Human Gene S1PR3 (ENST00000358157.3) from GENCODE V44
  Description: Homo sapiens sphingosine-1-phosphate receptor 3 (S1PR3), mRNA. (from RefSeq NM_005226)
RefSeq Summary (NM_005226): This gene encodes a member of the EDG family of receptors, which are G protein-coupled receptors. This protein has been identified as a functional receptor for sphingosine 1-phosphate and likely contributes to the regulation of angiogenesis and vascular endothelial cell function. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000358157.3
Gencode Gene: ENSG00000213694.7
Transcript (Including UTRs)
   Position: hg38 chr9:88,991,468-89,005,155 Size: 13,688 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg38 chr9:89,001,201-89,002,337 Size: 1,137 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr9:88,991,468-89,005,155)mRNA (may differ from genome)Protein (378 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Sphingosine 1-phosphate receptor 3; Short=S1P receptor 3; Short=S1P3; AltName: Full=Endothelial differentiation G-protein coupled receptor 3; AltName: Full=Sphingosine 1-phosphate receptor Edg-3; Short=S1P receptor Edg-3;
FUNCTION: Receptor for the lysosphingolipid sphingosine 1- phosphate (S1P). S1P is a bioactive lysophospholipid that elicits diverse physiological effect on most types of cells and tissues. When expressed in rat HTC4 hepatoma cells, is capable of mediating S1P-induced cell proliferation and suppression of apoptosis.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Expressed in all tissues, but most abundantly in heart, placenta, kidney, and liver.
SIMILARITY: Belongs to the G-protein coupled receptor 1 family.

-  Primer design for this transcript

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 33.30 RPKM in Esophagus - Muscularis
Total median expression: 283.49 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -149.50375-0.399 Picture PostScript Text
3' UTR -801.142818-0.284 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000276 - 7TM_GPCR_Rhodpsn
IPR004062 - EDG3_rcpt
IPR017452 - GPCR_Rhodpsn_supfam
IPR004061 - S1P_rcpt

Pfam Domains:
PF00001 - 7 transmembrane receptor (rhodopsin family)

ModBase Predicted Comparative 3D Structure on Q99500
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004871 signal transducer activity
GO:0004930 G-protein coupled receptor activity
GO:0005178 integrin binding
GO:0005515 protein binding
GO:0008289 lipid binding
GO:0038036 sphingosine-1-phosphate receptor activity

Biological Process:
GO:0001816 cytokine production
GO:0003376 sphingosine-1-phosphate signaling pathway
GO:0006954 inflammatory response
GO:0007165 signal transduction
GO:0007186 G-protein coupled receptor signaling pathway
GO:0007193 adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0007219 Notch signaling pathway
GO:0008284 positive regulation of cell proliferation
GO:0009653 anatomical structure morphogenesis
GO:0032651 regulation of interleukin-1 beta production
GO:1903141 negative regulation of establishment of endothelial barrier

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane

-  Descriptions from all associated GenBank mRNAs
  LF209790 - JP 2014500723-A/17293: Polycomb-Associated Non-Coding RNAs.
MA445367 - JP 2018138019-A/17293: Polycomb-Associated Non-Coding RNAs.
AK312798 - Homo sapiens cDNA, FLJ93220, highly similar to Homo sapiens endothelial differentiation, sphingolipidG-protein-coupled receptor, 3 (EDG3), mRNA.
BC060827 - Homo sapiens sphingosine-1-phosphate receptor 3, mRNA (cDNA clone MGC:71696 IMAGE:30342032), complete cds.
AL832194 - Homo sapiens mRNA; cDNA DKFZp686C042 (from clone DKFZp686C042).
AK094842 - Homo sapiens cDNA FLJ37523 fis, clone BRCAN2006401.
AK127854 - Homo sapiens cDNA FLJ45957 fis, clone PLACE7011269.
BC144432 - Homo sapiens chromosome 9 open reading frame 47, mRNA (cDNA clone MGC:177970 IMAGE:9052953), complete cds.
BC136895 - Homo sapiens chromosome 9 open reading frame 47, mRNA (cDNA clone MGC:168509 IMAGE:9020886), complete cds.
LF212528 - JP 2014500723-A/20031: Polycomb-Associated Non-Coding RNAs.
MA448105 - JP 2018138019-A/20031: Polycomb-Associated Non-Coding RNAs.
AY333281 - Homo sapiens chromosome 9 unknown mRNA.
LF331631 - JP 2014500723-A/139134: Polycomb-Associated Non-Coding RNAs.
MA567208 - JP 2018138019-A/139134: Polycomb-Associated Non-Coding RNAs.
AB385149 - Synthetic construct DNA, clone: pF1KB5664, Homo sapiens EDG3 gene for sphingosine 1-phosphate receptor Edg-3, complete cds, without stop codon, in Flexi system.
AF022139 - Homo sapiens lysosphingolipid receptor (EDG3) mRNA, partial cds.
KJ891084 - Synthetic construct Homo sapiens clone ccsbBroadEn_00478 S1PR3 gene, encodes complete protein.
BC069579 - Homo sapiens sphingosine-1-phosphate receptor 3, mRNA (cDNA clone MGC:97186 IMAGE:7262431), complete cds.
LF331632 - JP 2014500723-A/139135: Polycomb-Associated Non-Coding RNAs.
MA567209 - JP 2018138019-A/139135: Polycomb-Associated Non-Coding RNAs.
LF331633 - JP 2014500723-A/139136: Polycomb-Associated Non-Coding RNAs.
MA567210 - JP 2018138019-A/139136: Polycomb-Associated Non-Coding RNAs.
LF331634 - JP 2014500723-A/139137: Polycomb-Associated Non-Coding RNAs.
MA567211 - JP 2018138019-A/139137: Polycomb-Associated Non-Coding RNAs.
JD182948 - Sequence 163972 from Patent EP1572962.
JD410707 - Sequence 391731 from Patent EP1572962.
JD237169 - Sequence 218193 from Patent EP1572962.
JD310892 - Sequence 291916 from Patent EP1572962.
JD111650 - Sequence 92674 from Patent EP1572962.
JD469230 - Sequence 450254 from Patent EP1572962.
JD298873 - Sequence 279897 from Patent EP1572962.
JD470260 - Sequence 451284 from Patent EP1572962.
JD435253 - Sequence 416277 from Patent EP1572962.
JD496494 - Sequence 477518 from Patent EP1572962.
JD491334 - Sequence 472358 from Patent EP1572962.
LF331635 - JP 2014500723-A/139138: Polycomb-Associated Non-Coding RNAs.
MA567212 - JP 2018138019-A/139138: Polycomb-Associated Non-Coding RNAs.
JD383278 - Sequence 364302 from Patent EP1572962.
JD087629 - Sequence 68653 from Patent EP1572962.
JD453479 - Sequence 434503 from Patent EP1572962.
JD275380 - Sequence 256404 from Patent EP1572962.
JD513013 - Sequence 494037 from Patent EP1572962.
LF331636 - JP 2014500723-A/139139: Polycomb-Associated Non-Coding RNAs.
MA567213 - JP 2018138019-A/139139: Polycomb-Associated Non-Coding RNAs.
JD082879 - Sequence 63903 from Patent EP1572962.
JD303721 - Sequence 284745 from Patent EP1572962.
JD268313 - Sequence 249337 from Patent EP1572962.
LF331637 - JP 2014500723-A/139140: Polycomb-Associated Non-Coding RNAs.
MA567214 - JP 2018138019-A/139140: Polycomb-Associated Non-Coding RNAs.
JD301563 - Sequence 282587 from Patent EP1572962.
JD039252 - Sequence 20276 from Patent EP1572962.
JD421963 - Sequence 402987 from Patent EP1572962.
JD446440 - Sequence 427464 from Patent EP1572962.
JD236217 - Sequence 217241 from Patent EP1572962.
JD566225 - Sequence 547249 from Patent EP1572962.
JD410083 - Sequence 391107 from Patent EP1572962.
JD481608 - Sequence 462632 from Patent EP1572962.
JD472567 - Sequence 453591 from Patent EP1572962.
JD536073 - Sequence 517097 from Patent EP1572962.
JD096416 - Sequence 77440 from Patent EP1572962.
JD308886 - Sequence 289910 from Patent EP1572962.
JD175849 - Sequence 156873 from Patent EP1572962.
JD332257 - Sequence 313281 from Patent EP1572962.
JD332258 - Sequence 313282 from Patent EP1572962.
JD531524 - Sequence 512548 from Patent EP1572962.
JD332259 - Sequence 313283 from Patent EP1572962.
JD366669 - Sequence 347693 from Patent EP1572962.
JD517909 - Sequence 498933 from Patent EP1572962.
JD304288 - Sequence 285312 from Patent EP1572962.
JD553124 - Sequence 534148 from Patent EP1572962.
JD226830 - Sequence 207854 from Patent EP1572962.
JD258122 - Sequence 239146 from Patent EP1572962.
AK129921 - Homo sapiens cDNA FLJ26411 fis, clone HRT09683.
JD040254 - Sequence 21278 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04080 - Neuroactive ligand-receptor interaction

Reactome (by CSHL, EBI, and GO)

Protein Q99500 (Reactome details) participates in the following event(s):

R-HSA-419428 S1P-binding receptors bind S1P
R-HSA-749454 The Ligand:GPCR:Gi complex dissociates
R-HSA-749456 Liganded Gi-activating GPCRs bind inactive heterotrimeric G-protein Gi
R-HSA-380073 Liganded Gi-activating GPCR acts as a GEF for Gi
R-HSA-419408 Lysosphingolipid and LPA receptors
R-HSA-418594 G alpha (i) signalling events
R-HSA-373076 Class A/1 (Rhodopsin-like receptors)
R-HSA-388396 GPCR downstream signalling
R-HSA-500792 GPCR ligand binding
R-HSA-372790 Signaling by GPCR
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: EDG3, ENST00000358157.1, ENST00000358157.2, NM_005226, Q5SQD8, Q7Z5I2, Q99500, S1PR3_HUMAN, uc004aqe.1, uc004aqe.2, uc004aqe.3, uc004aqe.4, uc004aqe.5, uc004aqe.6
UCSC ID: ENST00000358157.3
RefSeq Accession: NM_005226
Protein: Q99500 (aka S1PR3_HUMAN)
CCDS: CCDS6680.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.