Smpdl3a (sphingomyelin phosphodiesterase, acid-like 3A) - Rat Genome Database

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Gene: Smpdl3a (sphingomyelin phosphodiesterase, acid-like 3A) Rattus norvegicus
Analyze
Symbol: Smpdl3a
Name: sphingomyelin phosphodiesterase, acid-like 3A
RGD ID: 1359277
Description: Predicted to enable phosphoric diester hydrolase activity and zinc ion binding activity. Predicted to be involved in nucleoside triphosphate catabolic process. Predicted to be located in extracellular space. Orthologous to human SMPDL3A (sphingomyelin phosphodiesterase acid like 3A); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: acid sphingomyelinase-like phosphodiesterase 3A; ASM-like phosphodiesterase 3a; MGC95161
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
mRatBN7.22037,132,592 - 37,155,567 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2037,132,592 - 37,155,567 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2038,164,650 - 38,187,612 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02037,555,362 - 37,578,323 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02038,282,400 - 38,305,383 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02040,779,022 - 40,800,842 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2040,778,927 - 40,800,868 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02042,510,561 - 42,532,381 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42036,821,916 - 36,844,891 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12036,835,715 - 36,858,691 (+)NCBI
Celera2038,445,334 - 38,468,295 (+)NCBICelera
Cytogenetic Map20q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzoates  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
choline  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
etoposide  (ISO)
fenthion  (ISO)
flutamide  (EXP)
folic acid  (ISO)
genistein  (EXP)
glafenine  (EXP)
L-methionine  (ISO)
lead diacetate  (ISO)
leflunomide  (EXP)
menadione  (ISO)
mercury dibromide  (ISO)
methidathion  (ISO)
mitomycin C  (ISO)
nickel sulfate  (ISO)
nitrofen  (EXP)
ozone  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
protein kinase inhibitor  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
sodium dichromate  (EXP,ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
testosterone  (EXP,ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
Tributyltin oxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
Tungsten carbide  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
extracellular region  (ISO,ISS)
extracellular space  (IBA,ISO,ISS)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
7. Increased expression of the acid sphingomyelinase-like protein ASML3a in bladder tumors. Wright KO, etal., J Urol 2002 Dec;168(6):2645-9.
Additional References at PubMed
PMID:15489334   PMID:19926744   PMID:23533145   PMID:24006456   PMID:25288789   PMID:26095358   PMID:26783088  


Genomics

Comparative Map Data
Smpdl3a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22037,132,592 - 37,155,567 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2037,132,592 - 37,155,567 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2038,164,650 - 38,187,612 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02037,555,362 - 37,578,323 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02038,282,400 - 38,305,383 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02040,779,022 - 40,800,842 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2040,778,927 - 40,800,868 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02042,510,561 - 42,532,381 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42036,821,916 - 36,844,891 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12036,835,715 - 36,858,691 (+)NCBI
Celera2038,445,334 - 38,468,295 (+)NCBICelera
Cytogenetic Map20q12NCBI
SMPDL3A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386122,789,258 - 122,809,720 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6122,789,049 - 122,809,720 (+)EnsemblGRCh38hg38GRCh38
GRCh376123,110,403 - 123,130,865 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366123,152,123 - 123,172,564 (+)NCBINCBI36Build 36hg18NCBI36
Build 346123,152,122 - 123,172,561NCBI
Celera6123,854,285 - 123,875,174 (+)NCBICelera
Cytogenetic Map6q22.31NCBI
HuRef6120,686,989 - 120,707,854 (+)NCBIHuRef
CHM1_16123,373,788 - 123,394,652 (+)NCBICHM1_1
T2T-CHM13v2.06123,977,551 - 123,998,013 (+)NCBIT2T-CHM13v2.0
Smpdl3a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391057,670,640 - 57,687,926 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1057,670,431 - 57,687,926 (+)EnsemblGRCm39 Ensembl
GRCm381057,794,544 - 57,811,830 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1057,794,335 - 57,811,830 (+)EnsemblGRCm38mm10GRCm38
MGSCv371057,514,350 - 57,531,636 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361057,483,015 - 57,500,236 (+)NCBIMGSCv36mm8
Celera1058,611,953 - 58,629,235 (+)NCBICelera
Cytogenetic Map10B4NCBI
cM Map1029.25NCBI
Smpdl3a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554364,655,732 - 4,663,638 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554364,655,730 - 4,663,993 (+)NCBIChiLan1.0ChiLan1.0
SMPDL3A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan16140,682,622 - 140,708,208 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06120,577,885 - 120,600,371 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16124,701,094 - 124,723,469 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6124,701,089 - 124,726,484 (+)Ensemblpanpan1.1panPan2
SMPDL3A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1162,091,947 - 62,110,081 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl162,092,121 - 62,109,773 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha162,901,586 - 62,919,687 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0162,296,228 - 62,314,394 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl162,171,111 - 62,314,381 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1162,230,501 - 62,248,649 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0162,018,563 - 62,036,619 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0162,666,962 - 62,685,313 (+)NCBIUU_Cfam_GSD_1.0
Smpdl3a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946112,987,002 - 113,004,982 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049368021,070,683 - 1,088,614 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049368021,070,919 - 1,089,222 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMPDL3A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl139,848,648 - 39,868,731 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1139,848,641 - 39,869,184 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2144,076,443 - 44,094,659 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMPDL3A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11350,996,472 - 51,017,056 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1350,996,674 - 51,016,108 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604023,291,116 - 23,312,930 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smpdl3a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247988,409,960 - 8,418,575 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247988,410,048 - 8,422,900 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Smpdl3a
117 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:39
Count of miRNA genes:36
Interacting mature miRNAs:37
Transcripts:ENSRNOT00000001081
Prediction methods:Miranda, Rnahybrid
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
70158Bp60Blood pressure QTL 603arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)203161428444396023Rat


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 27 53 37 19 37 8 11 21 25 22 11 8
Low 16 4 4 4 53 10 19
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001081   ⟹   ENSRNOP00000001081
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2037,132,592 - 37,155,567 (+)Ensembl
Rnor_6.0 Ensembl2040,778,927 - 40,800,868 (+)Ensembl
RefSeq Acc Id: NM_001005539   ⟹   NP_001005539
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22037,132,592 - 37,155,567 (+)NCBI
Rnor_6.02040,779,022 - 40,800,842 (+)NCBI
Rnor_5.02042,510,561 - 42,532,381 (+)NCBI
RGSC_v3.42036,821,916 - 36,844,891 (+)RGD
Celera2038,445,334 - 38,468,295 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001005539 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH82029 (Get FASTA)   NCBI Sequence Viewer  
  EDL92885 (Get FASTA)   NCBI Sequence Viewer  
  EDL92886 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000001081
GenBank Protein Q641Z7 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001005539   ⟸   NM_001005539
- Peptide Label: precursor
- UniProtKB: Q641Z7 (UniProtKB/Swiss-Prot),   A6K4D6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001081   ⟸   ENSRNOT00000001081
Protein Domains
Calcineurin-like phosphoesterase   Sphingomyelin phosphodiesterase C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q641Z7-F1-model_v2 AlphaFold Q641Z7 1-445 view protein structure

Transcriptome

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

Promoters
RGD ID:13701638
Promoter ID:EPDNEW_R12162
Type:initiation region
Name:Smpdl3a_1
Description:sphingomyelin phosphodiesterase, acid-like 3A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02040,779,026 - 40,779,086EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359277 AgrOrtholog
BioCyc Gene G2FUF-3580 BioCyc
Ensembl Genes ENSRNOG00000000815 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000001081 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.60.21.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7130096 IMAGE-MGC_LOAD
InterPro ASM-like_Pdiesterase_prd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ASM_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ASMase/PPN1_MPP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Calcineurin-like_PHP_ApaH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Metallo-depent_PP-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:294422 UniProtKB/Swiss-Prot
MGC_CLONE MGC:95161 IMAGE-MGC_LOAD
NCBI Gene 294422 ENTREZGENE
PANTHER ACID SPHINGOMYELINASE-LIKE PHOSPHODIESTERASE 3A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SPHINGOMYELIN PHOSPHODIESTERASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam ASMase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Metallophos UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Smpdl3a PhenoGen
PIRSF ASM-like_PDE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000815 RatGTEx
Superfamily-SCOP Metallo-dependent phosphatases UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A6K4D6 ENTREZGENE, UniProtKB/TrEMBL
  A6K4D7_RAT UniProtKB/TrEMBL
  ASM3A_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Smpdl3a  sphingomyelin phosphodiesterase, acid-like 3A    acid sphingomyelinase-like phosphodiesterase 3A  Name updated 1299863 APPROVED
2005-07-29 Smpdl3a  acid sphingomyelinase-like phosphodiesterase 3A      Symbol and Name status set to provisional 70820 PROVISIONAL