Smpd3 (sphingomyelin phosphodiesterase 3) - Rat Genome Database

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Gene: Smpd3 (sphingomyelin phosphodiesterase 3) Chinchilla lanigera
Analyze
Symbol: Smpd3
Name: sphingomyelin phosphodiesterase 3
RGD ID: 8980809
Description: ENCODES a protein that exhibits identical protein binding (ortholog); neutral sphingomyelin phosphodiesterase activity (ortholog); phosphatidic acid binding (ortholog); INVOLVED IN artery smooth muscle contraction (ortholog); BMP signaling pathway (ortholog); bone development (ortholog); PARTICIPATES IN ceramide signaling pathway; ASSOCIATED WITH autosomal dominant dyskeratosis congenita 6 (ortholog); chronic obstructive pulmonary disease (ortholog); genetic disease (ortholog); FOUND IN Golgi apparatus (ortholog); Golgi cis cisterna (ortholog); plasma membrane (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: sphingomyelin phosphodiesterase 3, neutral membrane (neutral sphingomyelinase II)
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554848,272,572 - 8,298,144 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554848,207,686 - 8,298,164 (+)NCBIChiLan1.0ChiLan1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
artery smooth muscle contraction  (ISO)
BMP signaling pathway  (ISO)
bone development  (ISO)
bone growth  (ISO)
bone mineralization  (ISO)
cartilage development  (ISO)
cellular response to hydrogen peroxide  (ISO)
cellular response to interleukin-1  (ISO)
cellular response to magnesium ion  (ISO)
cellular response to oxidised low-density lipoprotein particle stimulus  (ISO)
cellular response to peptide  (ISO)
cellular response to reactive oxygen species  (ISO)
cellular response to redox state  (ISO)
cellular response to tumor necrosis factor  (ISO)
ceramide metabolic process  (ISO)
chondrocyte development  (ISO)
chondrocyte development involved in endochondral bone morphogenesis  (ISO)
collagen metabolic process  (ISO)
dentinogenesis  (ISO)
DNA biosynthetic process  (ISO)
dopamine uptake  (ISO)
endochondral ossification  (ISO)
extracellular matrix assembly  (ISO)
G1 to G0 transition  (ISO)
hematopoietic progenitor cell differentiation  (ISO)
lung alveolus development  (ISO)
lung development  (ISO)
mitotic nuclear division  (ISO)
multicellular organism growth  (ISO)
negative regulation of cytosolic calcium ion concentration  (ISO)
negative regulation of hyaluronan biosynthetic process  (ISO)
negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction  (ISO)
ossification  (ISO)
peptide hormone secretion  (ISO)
platelet-derived growth factor receptor signaling pathway  (ISO)
polysaccharide transport  (ISO)
positive regulation of ceramide biosynthetic process  (ISO)
positive regulation of exosomal secretion  (ISO)
positive regulation of mitotic nuclear division  (ISO)
positive regulation of nitric oxide biosynthetic process  (ISO)
positive regulation of non-canonical NF-kappaB signal transduction  (ISO)
positive regulation of smooth muscle cell proliferation  (ISO)
regulation of cartilage development  (ISO)
regulation of hyaluronan biosynthetic process  (ISO)
regulation of leukocyte migration  (ISO)
regulation of protein phosphorylation  (ISO)
respiratory system development  (ISO)
signal transduction  (ISO)
skeletal system development  (ISO)
sphingolipid mediated signaling pathway  (ISO)
sphingolipid metabolic process  (ISO)
sphingomyelin catabolic process  (ISO)
sphingomyelin metabolic process  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Smpd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554848,272,572 - 8,298,144 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554848,207,686 - 8,298,164 (+)NCBIChiLan1.0ChiLan1.0
SMPD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381668,358,327 - 68,448,508 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1668,358,327 - 68,448,508 (-)EnsemblGRCh38hg38GRCh38
GRCh371668,392,230 - 68,482,411 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361666,949,731 - 67,039,905 (-)NCBINCBI36Build 36hg18NCBI36
Build 341666,949,732 - 67,039,905NCBI
Celera1652,900,779 - 52,990,952 (-)NCBICelera
Cytogenetic Map16q22.1NCBI
HuRef1654,265,453 - 54,355,875 (-)NCBIHuRef
CHM1_11669,800,294 - 69,890,458 (-)NCBICHM1_1
T2T-CHM13v2.01674,154,167 - 74,244,330 (-)NCBIT2T-CHM13v2.0
Smpd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398106,979,180 - 107,064,597 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8106,979,180 - 107,064,620 (-)EnsemblGRCm39 Ensembl
GRCm388106,252,548 - 106,337,965 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8106,252,548 - 106,337,988 (-)EnsemblGRCm38mm10GRCm38
MGSCv378108,776,448 - 108,861,888 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368109,141,677 - 109,227,117 (-)NCBIMGSCv36mm8
Celera8110,480,448 - 110,565,952 (-)NCBICelera
Cytogenetic Map8D3NCBI
cM Map853.12NCBI
Smpd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21934,162,337 - 34,245,786 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1934,162,341 - 34,245,749 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1940,977,903 - 41,061,312 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01941,631,214 - 41,714,614 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01943,930,363 - 44,013,762 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01938,237,963 - 38,321,572 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1938,237,965 - 38,321,528 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01949,107,658 - 49,191,221 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41936,112,166 - 36,195,564 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11936,117,046 - 36,200,445 (-)NCBI
Celera1933,589,416 - 33,672,639 (-)NCBICelera
RH 3.4 Map19304.3RGD
Cytogenetic Map19q12NCBI
SMPD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan11683,816,346 - 83,906,775 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01648,734,664 - 48,825,241 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11668,129,034 - 68,219,625 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1668,131,905 - 68,142,871 (-)Ensemblpanpan1.1panPan2
SMPD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1581,089,657 - 81,172,173 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl581,142,888 - 81,172,189 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha581,080,156 - 81,162,625 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0581,524,565 - 81,607,194 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl581,553,588 - 81,606,670 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1581,351,425 - 81,433,990 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0581,034,510 - 81,116,929 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0581,675,446 - 81,757,898 (+)NCBIUU_Cfam_GSD_1.0
Smpd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934940,833,996 - 40,920,586 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647518,671,428 - 18,755,208 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647518,667,563 - 18,755,132 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMPD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl628,938,290 - 29,025,357 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1628,938,287 - 29,025,397 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2626,117,915 - 26,204,889 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMPD3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1558,965,965 - 59,057,823 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl559,029,093 - 59,059,577 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604721,702,920 - 21,795,181 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smpd3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474617,920,835 - 17,948,468 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474617,857,779 - 17,948,469 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


RefSeq Acc Id: ENSCLAT00000006507   ⟹   ENSCLAP00000006401
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_0049554848,272,572 - 8,298,144 (+)Ensembl
RefSeq Acc Id: XM_005403580   ⟹   XP_005403637
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554848,207,686 - 8,298,164 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013503919   ⟹   XP_013359373
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554848,272,572 - 8,298,164 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013503920   ⟹   XP_013359374
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554848,270,625 - 8,298,164 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005403637 (Get FASTA)   NCBI Sequence Viewer  
  XP_013359373 (Get FASTA)   NCBI Sequence Viewer  
  XP_013359374 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCLAP00000006401
  ENSCLAP00000006401.1
RefSeq Acc Id: XP_005403637   ⟸   XM_005403580
- UniProtKB: A0A8C2UXW2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013359374   ⟸   XM_013503920
- UniProtKB: A0A8C2UXW2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013359373   ⟸   XM_013503919
- UniProtKB: A0A8C2UXW2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCLAP00000006401   ⟸   ENSCLAT00000006507

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000004522 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000006507 ENTREZGENE
  ENSCLAT00000006507.1 UniProtKB/TrEMBL
Gene3D-CATH 3.60.10.10 UniProtKB/TrEMBL
InterPro Endo/exonu/phosph_ase_sf UniProtKB/TrEMBL
  Endo/exonuclease/phosphatase UniProtKB/TrEMBL
  Sph/SMPD2-like UniProtKB/TrEMBL
  Sphingomyelinase/PLipase_C UniProtKB/TrEMBL
NCBI Gene Smpd3 ENTREZGENE
PANTHER SPHINGOMYELIN PHOSPHODIESTERASE 3 UniProtKB/TrEMBL
  SPHINGOMYELINASE FAMILY MEMBER UniProtKB/TrEMBL
Pfam Exo_endo_phos UniProtKB/TrEMBL
Superfamily-SCOP SSF56219 UniProtKB/TrEMBL
UniProt A0A8C2UXW2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-08-16 Smpd3  sphingomyelin phosphodiesterase 3    sphingomyelin phosphodiesterase 3, neutral membrane (neutral sphingomyelinase II)  Symbol and/or name change 5135510 APPROVED