟹ NP_001006998

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	159,892,946 - 159,896,789 (+)	NCBI
Rnor_6.0	1	170,383,682 - 170,387,525 (+)	NCBI
Rnor_5.0	1	177,389,588 - 177,393,431 (+)	NCBI
RGSC_v3.4	1	163,278,970 - 163,282,813 (+)	RGD
Celera	1	157,825,620 - 157,829,463 (+)	RGD

Sequence:

show sequence

TGTCTCCAGAGCTACTGGGGCCCCGAGGGCCAGCCAGGGCCTCGGCCTGCGGGGCCTGGAGGGG
CGATCCAGTCCTGTCTACGAGCTTGGCAATGCCCCACCACGGAGCGTCATCCGGCCAGGGCCAT
CTCAGAGCCGGCTGGGAGCAGAGACTGGAGAGGTCCTTACCGGCACCCAAATTGGGACTCCTTT
GGATGGGGCTGGGCTTGGCTCTGGTCCTGGCTCTGTTTGACTCCACGGTTCTCTGGGTTCCTGC
CAGAGCTTATCCTCTTCCCTCCCAAGGCCATTCTGTCAAATTCAGTGCGGTAGCGCCGCAGCTC
CAGAATGCCTTTGGGTGGAGGAACCTCACCTGCCCCGCCTGCAAAGTCTTATTTACTGCTCTCA
ACTATGGGCTGAAGAAGGAGCCCAATGTGGCACGAGTAGGCTCTGTGGCCATCAAGATGTGCAA
GATGCTGAACATAGCGCCACTAAATGTGTGCCAGTCAGCTGTTCATCTCTTTGAGGACGATGTG
GTGGACGTGTGGACACGCTCAGTTCTGAGCCCTTCAGAAGCTTGTGGCTTGCTTCTGGGCTCCT
CTTGTGGGCACTGGGACATCTTTTCAACTTGGAACATCTCTTTGCCATCAGTGCCGAAGCCACC
CCCAAAGCCACCGAGCCCACCAGCCCCAGGTGCCCCTGTCAGCCGTGTCCTCTTCCTTACTGAC
CTTCACTGGGACCATGACTACCTGGAGGGCACAGACCCTAACTGTGCAGATCCCCTCTGCTGCC
GCAGGGGGTCTGGATGGCCGCCCAACTCACGGACAGGGGCTGGGTACTGGGGAGAGTACAGCAA
GTGTGACCTGCCCCTGCGAACGCTAGAGAGCCTGTTGAAAGGGCTGGGCCCCGCCGGCCCTTTT
GAAATGGTGTACTGGACAGGAGACATCCCTGCCCATGATGTCTGGCAACAGTCTCGACAAGATC
AGCTAAGGGCCCTGAACACCATCACAGACCTCGTGTGGAAGTTCTTGGGCCCTGTACCGGTGTA
CCCTGCTGTGGGCAACCATGAGAGTACTCCTGTCAATGGCTTCCCTCCCCCCTTCATAAAGGGA
AACCAGTCTTCACAATGGCTTTATGAAGCCATGGCCAAGGCATGGGAACCCTGGTTACCAGCTG
ACGCCCTTCACACCCTCAGAATTGGGGGCTTCTATGCCCTCACCCCACGCCCTGGCCTCCGCCT
CATCTCTCTCAATATGAATTTTTGTTCCCGTGAGAACTTTTGGCTCTTGATCAACTCCACAGAT
CCTGCTGGACAACTCCAGTGGCTGGTGGACGAGCTTCAGGCTGCTGAGAATCGAGGAGACAAAG
TGCATATAATTGGGCACATTCCTCCAGGACATTGCCTCAAGAGCTGGAGTTGGAACTATTACAA
AATTATAGCCAGGTATGAAAACACTCTGGCTGGTCAGTTCTTTGGCCACACTCATGTGGATGAG
TTTGAGATCTTCTATGATGAGGAAACTCTGAGCCGCCCACTAGCCGTAGCCTTCCTGGGACCCA
GTGCTACCACCTTTATCAACCTTAATCCTGGCTACCGAGTTTACCAAATAGATGGAAACTACCC
GGGAAGCTCTCATGTGGTCCTGGACCATGAGACCTACATCCTGAATCTGACCCAGGCCAATGCG
CCGGGGGGCACGCCCAGCTGGAAGCGGCTCTACAGGGCTCGGGAAACCTATGGACTTCCAGATG
CGATGCCTGCCTCCTGGCACAACCTGGTCTACCGCATGAGGGCTGATGAGCAGCTCTTCCAGAC
CTTCTGGTTTCTCTACCATAAGGGCCACCCACCTTCAGAGCCCTGCGGCACACCCTGCCGCCTG
GCCACTCTGTGTGCCCAGCTCTCAGCACGTGCAGACAGCCCTGCTCTGTGTCGCCACTTGATGC
CCAATGGGAGCCTCCCAGATGCCCATAGCTTGTGGTCACGGCCCCTGCTGTGCTAGTGTGGGAA
AAGTTCACATATTAGCAAAGGGATGGATTCCTGAGTATCGCTGATCTACCTGAGGCAAAAGCTT
TCGGGGAAGGAGCCAGCCAGGCCAGGGAACAAGCCTCCTCATGAAAGCTTGTTTGGCTAGACTG
AGGGAGGTTTTGGCTGTCCTATTTATGCCCAGTATCTGGATTACCCCTGGGGCTGATGTCTTTA
AGGCCACAAAGCCGAGGTCTTAGTGCTCTGGATTGTAGACAGGAGCTATTGCCCCAGCCTGTGC
TATGCACCTCTGAACTCTGTACTGTTACCTGATCCTGCCAGGCTGTTAAAATAAAGAGACTCAT
ACTTCAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001006998	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH83780	(Get FASTA)	NCBI Sequence Viewer
	EDM18044	(Get FASTA)	NCBI Sequence Viewer
	EDM18045	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001006998 ⟸ NM_001006997

- UniProtKB:

Q5XIA6 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MPHHGASSGQGHLRAGWEQRLERSLPAPKLGLLWMGLGLALVLALFDSTVLWVPARAYPLPSQG
HSVKFSAVAPQLQNAFGWRNLTCPACKVLFTALNYGLKKEPNVARVGSVAIKMCKMLNIAPLNV
CQSAVHLFEDDVVDVWTRSVLSPSEACGLLLGSSCGHWDIFSTWNISLPSVPKPPPKPPSPPAP
GAPVSRVLFLTDLHWDHDYLEGTDPNCADPLCCRRGSGWPPNSRTGAGYWGEYSKCDLPLRTLE
SLLKGLGPAGPFEMVYWTGDIPAHDVWQQSRQDQLRALNTITDLVWKFLGPVPVYPAVGNHEST
PVNGFPPPFIKGNQSSQWLYEAMAKAWEPWLPADALHTLRIGGFYALTPRPGLRLISLNMNFCS
RENFWLLINSTDPAGQLQWLVDELQAAENRGDKVHIIGHIPPGHCLKSWSWNYYKIIARYENTL
AGQFFGHTHVDEFEIFYDEETLSRPLAVAFLGPSATTFINLNPGYRVYQIDGNYPGSSHVVLDH
ETYILNLTQANAPGGTPSWKRLYRARETYGLPDAMPASWHNLVYRMRADEQLFQTFWFLYHKGH
PPSEPCGTPCRLATLCAQLSARADSPALCRHLMPNGSLPDAHSLWSRPLLC

hide sequence

RefSeq Acc Id:

ENSRNOP00000024224 ⟸ ENSRNOT00000024224

Protein Domains

Saposin B-type

Transcriptome

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

Promoters

RGD ID:

13690285

Promoter ID:

EPDNEW_R810

Type:

initiation region

Name:

Smpd1_1

Description:

sphingomyelin phosphodiesterase 1

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	170,383,634 - 170,383,694	EPDNEW

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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CSV

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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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CSV

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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

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
1	177391762	177391763	T	G	snv	ACI/EurMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW)

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
1	163281144	163281145	T	G	snv	ACI/EurMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1549719	AgrOrtholog
Ensembl Genes	ENSRNOG00000017977	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000024224	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000024224	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	3.60.21.10	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7096039	IMAGE-MGC_LOAD
InterPro	ASMase/PPN1_MPP	UniProtKB/TrEMBL
	M-pesterase	UniProtKB/TrEMBL
	Metallo-depent_PP-like	UniProtKB/TrEMBL
	Saposin-like	UniProtKB/TrEMBL
	SaposinB	UniProtKB/TrEMBL
	Sphingomy_PDE	UniProtKB/TrEMBL
KEGG Report	rno:308909	UniProtKB/TrEMBL
MGC_CLONE	MGC:94748	IMAGE-MGC_LOAD
NCBI Gene	308909	ENTREZGENE
Pfam	Metallophos	UniProtKB/TrEMBL
PharmGKB	SMPD1	RGD
PhenoGen	Smpd1	PhenoGen
PIRSF	Sphingomy_PDE	UniProtKB/TrEMBL
PROSITE	SAP_B	UniProtKB/TrEMBL
SMART	SapB	UniProtKB/TrEMBL
Superfamily-SCOP	Saposin_like	UniProtKB/TrEMBL
UniProt	Q5XIA6	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)