Human Gene S1PR4 (ENST00000246115.5_4) from GENCODE V47lift37
  Description: sphingosine-1-phosphate receptor 4 (from RefSeq NM_003775.4)
Gencode Transcript: ENST00000246115.5_4
Gencode Gene: ENSG00000125910.6_7
Transcript (Including UTRs)
   Position: hg19 chr19:3,178,767-3,180,330 Size: 1,564 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr19:3,178,791-3,179,945 Size: 1,155 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:3,178,767-3,180,330)mRNA (may differ from genome)Protein (384 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: S1PR4_HUMAN
DESCRIPTION: RecName: Full=Sphingosine 1-phosphate receptor 4; Short=S1P receptor 4; Short=S1P4; AltName: Full=Endothelial differentiation G-protein coupled receptor 6; AltName: Full=Sphingosine 1-phosphate receptor Edg-6; Short=S1P receptor Edg-6;
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. May be involved in cell migration processes that are specific for lymphocytes.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Specifically expressed in fetal and adult lymphoid and hematopoietic tissue as well as in lung. Considerable level of expression in adult and fetal spleen as well as adult peripheral leukocytes and lung. Lower expression in adult thymus, lymph node, bone marrow, and appendix as well as in fetal liver, thymus, and lung.
SIMILARITY: Belongs to the G-protein coupled receptor 1 family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 123.90 RPKM in Whole Blood
Total median expression: 238.77 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -6.5024-0.271 Picture PostScript Text
3' UTR -175.90385-0.457 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
IPR004064 - EDG6_rcpt
IPR017452 - GPCR_Rhodpsn_supfam
IPR004061 - S1P_rcpt

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

SCOP Domains:
81321 - Family A G protein-coupled receptor-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2DCO - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O95977
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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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004871 signal transducer activity
GO:0004930 G-protein coupled receptor activity
GO:0008289 lipid binding
GO:0038036 sphingosine-1-phosphate receptor activity

Biological Process:
GO:0003376 sphingosine-1-phosphate signaling pathway
GO:0006955 immune response
GO:0007165 signal transduction
GO:0007186 G-protein coupled receptor signaling pathway
GO:0007189 adenylate cyclase-activating G-protein coupled receptor signaling pathway
GO:0007202 activation of phospholipase C activity
GO:0007204 positive regulation of cytosolic calcium ion concentration

Cellular Component:
GO:0005739 mitochondrion
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
  BC014970 - Homo sapiens sphingosine-1-phosphate receptor 4, mRNA (cDNA clone MGC:23096 IMAGE:4849349), complete cds.
AJ000479 - Homo sapiens mRNA for putative G-protein coupled receptor, EDG6.
KJ892597 - Synthetic construct Homo sapiens clone ccsbBroadEn_01991 S1PR4 gene, encodes complete protein.
FJ200495 - Homo sapiens sphingosine-1-phosphate receptor 4 variant mRNA, complete cds.
JD025807 - Sequence 6831 from Patent EP1572962.
JD030635 - Sequence 11659 from Patent EP1572962.
JD020474 - Sequence 1498 from Patent EP1572962.
JD031236 - Sequence 12260 from Patent EP1572962.
JD219229 - Sequence 200253 from Patent EP1572962.
JD409669 - Sequence 390693 from Patent EP1572962.
JD119711 - Sequence 100735 from Patent EP1572962.
JD545684 - Sequence 526708 from Patent EP1572962.
JD121235 - Sequence 102259 from Patent EP1572962.
JD394938 - Sequence 375962 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O95977 (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: D6W612, EDG6, ENST00000246115.1, ENST00000246115.2, ENST00000246115.3, ENST00000246115.4, NM_003775, O95977, S1PR4_HUMAN, uc317esu.1, uc317esu.2
UCSC ID: ENST00000246115.5_4
RefSeq Accession: NM_003775.4
Protein: O95977 (aka S1PR4_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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