Smpd2 (sphingomyelin phosphodiesterase 2) - Rat Genome Database

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Gene: Smpd2 (sphingomyelin phosphodiesterase 2) Rattus norvegicus
Analyze
Symbol: Smpd2
Name: sphingomyelin phosphodiesterase 2
RGD ID: 619753
Description: Enables sphingomyelin phosphodiesterase activity. Involved in ceramide biosynthetic process; intracellular signal transduction; and response to mechanical stimulus. Located in caveola. Orthologous to human SMPD2 (sphingomyelin phosphodiesterase 2); PARTICIPATES IN tumor necrosis factor mediated signaling pathway; sphingolipid metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously 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 ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22044,986,229 - 44,989,343 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2044,986,231 - 44,989,441 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2046,703,734 - 46,706,848 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02046,353,909 - 46,357,023 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02047,060,705 - 47,063,816 (-)NCBIRnor_WKY
Rnor_6.02046,212,070 - 46,215,183 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2046,211,892 - 46,215,120 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02047,904,390 - 47,907,503 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42045,448,774 - 45,451,887 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12045,471,784 - 45,474,898 (-)NCBI
Celera2054,964,269 - 54,967,382 (+)NCBICelera
Cytogenetic Map20q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
caveola  (IBA,IDA)
cell periphery  (IBA)
endoplasmic reticulum  (IBA)
membrane  (IBA,IDA,IEA)
plasma membrane  (ISO,TAS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Transient mechanoactivation of neutral sphingomyelinase in caveolae to generate ceramide. Czarny M, etal., J Biol Chem. 2003 Feb 14;278(7):4424-30. Epub 2002 Dec 6.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Cloning and expression of rat neutral sphingomyelinase: enzymological characterization and identification of essential histidine residues. Mizutani Y, etal., Biochim Biophys Acta 2000 May 31;1485(2-3):236-46.
6. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
7. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
8. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
9. GOA pipeline RGD automated data pipeline
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Sphingomyelinase treatment of rat hepatocytes inhibits cell-swelling-stimulated glycogen synthesis by causing cell shrinkage. 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   PMID:34089907  


Genomics

Comparative Map Data
Smpd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22044,986,229 - 44,989,343 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2044,986,231 - 44,989,441 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2046,703,734 - 46,706,848 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02046,353,909 - 46,357,023 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02047,060,705 - 47,063,816 (-)NCBIRnor_WKY
Rnor_6.02046,212,070 - 46,215,183 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2046,211,892 - 46,215,120 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02047,904,390 - 47,907,503 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42045,448,774 - 45,451,887 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12045,471,784 - 45,474,898 (-)NCBI
Celera2054,964,269 - 54,967,382 (+)NCBICelera
Cytogenetic Map20q12NCBI
SMPD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386109,440,724 - 109,443,919 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl6109,440,724 - 109,443,919 (+)EnsemblGRCh38hg38GRCh38
GRCh376109,761,927 - 109,765,122 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366109,868,624 - 109,871,815 (+)NCBINCBI36Build 36hg18NCBI36
Build 346109,868,658 - 109,871,814NCBI
Celera6110,508,515 - 110,511,706 (+)NCBICelera
Cytogenetic Map6q21NCBI
HuRef6107,328,017 - 107,331,208 (+)NCBIHuRef
CHM1_16110,025,014 - 110,028,205 (+)NCBICHM1_1
T2T-CHM13v2.06110,618,762 - 110,621,957 (+)NCBIT2T-CHM13v2.0
Smpd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391041,363,168 - 41,366,410 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1041,361,638 - 41,366,365 (-)EnsemblGRCm39 Ensembl
GRCm381041,487,172 - 41,490,370 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1041,485,642 - 41,490,369 (-)EnsemblGRCm38mm10GRCm38
MGSCv371041,206,978 - 41,210,146 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361041,175,587 - 41,178,755 (-)NCBIMGSCv36mm8
Celera1042,373,425 - 42,376,593 (-)NCBICelera
Cytogenetic Map10B1NCBI
Smpd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541134,481,823 - 34,484,406 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541134,481,431 - 34,484,423 (+)NCBIChiLan1.0ChiLan1.0
SMPD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16111,292,130 - 111,295,408 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6111,292,130 - 111,295,408 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06107,243,751 - 107,246,941 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SMPD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11266,347,628 - 66,350,322 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1266,323,022 - 66,350,322 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1266,167,530 - 66,170,223 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01267,230,786 - 67,233,489 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1267,230,194 - 67,233,489 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11266,580,755 - 66,583,447 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01266,429,591 - 66,432,296 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01266,701,323 - 66,704,026 (+)NCBIUU_Cfam_GSD_1.0
Smpd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946101,290,250 - 101,293,611 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365645,564,784 - 5,568,956 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049365645,565,205 - 5,568,474 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMPD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl175,508,350 - 75,512,153 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1175,508,303 - 75,511,572 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2184,786,677 - 84,789,541 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SMPD2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11364,424,236 - 64,427,435 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1364,424,250 - 64,427,366 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604036,716,021 - 36,719,229 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smpd2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624916697,006 - 701,012 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624916697,861 - 701,015 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Smpd2
12 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat

Markers in Region
RH130593  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22044,986,322 - 44,986,507 (+)MAPPERmRatBN7.2
Rnor_6.02046,212,164 - 46,212,348NCBIRnor6.0
Rnor_5.02047,904,484 - 47,904,668UniSTSRnor5.0
RGSC_v3.42045,448,868 - 45,449,052UniSTSRGSC3.4
Celera2054,967,104 - 54,967,288UniSTS
RH 3.4 Map20484.92UniSTS
Cytogenetic Map20q12UniSTS


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

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000336   ⟹   ENSRNOP00000000336
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2044,986,234 - 44,989,441 (-)Ensembl
Rnor_6.0 Ensembl2046,211,892 - 46,215,120 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112826   ⟹   ENSRNOP00000093225
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2044,986,231 - 44,989,180 (-)Ensembl
RefSeq Acc Id: NM_031360   ⟹   NP_112650
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22044,986,229 - 44,989,343 (-)NCBI
Rnor_6.02046,212,070 - 46,215,183 (-)NCBI
Rnor_5.02047,904,390 - 47,907,503 (-)NCBI
RGSC_v3.42045,448,774 - 45,451,887 (-)RGD
Celera2054,964,269 - 54,967,382 (+)RGD
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: Q5BKB2 (UniProtKB/Swiss-Prot),   Q9ET64 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000336   ⟸   ENSRNOT00000000336
RefSeq Acc Id: ENSRNOP00000093225   ⟸   ENSRNOT00000112826
Protein Domains
Endo/exonuclease/phosphatase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9ET64-F1-model_v2 AlphaFold Q9ET64 1-422 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619753 AgrOrtholog
BioCyc Gene G2FUF-3396 BioCyc
BioCyc Pathway PWY3DJ-11281 [sphingomyelin metabolism] BioCyc
Ensembl Genes ENSRNOG00000000306 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000336 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000093225.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000336 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000112826.1 UniProtKB/TrEMBL
Gene3D-CATH 3.60.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7378100 IMAGE-MGC_LOAD
InterPro Endo/exonu/phosph_ase_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Endo/exonuclease/phosphatase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMPD2-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:83537 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108644 IMAGE-MGC_LOAD
NCBI Gene 83537 ENTREZGENE
PANTHER PTHR12393 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Exo_endo_phos UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Smpd2 PhenoGen
Superfamily-SCOP SSF56219 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6GKK3_RAT UniProtKB/TrEMBL
  NSMA_RAT UniProtKB/Swiss-Prot
  Q5BKB2 ENTREZGENE
  Q9ET64 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