SMPD1 (sphingomyelin phosphodiesterase 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: SMPD1 (sphingomyelin phosphodiesterase 1) Canis lupus familiaris
Analyze
Symbol: SMPD1
Name: sphingomyelin phosphodiesterase 1
RGD ID: 12166714
Description: ENCODES a protein that exhibits acid sphingomyelin phosphodiesterase activity (inferred); hydrolase activity (inferred); hydrolase activity, acting on glycosyl bonds (inferred); INVOLVED IN ceramide biosynthetic process (ortholog); ceramide metabolic process (ortholog); cholesterol metabolic process (ortholog); PARTICIPATES IN ceramide signaling pathway; FasL mediated signaling pathway; Trail mediated signaling pathway; ASSOCIATED WITH Experimental Diabetes Mellitus (ortholog); Gaucher's disease (ortholog); genetic disease (ortholog); FOUND IN extracellular space (ortholog); lamellar body (ortholog); lysosome (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: acid sphingomyelinase; sphingomyelin phosphodiesterase; sphingomyelin phosphodiesterase 1, acid lysosomal (acid sphingomyelinase)
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12129,714,418 - 29,719,035 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2129,714,557 - 29,719,033 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2129,416,446 - 29,421,072 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02130,540,703 - 30,545,329 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2130,540,764 - 30,545,592 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12129,861,608 - 29,866,232 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02130,027,386 - 30,032,012 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02130,222,733 - 30,227,359 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202   PMID:37308057  


Genomics

Comparative Map Data
SMPD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12129,714,418 - 29,719,035 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2129,714,557 - 29,719,033 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2129,416,446 - 29,421,072 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02130,540,703 - 30,545,329 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2130,540,764 - 30,545,592 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12129,861,608 - 29,866,232 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02130,027,386 - 30,032,012 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02130,222,733 - 30,227,359 (+)NCBIUU_Cfam_GSD_1.0
SMPD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38116,390,474 - 6,394,996 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl116,390,440 - 6,394,998 (+)EnsemblGRCh38hg38GRCh38
GRCh37116,411,704 - 6,416,226 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36116,368,231 - 6,372,802 (+)NCBINCBI36Build 36hg18NCBI36
Build 34116,368,230 - 6,372,801NCBI
Celera116,530,711 - 6,535,296 (+)NCBICelera
Cytogenetic Map11p15.4NCBI
HuRef116,070,739 - 6,075,337 (+)NCBIHuRef
CHM1_1116,410,778 - 6,415,363 (+)NCBICHM1_1
T2T-CHM13v2.0116,448,931 - 6,453,455 (+)NCBIT2T-CHM13v2.0
Smpd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397105,203,567 - 105,207,596 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl7105,203,567 - 105,207,596 (+)EnsemblGRCm39 Ensembl
GRCm387105,554,360 - 105,558,389 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7105,554,360 - 105,558,389 (+)EnsemblGRCm38mm10GRCm38
MGSCv377112,702,874 - 112,706,903 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv367105,428,236 - 105,432,203 (+)NCBIMGSCv36mm8
Celera7105,825,502 - 105,829,531 (+)NCBICelera
Cytogenetic Map7E3NCBI
cM Map755.9NCBI
Smpd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81169,304,772 - 169,308,615 (+)NCBIGRCr8
mRatBN7.21159,892,946 - 159,896,789 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1159,892,859 - 159,896,794 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1167,915,425 - 167,919,268 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01175,101,419 - 175,105,262 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01168,003,243 - 168,007,086 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01170,383,682 - 170,387,525 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1170,383,682 - 170,387,524 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01177,389,588 - 177,393,431 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41163,278,970 - 163,282,813 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1157,825,620 - 157,829,463 (+)NCBICelera
Cytogenetic Map1q32NCBI
Smpd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541422,117,930 - 22,121,744 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541422,117,929 - 22,121,744 (+)NCBIChiLan1.0ChiLan1.0
SMPD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v298,826,802 - 8,831,484 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1118,790,673 - 8,795,342 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0116,521,812 - 6,526,349 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1116,205,278 - 6,209,950 (+)NCBIpanpan1.1PanPan1.1panPan2
Smpd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494756,222,931 - 56,227,200 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936842447,991 - 452,630 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936842448,315 - 452,557 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMPD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl93,324,442 - 3,328,457 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.193,324,091 - 3,328,493 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.293,961,624 - 3,964,422 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SMPD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1158,431,677 - 58,436,233 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl158,432,068 - 58,436,236 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666038156,257,313 - 156,261,990 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smpd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248177,909,468 - 7,913,417 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248177,909,777 - 7,913,419 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SMPD1
41 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 4 4 22 6 4 6 6 1 12 10 6
Low 1 1 2 5 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000010359   ⟹   ENSCAFP00000009604
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl2129,714,557 - 29,719,033 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845013044   ⟹   ENSCAFP00845010161
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl2130,540,764 - 30,545,592 (+)Ensembl
RefSeq Acc Id: XM_038430362   ⟹   XP_038286290
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.02130,540,703 - 30,545,329 (+)NCBI
RefSeq Acc Id: XM_038505692   ⟹   XP_038361620
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.12129,861,608 - 29,866,232 (+)NCBI
RefSeq Acc Id: XM_038568897   ⟹   XP_038424825
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.02130,222,733 - 30,227,359 (+)NCBI
RefSeq Acc Id: XM_038633063   ⟹   XP_038488991
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.02130,027,386 - 30,032,012 (+)NCBI
RefSeq Acc Id: XM_542452   ⟹   XP_542452
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.12129,714,418 - 29,719,035 (+)NCBI
Dog10K_Boxer_Tasha2129,416,446 - 29,421,072 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_542452   ⟸   XM_542452
- UniProtKB: A0A8C0MWB3 (UniProtKB/TrEMBL),   A0A8C0K937 (UniProtKB/TrEMBL),   A0A8I3RTW7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000009604   ⟸   ENSCAFT00000010359
RefSeq Acc Id: XP_038361620   ⟸   XM_038505692
RefSeq Acc Id: XP_038488991   ⟸   XM_038633063
RefSeq Acc Id: XP_038286290   ⟸   XM_038430362
- UniProtKB: A0A8C0MWB3 (UniProtKB/TrEMBL),   A0A8C0K937 (UniProtKB/TrEMBL),   A0A8I3RTW7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038424825   ⟸   XM_038568897
- UniProtKB: A0A8C0K937 (UniProtKB/TrEMBL),   A0A8C0MWB3 (UniProtKB/TrEMBL),   A0A8I3RTW7 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845010161   ⟸   ENSCAFT00845013044
Protein Domains
Saposin B-type

Promoters
RGD ID:13687222
Promoter ID:EPDNEW_C5290
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:
Dog AssemblyChrPosition (strand)Source
CanFam3.12129,714,470 - 29,714,530EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000006411 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030009197 UniProtKB/TrEMBL
  ENSCAFG00040018866 UniProtKB/TrEMBL
  ENSCAFG00845007383 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000010359.5 UniProtKB/TrEMBL
  ENSCAFT00030017073.1 UniProtKB/TrEMBL
  ENSCAFT00040034928.1 UniProtKB/TrEMBL
  ENSCAFT00845013044 ENTREZGENE
  ENSCAFT00845013044.1 UniProtKB/TrEMBL
Gene3D-CATH 3.60.21.10 UniProtKB/TrEMBL
InterPro ASMase/PPN1_MPP UniProtKB/TrEMBL
  Calcineurin-like_PHP_ApaH UniProtKB/TrEMBL
  Metallo-depent_PP-like UniProtKB/TrEMBL
  Saposin-like UniProtKB/TrEMBL
  SaposinB_dom UniProtKB/TrEMBL
  Sphingomy_PDE UniProtKB/TrEMBL
KEGG Report cfa:485334 UniProtKB/TrEMBL
NCBI Gene SMPD1 ENTREZGENE
PANTHER SPHINGOMYELIN PHOSPHODIESTERASE UniProtKB/TrEMBL
  SPHINGOMYELIN PHOSPHODIESTERASE UniProtKB/TrEMBL
Pfam Metallophos UniProtKB/TrEMBL
PIRSF Sphingomy_PDE UniProtKB/TrEMBL
PROSITE SAP_B UniProtKB/TrEMBL
SMART SapB UniProtKB/TrEMBL
Superfamily-SCOP SSF47862 UniProtKB/TrEMBL
  SSF56300 UniProtKB/TrEMBL
UniProt A0A8C0K937 ENTREZGENE
  A0A8C0MWB3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3RTW7 ENTREZGENE, UniProtKB/TrEMBL
  O46601_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:46569 ENTREZGENE