Human Gene PTGDS (ENST00000371625.8) from GENCODE V44
  Description: Homo sapiens prostaglandin D2 synthase (PTGDS), mRNA. (from RefSeq NM_000954)
RefSeq Summary (NM_000954): The protein encoded by this gene is a glutathione-independent prostaglandin D synthase that catalyzes the conversion of prostaglandin H2 (PGH2) to postaglandin D2 (PGD2). PGD2 functions as a neuromodulator as well as a trophic factor in the central nervous system. PGD2 is also involved in smooth muscle contraction/relaxation and is a potent inhibitor of platelet aggregation. This gene is preferentially expressed in brain. Studies with transgenic mice overexpressing this gene suggest that this gene may be also involved in the regulation of non-rapid eye movement sleep. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000371625.8
Gencode Gene: ENSG00000107317.13
Transcript (Including UTRs)
   Position: hg38 chr9:136,977,504-136,981,742 Size: 4,239 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg38 chr9:136,977,579-136,980,855 Size: 3,277 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:136,977,504-136,981,742)mRNA (may differ from genome)Protein (190 aa)
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HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PTGDS_HUMAN
DESCRIPTION: RecName: Full=Prostaglandin-H2 D-isomerase; EC=5.3.99.2; AltName: Full=Beta-trace protein; AltName: Full=Cerebrin-28; AltName: Full=Glutathione-independent PGD synthase; AltName: Full=Lipocalin-type prostaglandin-D synthase; AltName: Full=Prostaglandin-D2 synthase; Short=PGD2 synthase; Short=PGDS; Short=PGDS2; Flags: Precursor;
FUNCTION: Catalyzes the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation. Involved in a variety of CNS functions, such as sedation, NREM sleep and PGE2-induced allodynia, and may have an anti-apoptotic role in oligodendrocytes. Binds small non-substrate lipophilic molecules, including biliverdin, bilirubin, retinal, retinoic acid and thyroid hormone, and may act as a scavenger for harmful hydrophopic molecules and as a secretory retinoid and thyroid hormone transporter. Possibly involved in development and maintenance of the blood-brain, blood-retina, blood-aqueous humor and blood-testis barrier. It is likely to play important roles in both maturation and maintenance of the central nervous system and male reproductive system.
CATALYTIC ACTIVITY: (5Z,13E,15S)-9-alpha,11-alpha-epidioxy-15- hydroxyprosta-5,13-dienoate = (5Z,13E,15S)-9-alpha,15-dihydroxy- 11-oxoprosta-5,13-dienoate.
SUBUNIT: Monomer.
SUBCELLULAR LOCATION: Rough endoplasmic reticulum. Nucleus membrane. Golgi apparatus. Cytoplasm, perinuclear region. Secreted. Note=Detected on rough endoplasmic reticulum of arachnoid and menigioma cells. Localized to the nuclear envelope, Golgi apparatus, secretory vesicles and spherical cytoplasmic structures in arachnoid trabecular cells, and to circular cytoplasmic structures in meningeal macrophages and perivascular microglial cells. In oligodendrocytes, localized to the rough endoplasmic reticulum and nuclear envelope. In retinal pigment epithelial cells, localized to distinct cytoplasmic domains including the perinuclear region. Also secreted.
TISSUE SPECIFICITY: Abundant in the brain and CNS, where it is expressed in tissues of the blood-brain barrier and secreted into the cerebro-spinal fluid. Abundantly expressed in the heart. In the male reproductive system, it is expressed in the testis, epididymis and prostate, and is secreted into the seminal fluid. Expressed in the eye and secreted into the aqueous humor. Lower levels detected in various tissue fluids such as serum, normal urine, ascitic fluid and tear fluid. Also found in a number of other organs including ovary, fimbriae of the fallopian tubes, kidney, leukocytes.
DEVELOPMENTAL STAGE: Expression in the amniotic fluid increases dramatically during weeks 12 to 25 of pregnancy. Levels decrease slowly after 25 weeks.
INDUCTION: By IL1B/interleukin-1 beta and thyroid hormone. Probably induced by dexamethasone, dihydrotestosterone (DHT), progesterone, retinoic acid and retinal. Repressed by the Notch- Hes signaling pathway.
DOMAIN: Forms a beta-barrel structure that accommodates hydrophobic ligands in its interior.
PTM: Both N-glycosylation recognition sites are almost quantitatively occupied by N-glycans of the biantennary complex type, with a considerable proportion of structures bearing a bisecting GlcNAc. N-glycan at Asn-78: dHex1Hex5HexNAc4. Agalacto structure as well as sialylated and nonsialylated oligosaccharides bearing alpha2-3- and/or alpha2-6-linked NeuNAc are present.
MISCELLANEOUS: It has been proposed that the urinary and serum levels may provide a sensitive indicator of renal damage in diabetes mellitus and hypertension. Elevated levels in the coronary circulation may also be associated with angina. Changes in charge and molecular weight microheterogeneity, due to modification of the N-linked oligosaccharides, may be associated with neurodegenerative disease and multiple sclerosis. Detected in meningioma but not in other brain tumors and may be considered a specific cell marker for meningioma. Expression levels in amniotic fluid are altered in abnormal pregnancies. Levels are lower in pregnancies with trisomic fetuses and fetuses with renal abnormalities.
SIMILARITY: Belongs to the calycin superfamily. Lipocalin family.
WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/ptgds/";

-  Primer design for this transcript
 

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-  MalaCards Disease Associations
  MalaCards Gene Search: PTGDS
Diseases sorted by gene-association score: egg allergy (22), normal pressure hydrocephalus (21), cerebrospinal fluid leak (18), macular holes (9), congenital disorder of glycosylation, type in (9), complete androgen insensitivity syndrome (9), orbital cyst (8), deafness, autosomal recessive 79 (8), optic nerve sheath meningioma (6), communicating hydrocephalus (6), deafness, autosomal recessive 33 (6), bacterial meningitis (6), demyelinating polyneuropathy (6), meningitis (3), hydrocephalus (2), cryptorchidism (2)

-  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: 1271.54 RPKM in Testis
Total median expression: 11188.22 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 -18.6075-0.248 Picture PostScript Text
3' UTR -43.60164-0.266 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
IPR012674 - Calycin
IPR011038 - Calycin-like
IPR002345 - Lipocalin
IPR022272 - Lipocalin_CS
IPR000566 - Lipocln_cytosolic_FA-bd_dom
IPR002972 - PstgldnD_synth

Pfam Domains:
PF00061 - Lipocalin / cytosolic fatty-acid binding protein family

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2WWP - X-ray MuPIT 3O19 - X-ray MuPIT 3O22 - X-ray MuPIT 3O2Y - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P41222
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-  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     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004667 prostaglandin-D synthase activity
GO:0005501 retinoid binding
GO:0005504 fatty acid binding
GO:0005515 protein binding
GO:0016853 isomerase activity
GO:0036094 small molecule binding

Biological Process:
GO:0001516 prostaglandin biosynthetic process
GO:0006629 lipid metabolic process
GO:0006631 fatty acid metabolic process
GO:0006633 fatty acid biosynthetic process
GO:0006693 prostaglandin metabolic process
GO:0019371 cyclooxygenase pathway
GO:0045187 regulation of circadian sleep/wake cycle, sleep

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005791 rough endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0031965 nuclear membrane
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BC041463 - Homo sapiens prostaglandin D2 synthase 21kDa (brain), mRNA (cDNA clone IMAGE:5211974).
HM005686 - Homo sapiens clone HTL-T-63n testis tissue sperm-binding protein Li 63n mRNA, complete cds.
HW061239 - JP 2012529430-A/114: METHODS FOR TREATING CHRONIC KIDNEY DISEASE.
JB252047 - Sequence 114 from Patent EP2440214.
LP764946 - Sequence 114 from Patent EP3276004.
AK075333 - Homo sapiens cDNA PSEC0009 fis, clone NT2RM1000731, highly similar to Prostaglandin-H2 D-isomerase precursor (EC 5.3.99.2).
M61900 - Homo sapiens prostaglandin D synthase precursor, mRNA, complete cds.
AK312817 - Homo sapiens cDNA, FLJ93254, Homo sapiens prostaglandin D2 synthase 21kDa (brain) (PTGDS), mRNA.
JD140528 - Sequence 121552 from Patent EP1572962.
BC005939 - Homo sapiens prostaglandin D2 synthase 21kDa (brain), mRNA (cDNA clone MGC:14559 IMAGE:4294999), complete cds.
AB464076 - Synthetic construct DNA, clone: pF1KB8266, Homo sapiens PTGDS gene for prostaglandin D2 synthase 21kDa, without stop codon, in Flexi system.
KJ897416 - Synthetic construct Homo sapiens clone ccsbBroadEn_06810 PTGDS gene, encodes complete protein.
AY026356 - Homo sapiens prostaglandin D synthase mRNA, complete cds.
BT019921 - Homo sapiens prostaglandin D2 synthase 21kDa (brain) mRNA, complete cds.
BT019922 - Homo sapiens prostaglandin D2 synthase 21kDa (brain) mRNA, complete cds.
JD482176 - Sequence 463200 from Patent EP1572962.
JD428109 - Sequence 409133 from Patent EP1572962.
JD521500 - Sequence 502524 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00590 - Arachidonic acid metabolism
hsa01100 - Metabolic pathways

BioCyc Knowledge Library
PWY66-374 - C20 prostanoid biosynthesis

Reactome (by CSHL, EBI, and GO)

Protein P41222 (Reactome details) participates in the following event(s):

R-HSA-2161620 PGH2 is isomerised to PGD2 by PTGDS
R-HSA-2162123 Synthesis of Prostaglandins (PG) and Thromboxanes (TX)
R-HSA-2142753 Arachidonic acid metabolism
R-HSA-8978868 Fatty acid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B2R727, ENST00000371625.1, ENST00000371625.2, ENST00000371625.3, ENST00000371625.4, ENST00000371625.5, ENST00000371625.6, ENST00000371625.7, NM_000954, P41222, PDS, PTGDS_HUMAN, Q5SQ10, Q7M4P3, Q9UC22, Q9UCC9, Q9UCD9, uc004cke.1, uc004cke.2, uc004cke.3, uc004cke.4, uc004cke.5
UCSC ID: ENST00000371625.8
RefSeq Accession: NM_000954
Protein: P41222 (aka PTGDS_HUMAN)
CCDS: CCDS7019.1

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