Smpd2 (sphingomyelin phosphodiesterase 2)

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Gene: Smpd2 (sphingomyelin phosphodiesterase 2) Rattus norvegicus

Analyze

Symbol:

Smpd2

Name:

sphingomyelin phosphodiesterase 2

RGD ID:

619753

Description:

Exhibits sphingomyelin phosphodiesterase activity. Involved in ceramide biosynthetic process; intracellular signal transduction; and response to mechanical stimulus. Localizes to caveola. Orthologous to human SMPD2 (sphingomyelin phosphodiesterase 2); PARTICIPATES IN tumor necrosis factor mediated signaling pathway; sphingolipid metabolic pathway; INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; acrylamide.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

lyso-PAF-PLC; lyso-platelet-activating factor-phospholipase C; N-SMase; neutral sphingomyelinase; nSMase; sphingomyelin phosphodiesterase 2, neutral; sphingomyelin phosphodiesterase 2, neutral membrane

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):	SMPD2 (sphingomyelin phosphodiesterase 2)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Smpd2 (sphingomyelin phosphodiesterase 2, neutral)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Smpd2 (sphingomyelin phosphodiesterase 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SMPD2 (sphingomyelin phosphodiesterase 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SMPD2 (sphingomyelin phosphodiesterase 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Smpd2 (sphingomyelin phosphodiesterase 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SMPD2 (sphingomyelin phosphodiesterase 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	SMPD2 (sphingomyelin phosphodiesterase 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Smpd2 (sphingomyelin phosphodiesterase 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	SMPD2 (sphingomyelin phosphodiesterase 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Smpd2 (sphingomyelin phosphodiesterase 2, neutral)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	smpd2a (sphingomyelin phosphodiesterase 2a, neutral membrane (neutral sphingomyelinase))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	smpd2b (sphingomyelin phosphodiesterase 2b, neutral membrane (neutral sphingomyelinase))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	CG12034	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Saccharomyces cerevisiae (baker's yeast):	ISC1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	T27F6.6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|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	20	44,986,229 - 44,989,343 (-)	NCBI
Rnor_6.0 Ensembl	20	46,211,892 - 46,215,120 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	20	46,212,070 - 46,215,183 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	20	47,904,390 - 47,907,503 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	20	45,448,774 - 45,451,887 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	20	45,471,784 - 45,474,898 (-)	NCBI
Celera	20	54,964,269 - 54,967,382 (+)	NCBI		Celera
Cytogenetic Map	20	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(25R)-cholest-5-ene-3beta,26-diol (ISO)

1,2-dimethylhydrazine (ISO)

17beta-hydroxy-5alpha-androstan-3-one (ISO)

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

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

26-hydroxycholesterol (ISO)

3,3',4,4'-tetrachlorobiphenyl (ISO)

5-aza-2'-deoxycytidine (ISO)

acrylamide (EXP)

ammonium chloride (EXP)

ampicillin (EXP)

antirheumatic drug (ISO)

benzo[a]pyrene (EXP,ISO)

benzo[b]fluoranthene (ISO)

bezafibrate (EXP)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP)

C60 fullerene (EXP)

carmustine (ISO)

chrysene (ISO)

cisplatin (ISO)

clofibrate (ISO)

dexamethasone (ISO)

dextran sulfate (ISO)

fenofibrate (ISO)

flavonoids (EXP)

folic acid (ISO)

gentamycin (EXP)

metronidazole (EXP)

NAD zwitterion (ISO)

NAD(+) (ISO)

neomycin (EXP)

phenobarbital (ISO)

pirinixic acid (ISO)

sodium dichromate (ISO)

sphingosine 1-phosphate (ISO)

sunitinib (ISO)

tetrachloromethane (EXP)

tetraphene (ISO)

thalidomide (ISO)

trichloroethene (EXP)

valproic acid (ISO)

vancomycin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

ceramide biosynthetic process (IBA,IDA)

intracellular signal transduction (IMP)

response to mechanical stimulus (IMP)

sphingolipid catabolic process (IBA)

sphingomyelin catabolic process (ISO)

sphingomyelin metabolic process (IBA)

Cellular Component

caveola (IBA,IDA)

cell periphery (IBA)

endoplasmic reticulum (IBA)

integral component of membrane (IEA)

membrane (IBA,IDA)

plasma membrane (TAS)

Molecular Function

metal ion binding (IEA)

phospholipase activity (IBA)

protein binding (ISO)

sphingomyelin phosphodiesterase activity (IBA,IDA,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

sphingolipid metabolic pathway (IEA)

tumor necrosis factor mediated signaling pathway (ISO)

References

References - curated


1.	Czarny M, etal., J Biol Chem. 2003 Feb 14;278(7):4424-30. Epub 2002 Dec 6.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	GOA data from the GO Consortium
4.	MGD data from the GO Consortium
5.	Mizutani Y, etal., Biochim Biophys Acta 2000 May 31;1485(2-3):236-46.
6.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
7.	Pipeline to import KEGG annotations from KEGG into RGD
8.	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
9.	RGD automated data pipeline
10.	RGD automated import pipeline for gene-chemical interactions
11.	Van Sluijters DA, etal., Eur J Biochem 1999 Dec;266(2):653-9.

Additional References at PubMed

PMID:7673191	PMID:8079174	PMID:12477932	PMID:15764706	PMID:17668873	PMID:17693623	PMID:17707397	PMID:19088082	PMID:22627111	PMID:23973266	PMID:24316227	PMID:25354938
PMID:28277984

Genomics

Comparative Map Data

Smpd2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	20	44,986,229 - 44,989,343 (-)	NCBI
Rnor_6.0 Ensembl	20	46,211,892 - 46,215,120 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	20	46,212,070 - 46,215,183 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	20	47,904,390 - 47,907,503 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	20	45,448,774 - 45,451,887 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	20	45,471,784 - 45,474,898 (-)	NCBI
Celera	20	54,964,269 - 54,967,382 (+)	NCBI		Celera
Cytogenetic Map	20	q12	NCBI

SMPD2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	6	109,440,724 - 109,443,919 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	6	109,440,721 - 109,443,922 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	6	109,761,927 - 109,765,122 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	109,868,624 - 109,871,815 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	6	109,868,658 - 109,871,814	NCBI
Celera	6	110,508,515 - 110,511,706 (+)	NCBI
Cytogenetic Map	6	q21	NCBI
HuRef	6	107,328,017 - 107,331,208 (+)	NCBI		HuRef
CHM1_1	6	110,025,014 - 110,028,205 (+)	NCBI		CHM1_1

Smpd2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	41,363,168 - 41,366,410 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	10	41,361,638 - 41,366,365 (-)	Ensembl
GRCm38	10	41,487,172 - 41,490,370 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	41,485,642 - 41,490,369 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	41,206,978 - 41,210,146 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	10	41,175,587 - 41,178,755 (-)	NCBI			mm8
Celera	10	42,373,425 - 42,376,593 (-)	NCBI		Celera
Cytogenetic Map	10	B1	NCBI

Smpd2
(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_004955411	34,481,823 - 34,484,406 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955411	34,481,431 - 34,484,423 (+)	NCBI	ChiLan1.0	ChiLan1.0

SMPD2
(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	6	111,292,130 - 111,295,408 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	111,292,130 - 111,295,408 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	6	107,243,751 - 107,246,941 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

SMPD2
(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	12	66,323,022 - 66,350,322 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	12	66,347,628 - 66,350,322 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Smpd2
(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_004936564	5,565,205 - 5,568,474 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SMPD2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	75,508,350 - 75,512,159 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	75,508,303 - 75,511,572 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	84,786,677 - 84,789,541 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SMPD2
(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	13	64,424,236 - 64,427,435 (-)	NCBI
ChlSab1.1 Ensembl	13	64,424,250 - 64,427,366 (-)	Ensembl

Smpd2
(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_004624916	697,861 - 701,015 (+)	NCBI

Position Markers

RH130593

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	20	46,212,164 - 46,212,348	NCBI	Rnor6.0
Rnor_5.0	20	47,904,484 - 47,904,668	UniSTS	Rnor5.0
RGSC_v3.4	20	45,448,868 - 45,449,052	UniSTS	RGSC3.4
Celera	20	54,967,104 - 54,967,288	UniSTS
RH 3.4 Map	20	484.92	UniSTS
Cytogenetic Map	20	q12	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
2305926	Iddm37	Insulin dependent diabetes mellitus QTL 37	6		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	20	2018654	47018654	Rat
1641915	Colcr9	Colorectal carcinoma resistance QTL 9	2.97	0.0024	intestine integrity trait (VT:0010554)	benign colorectal tumor number (CMO:0001795)	20	2999707	47999707	Rat
1598816	Memor12	Memory QTL 12	2.4		exploratory behavior trait (VT:0010471)	average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)	20	4108956	49108956	Rat
9590092	Insglur9	Insulin/glucose ratio QTL 9	18.38	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	20	13834309	56205956	Rat
7411652	Foco24	Food consumption QTL 24		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	13834309	56205956	Rat
2317880	Alcrsp25	Alcohol response QTL 25	2.3		response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	17827096	56205956	Rat
4889610	Pancm3	Pancreatic morphology QTL 3	3.75	0.001	pancreas mass (VT:0010144)	pancreas wet weight (CMO:0000626)	20	18872150	49108956	Rat
2303626	Vencon10	Ventilatory control QTL 10		0.001	respiration trait (VT:0001943)	respiration rate (CMO:0000289)	20	20858470	56205956	Rat
2303578	Gluco50	Glucose level QTL 50	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	20	26608843	56205956	Rat
2303587	Bw93	Body weight QTL 93	13		body mass (VT:0001259)	body weight (CMO:0000012)	20	26608843	56205956	Rat
2300188	Bmd68	Bone mineral density QTL 68	6.4	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	20	26608843	56205956	Rat
1331747	Hrtrt16	Heart rate QTL 16	3.163		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	20	26712323	56205956	Rat
1598869	Memor6	Memory QTL 6	3.1		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	20	30913481	56205956	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	112
Count of miRNA genes:	93
Interacting mature miRNAs:	100
Transcripts:	ENSRNOT00000000336
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	15	12	4	19	4			13	34	39	11
Low		28	45	37		37	8	11	61	1	2		8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031360	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB047002	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC091139	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474025	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000330	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000000336 ⟹ ENSRNOP00000000336

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	46,211,892 - 46,215,120 (-)	Ensembl

RefSeq Acc Id:

NM_031360 ⟹ NP_112650

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	20	44,986,229 - 44,989,343 (-)	NCBI
Rnor_6.0	20	46,212,070 - 46,215,183 (-)	NCBI
Rnor_5.0	20	47,904,390 - 47,907,503 (-)	NCBI
RGSC_v3.4	20	45,448,774 - 45,451,887 (-)	RGD
Celera	20	54,964,269 - 54,967,382 (+)	RGD

Sequence:

show sequence

CACCGAAGGCTCTAAGAACCTGGAACGGTCCACCCGAGACTCCTTCCGGGACTGCCGGCGGCCT
CGAGCAGCCAGCCCAGCACTAGCGGCCGATCTCCTTTCAGGTGGGAGGACGGCCTGTTGTCCCA
GTAACGCAGGAGTCGTCCCCCCCCCCCCCCGCCCCAAACCAGCTCGCGTTCCTGGGTCGGGGCA
GCGCGGGACAGCGCCGGCAACCTGTGCGCGCGGTCAGCCTCGCCACCCTTGCTCCGAAGCACTC
CAACCATGAAGCACAACTTTTCTCTGCGGCTGAGGGTTTTCAACCTCAACTGCTGGGACATCCC
CTACCTAAGCAAGCATAGGGCCGACCGCATGAAGCGCTTGGGAGACTTTCTGAACTTGGAGAGC
TTTGACCTGGCTCTGCTGGAGGAGGTGTGGAGTGAGCAGGACTTCCAGTACTTAAAGCAAAAGC
TATCGCTCACCTACCCGGATGCACACTACTTCAGAAGCGGAATCATTGGCAGTGGCCTCTGTGT
GTTCTCCAGACACCCAATCCAGGAAATTGTCCAGCACGTCTATACTCTCAATGGTTACCCCTAC
AAGTTCTATCATGGAGACTGGTTCTGTGGGAAGGCTGTGGGGCTGCTGGTGCTCCATCTAAGCG
GACTGGTGCTCAACGCCTACGTGACCCATCTGCACGCTGAGTACAGCCGGCAGAAGGATATCTA
CTTCGCACACCGTGTGGCCCAAGCTTGGGAACTGGCCCAGTTCATCCACCACACATCCAAGAAA
GCAAATGTGGTCCTGTTGTGCGGGGATCTCAACATGCACCCCAAAGACCTGGGCTGCTGCCTAC
TGAAAGAGTGGACGGGGCTCCGTGATGCCTTTGTTGAGACCGAGGACTTTAAGGGCTCAGAGGA
CGGCTGTACCATGGTACCCAAGAACTGCTACGTCAGCCAGCAGGACCTGGGGCCGTTTCCCTTT
GGCGTCCGTATCGACTACGTGCTTTACAAGGCAGTCTCTGGCTTCCACATCTGCTGTAAGACTC
TGAAAACCACTACGGGCTGTGACCCCCACAATGGCACCCCCTTCTCTGACCACGAGGCCCTCAT
GGCTACTTTGTGTGTGAAGCACAGCCCCCCTCAGGAAGACCCTTGCTCTGCCCATGGATCAGCG
GAAAGGTCAGCATTGATCAGCGCGCTAAGGGAGGCGAGGACAGAGCTGGGGCGAGGCATAGCTC
AAGCTCGCTGGTGGGCTGCACTCTTTGGCTATGTGATGATTTTGGGGCTGTCCCTCCTGGTGTT
GCTGTGTGTCCTGGCTGCAGGAGAAGAGGCCAGGGAAGTGGCCATAATGCTCTGGACACCCAGT
GTGGGTCTGGTGCTGGGGGCAGGCGCAGTCTACCTGTTCCACAAGCAGGAGGCCAAAAGCTTAT
GTCGGGCCCAGGCTGAGATACAACATGTTCTGACAAGGACAACGGAGACCCAGGACCTAGGCTC
AGAGCCTCACCCAACCCACTGCCGGCAGCAGGAGGCGGACAGAGCTGAAGAAAAATAAAACTTG
CTTGACACACTCTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_112650	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH91139	(Get FASTA)	NCBI Sequence Viewer
	BAB08219	(Get FASTA)	NCBI Sequence Viewer
	EDL99734	(Get FASTA)	NCBI Sequence Viewer
	EDL99735	(Get FASTA)	NCBI Sequence Viewer
	Q9ET64	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_112650 ⟸ NM_031360

- UniProtKB:

Q9ET64 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MKHNFSLRLRVFNLNCWDIPYLSKHRADRMKRLGDFLNLESFDLALLEEVWSEQDFQYLKQKLS
LTYPDAHYFRSGIIGSGLCVFSRHPIQEIVQHVYTLNGYPYKFYHGDWFCGKAVGLLVLHLSGL
VLNAYVTHLHAEYSRQKDIYFAHRVAQAWELAQFIHHTSKKANVVLLCGDLNMHPKDLGCCLLK
EWTGLRDAFVETEDFKGSEDGCTMVPKNCYVSQQDLGPFPFGVRIDYVLYKAVSGFHICCKTLK
TTTGCDPHNGTPFSDHEALMATLCVKHSPPQEDPCSAHGSAERSALISALREARTELGRGIAQA
RWWAALFGYVMILGLSLLVLLCVLAAGEEAREVAIMLWTPSVGLVLGAGAVYLFHKQEAKSLCR
AQAEIQHVLTRTTETQDLGSEPHPTHCRQQEADRAEEK

hide sequence

RefSeq Acc Id:

ENSRNOP00000000336 ⟸ ENSRNOT00000000336

Transcriptome

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
20	47904734	47904735	C	T	snv	MNS/Gib (KNAW)

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
20	46212414	46212415	C	T	snv	MNS/Gib (RGD)

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
20	45449118	45449119	C	T	snv	MNS/Gib (ICL)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:619753	AgrOrtholog
Ensembl Genes	ENSRNOG00000000306	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000000336	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000000336	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	3.60.10.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7378100	IMAGE-MGC_LOAD
InterPro	Endo/exonu/phosph_ase_sf	UniProtKB/Swiss-Prot
	Endo/exonuclease/phosphatase	UniProtKB/Swiss-Prot
	SMPD2-like	UniProtKB/Swiss-Prot
KEGG Report	rno:83537	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:108644	IMAGE-MGC_LOAD
NCBI Gene	83537	ENTREZGENE
PANTHER	PTHR12393	UniProtKB/Swiss-Prot
Pfam	Exo_endo_phos	UniProtKB/Swiss-Prot
PhenoGen	Smpd2	PhenoGen
Superfamily-SCOP	SSF56219	UniProtKB/Swiss-Prot
UniProt	NSMA_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary	Q5BKB2	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-03-16	Smpd2	sphingomyelin phosphodiesterase 2	Smpd2	sphingomyelin phosphodiesterase 2, neutral membrane	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2011-01-19	Smpd2	sphingomyelin phosphodiesterase 2, neutral membrane	Smpd2	sphingomyelin phosphodiesterase 2, neutral	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-01-20	Smpd2	sphingomyelin phosphodiesterase 2, neutral		neutral sphingomyelinase	Name updated	1299863	APPROVED
2002-08-07	Smpd2	neutral sphingomyelinase			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 Annotations - KEGG (archival)

Imported Annotations - PID (archival)