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 enable acid sphingomyelin phosphodiesterase activity and zinc ion binding activity. Involved in several processes, including ceramide biosynthetic process; response to cocaine; and response to drug. Located in extracellular space and lamellar body. Used to study Wilson disease. Human ortholog(s) of this gene implicated in Niemann-Pick disease; Niemann-Pick disease type A; and Niemann-Pick disease type B. Orthologous to human SMPD1 (sphingomyelin phosphodiesterase 1); PARTICIPATES IN ceramide signaling pathway; FasL mediated signaling pathway; Trail mediated signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 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 (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:

mRatBN7.2 - mRatBN7.2 Assembly

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	mRatBN7.2
mRatBN7.2 Ensembl	1	159,892,859 - 159,896,794 (+)	Ensembl
Rnor_6.0	1	170,383,682 - 170,387,525 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	170,383,682 - 170,387,524 (+)	Ensembl	Rnor6.0		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)

intellectual disability (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)

2,3,7,8-Tetrachlorodibenzofuran (ISO)

2-hydroxypropanoic acid (ISO)

3',4',5-trihydroxy-3,7-dimethoxyflavone (ISO)

3,3',4,4',5-pentachlorobiphenyl (EXP)

3,3-diphenyl-N-(1-phenylethyl)-1-propanamine (ISO)

3,4-methylenedioxymethamphetamine (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-diaminodiphenylmethane (ISO)

7-ketocholesterol (ISO)

afimoxifene (ISO)

all-trans-retinoic acid (ISO)

amitriptyline (ISO)

aristolochic acid (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)

ivermectin (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)

temozolomide (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 (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 interleukin-1 (ISO)

response to ionizing radiation (ISO)

response to tumor necrosis factor (ISO)

response to type I interferon (ISO)

response to virus (ISO)

response to xenobiotic stimulus (IEP)

sphingomyelin catabolic process (IBA,ISO)

termination of signal transduction (ISO)

viral entry into host cell (ISO)

wound healing (ISO)

Cellular Component

endolysosome (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	mRatBN7.2
mRatBN7.2 Ensembl	1	159,892,859 - 159,896,794 (+)	Ensembl
Rnor_6.0	1	170,383,682 - 170,387,525 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	170,383,682 - 170,387,524 (+)	Ensembl	Rnor6.0		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
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
GRCm39 Ensembl	7	105,203,567 - 105,207,596 (+)	Ensembl
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	21	29,714,418 - 29,719,035 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	21	29,714,557 - 29,719,033 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	21	29,416,446 - 29,421,072 (+)	NCBI
ROS_Cfam_1.0	21	30,540,703 - 30,545,329 (+)	NCBI
UMICH_Zoey_3.1	21	29,861,608 - 29,866,232 (+)	NCBI
UNSW_CanFamBas_1.0	21	30,027,386 - 30,032,012 (+)	NCBI
UU_Cfam_GSD_1.0	21	30,222,733 - 30,227,359 (+)	NCBI

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
HiC_Itri_2	NW_024404947	56,222,931 - 56,227,200 (-)	NCBI
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 - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	1	58,431,677 - 58,436,233 (-)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	1	58,432,068 - 58,436,236 (-)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666038	156,257,313 - 156,261,990 (-)	NCBI	Vero_WHO_p1.0

Smpd1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624817	7,909,777 - 7,913,419 (+)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

AF206720

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	159,897,088 - 159,897,230 (+)	MAPPER	mRatBN7.2
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
mRatBN7.2	1	159,896,553 - 159,896,734 (+)	MAPPER	mRatBN7.2
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
mRatBN7.2	1	159,893,020 - 159,894,288 (+)	MAPPER	mRatBN7.2
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
mRatBN7.2	1	159,897,030 - 159,897,222 (+)	MAPPER	mRatBN7.2
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
mRatBN7.2	1	159,892,930 - 159,893,039 (+)	MAPPER	mRatBN7.2
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
mRatBN7.2	1	159,896,107 - 159,896,914 (+)	MAPPER	mRatBN7.2
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
mRatBN7.2	1	159,895,451 - 159,896,203 (+)	MAPPER	mRatBN7.2
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 (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
70209	Niddm23	Non-insulin dependent diabetes mellitus QTL 23	2.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	94494440	198324465	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	32356093	162846471	Rat
71118	Thym1	Thymus enlargement QTL 1	10.17	0.001	thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	136829932	181829932	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	115585465	172949803	Rat
631205	Bp196	Blood pressure QTL 196	4	0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	118944897	199050459	Rat
631206	Niddm40	Non-insulin dependent diabetes mellitus QTL 40			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	136745990	163747690	Rat
2302378	Insul11	Insulin level QTL 11	3.25		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	144267353	251128347	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	121767634	166767634	Rat
70160	Bw18	Body weight QTL 18	5.7		body mass (VT:0001259)	body weight (CMO:0000012)	1	144267353	196383635	Rat
724521	Uae1	Urinary albumin excretion QTL 1	3.8	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	90508614	173018436	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	150700142	252085212	Rat
724550	Thym3	Thymus enlargement QTL 3	7.82	0.001	thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	136829932	181829932	Rat
1331749	Hrtrt11	Heart rate QTL 11	2.973		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	94494440	198211706	Rat
1331751	Bp199	Blood pressure QTL 199	3.60022		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	94494440	181830018	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	144267353	222987745	Rat
631654	Bp107	Blood pressure QTL 107			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	125611501	170611501	Rat
1331793	Bp200	Blood pressure QTL 200	3.71601		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	94494440	172949803	Rat
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	156677124	256448636	Rat
731168	Bp154	Blood pressure QTL 154	3.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	94642722	214537671	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	130636910	175636910	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	130636910	175636910	Rat
631519	Pia11	Pristane induced arthritis QTL 11	5.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	136830018	181830018	Rat
631544	Bp84	Blood pressure QTL 84	5.6		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	123350408	181759564	Rat
631548	Bp88	Blood pressure QTL 88	5	0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	156677124	176484451	Rat
631549	Bp89	Blood pressure QTL 89	5.7		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	123350581	201284552	Rat
1641895	Bp298	Blood pressure QTL 298			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	123350408	182418476	Rat
1598850	Bp297	Blood pressure QTL 297	2.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	121006655	166006655	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	143506580	212458660	Rat
1598866	Bp287	Blood pressure QTL 287	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	121006655	166006655	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49393289	199050459	Rat
634315	Niddm45	Non-insulin dependent diabetes mellitus QTL 45	7.16		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	144267916	172949660	Rat
634348	Bp138	Blood pressure QTL 138			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	125611501	168883176	Rat
1578759	Uae30	Urinary albumin excretion QTL 30	3.3	0.003	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	150700247	252085048	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	123350408	182418476	Rat
1578778	Pur4	Proteinuria QTL 4	3.3	0.003	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	1	150700247	252085048	Rat
1578780	Cm52	Cardiac mass QTL 52	3.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	1	81591954	219808434	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	115540693	185145286	Rat
1354591	Cm36	Cardiac mass QTL 36	4.1		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	102813953	201278233	Rat
1354602	Bw35	Body weight QTL 35	12.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	151162512	201278233	Rat
1354606	Bp246	Blood pressure QTL 246	3.6		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	102813953	218753816	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	151162512	256448636	Rat
1354615	Cm32	Cardiac mass QTL 32	5.2		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	1	102813953	201278233	Rat
1354618	Kidm15	Kidney mass QTL 15	5		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	1	156677124	201278233	Rat
1354620	Kidm19	Kidney mass QTL 19	4		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	151162512	201278233	Rat
1354634	Kidm12	Kidney mass QTL 12	3.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	1	151162512	201278233	Rat
1354636	Lmblg1	Limb length QTL 1	6.4		tibia length (VT:0004357)	tibia length (CMO:0000450)	1	151162512	201278233	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	151162512	256448636	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	151162512	256448636	Rat
1558645	Bw55	Body weight QTL 55	3.2	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	1	133680936	178680936	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	153136852	260522016	Rat
1358189	Cstrr1	Cold stress response QTL 1		0.0001	catecholamine amount (VT:0010543)	urine norepinephrine level (CMO:0001629)	1	123350408	182418476	Rat
2312420	Pur17	Proteinuria QTL 17	7.1	0.0001	urine protein amount (VT:0005160)	urine total protein excretion rate (CMO:0000756)	1	156677124	218753816	Rat
2313060	Bss71	Bone structure and strength QTL 71	2.6	0.0001	long bone metaphysis morphology trait (VT:0000133)	tibia midshaft total cross-sectional area (CMO:0001715)	1	118944747	163944747	Rat
2303622	Vencon6	Ventilatory control QTL 6		0.001	respiration trait (VT:0001943)	respiration rate (CMO:0000289)	1	154561505	199561505	Rat
1358886	Bp260	Blood pressure QTL 260	3.67		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	151162766	225824951	Rat
1358902	Bw47	Body weight QTL 47	1.67		body mass (VT:0001259)	body weight (CMO:0000012)	1	90508614	180359386	Rat
1582204	Livw1	Liver weight QTL 1	3.6	0.0003	liver mass (VT:0003402)	liver weight to body weight ratio (CMO:0000633)	1	155422851	172949803	Rat
2293140	Bp313	Blood pressure QTL 313			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	121833674	166833674	Rat
61343	Bp28	Blood pressure QTL 28			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	151646613	196646613	Rat
61347	Bp197	Blood pressure QTL 197	4.2		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	1	158633083	203633083	Rat
61348	Bp30	Blood pressure QTL 30	2.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	144017057	197814409	Rat
61379	Bp44	Blood pressure QTL 44	19.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	144267916	174133260	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	155866514	200866514	Rat
6893347	Bw98	Body weight QTL 98	0.2	0.53	body mass (VT:0001259)	body weight (CMO:0000012)	1	133680936	178680936	Rat
6893361	Bw104	Body weight QTL 104	0.59	0.27	body mass (VT:0001259)	body weight (CMO:0000012)	1	133680936	178680936	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	100357752	183970443	Rat
7794788	Mcs32	Mammary carcinoma susceptibility QTL 32	2.61		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	1	115540693	238914717	Rat
9685799	Bp375	Blood pressure QTL 375			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	125611501	170611501	Rat
9685802	Bp376	Blood pressure QTL 376			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	126540680	171540680	Rat
7771612	Cm80	Cardiac mass QTL 80	8.4		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	1	149448574	221264292	Rat
7421630	Bp362	Blood pressure QTL 362		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	118608292	241799120	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	32737458	199368955	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
mRatBN7.2 Ensembl	1	159,892,859 - 159,896,794 (+)	Ensembl
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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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-Lx/CubMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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)

DA/OlaHsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

F344/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

FXLE16/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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/FarMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

HXB10/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LEXF10A/StmMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LH/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LL/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LN/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

M520/NRrrcMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

MWF/Hsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

SHR/OlalpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

WAG/RijCrl (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000024224	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000024224	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
	SSF56300	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)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)