Homo sapiens complex locus PTGS2, encoding prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase).
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SUMMARY back to top
RefSeq summary
[PTGS2] Prostaglandin-endoperoxide synthase (PTGS), also known as cyclooxygenase, is the key enzyme in prostaglandin biosynthesis, and acts both as a dioxygenase and as a peroxidase. There are two isozymes of PTGS: a constitutive PTGS1 and an inducible PTGS2, which differ in their regulation of expression and tissue distribution. This gene encodes the inducible isozyme. It is regulated by specific stimulatory events, suggesting that it is responsible for the prostanoid biosynthesis involved in inflammation and mitogenesis. [provided by RefSeq].

RefSeq annotates one representative transcript (NM included in AceView variant.a), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 5 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus is complex: it appears to produce several proteins with no sequence overlap.
Expression: According to AceView, this gene is expressed at high level, 1.7 times the average gene in this release. The sequence of this gene is defined by 192 GenBank accessions from 179 cDNA clones, some from coronary artery (seen 15 times), prostate (13), lung (12), islets of langerhans (6), pancreas (6), placenta (6), breast carcinoma (5) and 63 other tissues. We annotate structural defects or features in 24 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 11 distinct gt-ag introns. Transcription produces 8 different mRNAs, 5 alternatively spliced variants and 3 unspliced forms. There are 2 probable alternative promotors, 2 non overlapping alternative last exons and 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, overlapping exons with different boundaries, splicing versus retention of one intron.
Note that mRNA .cAug10 was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
Function: There are 1165 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Adenoma; Aggressive Periodontitis; Alzheimer Disease; Angina Pectoris; Aortic Aneurysm, Abdominal; Asthma; Barrett Esophagus; Bone Marrow Neoplasms; Brain Diseases and 56 others), proposed to participate in pathways (Arachidonic acid metabolism, Leishmaniasis, Mechanism of Acetaminophen Activity and Toxicity, Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa(alpha), Pathways in cancer, Small cell lung cancer, VEGF signaling pathway) and processes (anagen, bone mineralization, decidualization, embryo implantation, fatty acid biosynthetic process, memory, negative regulation of calcium ion transport, negative regulation of cell proliferation, negative regulation of synaptic transmission, dopaminergic, ovulation, oxidation reduction, positive regulation of apoptosis, positive regulation of fever, positive regulation of prostaglandin biosynthetic process, positive regulation of smooth muscle cell proliferation, positive regulation of smooth muscle contraction, positive regulation of synaptic plasticity, positive regulation of synaptic transmission, glutamatergic, positive regulation of vasoconstriction, regulation of blood pressure, regulation of cell cycle, response to cytokine stimulus, response to drug, response to estradiol stimulus, response to fructose stimulus, response to glucocorticoid stimulus, response to lipopolysaccharide, response to manganese ion, response to organic cyclic substance, response to organic nitrogen, response to oxidative stress, response to vitamin D). Proteins are expected to have molecular functions (heme binding, lipid binding, metal ion binding, oxidoreductase activity, oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen, protein binding) and to localize in various compartments (extracellular space, membrane, caveola, cytoplasm and 6 others). Putative protein interactors have been described (CAV2ANDCAV1, COPS3, COPS5ANDLRRC67, COPS7A, CUL1, CUL4A, LY6G6EANDBAT5, NUCB1, PSMC5, PSMD1, PTGS2, TP53, XPNPEP3ANDRBX1, ZFP36).
Protein coding potential: 5 spliced and the unspliced mRNAs putatively encode good proteins, altogether 6 different isoforms (4 complete, 2 COOH complete), some containing domains Animal haem peroxidase, EGF-like domain [Pfam], some transmembrane domains [Psort2]; 2 of the 4 complete proteins appear to be secreted. The remaining 2 mRNA variants (2 unspliced) appear not to encode good proteins. Finally proteins from this gene may be modulated by phosphorylation, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 1, links to other databases and other names
Map: This gene PTGS2 maps on chromosome 1, at 1q25.2-q25.3 according to Entrez Gene. In AceView, it covers 8.64 kb, from 186649554 to 186640919 (NCBI 37, August 2010), on the reverse strand.
Links to: , manual annotations from GAD, KEGG_00590, KEGG_04370, KEGG_05140, KEGG_05200, KEGG_05222, PhosphoSite, the SNP view, gene overviews from Entrez Gene 5743, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as PTGS2, COX2, COX-2, PHS-2, PGG/HS, PGHS-2, hCox-2 or GRIPGHS, LOC5743. It has been described as prostaglandin G/H synthase 2, PHS II, PGH synthase 2, cyclooxygenase-2, cyclooxygenase 2b, prostaglandin H2 synthase 2, prostaglandin G/H synthase and cyclooxygenase.
EC number: This gene encodes protein number: 1.14.99.1.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Ptgs2 (e=0.0).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene 4I514 (e=6 10-19), which may contain interesting functional annotation.
The closest A.thaliana gene, according to BlastP, is the AceView gene AT1G73680 (e=2 10-12), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
PTGS2 Gene expression in 15 primates, 16 tissues, from the NHPRTR project in sFPKM BAB SkeletalMuscle WholeBlood CHP Kidney Liver Lung Spleen CMC CMM Cerebellum HUM Brain Colon Heart LymphNode Ovary Testis JMI BoneMarrow MLM OWL PTM RMC RMI Pituitary SQM Thymus MST SMY RTL 0.14 4.71 6.21 2.05 26.6 7.64 4.71 7.64 10.8 5.40 14.3 1.35 3.33 0.42 122 9.41 0.36 1.26 2.90 40.3 3.10 5.79 0.36 1.66 16.4 10.1 8.78 2.35 0.51 16.4 0.48 0.17 0.21 5.04 0.16 5.79 1.45 0.14 0.68 0.24 1.26 1.91 6.65 1.55 1.55 0.17 7.13 2.05 10.8 0.18 2.52 7.64 4.39 1.26 86.5 1.10 1.35 1.91 4.71 2.90 6.21 1.10 0.19 1.78 2.19 0.13 0.07 2.90 0.72 0.27 1.02 4.71 4.10 2.70 1.35 0.06 0.78 1.26 0.45 0.72 1.66 0.48 0.26 5.79 1.02 3.33 0.26 1.55 0.39 2.19 0.36 0.07 2.35 3.10 0.19 2.35 0.78 2.90 0.22 0.96 0.68 0.27 5.04 1.66 0.45 2.70 1.26 0.72 2.90 0.39 0.13 3.57 2.70 4.39 0.16 1.26 0.15 6.21 0.78 0.36 0.45 0.14 1.78 1.91 1.35 0.96 2.70 1.91 0.83 122 0.96 0.10 3.82 3.82 5.40 0.22 1.55 0.42 5.04 0.08 1.55 1.66 1.66 0.34 0.89 0.59 1.66 2.52 6.65 1.91 20.2 Expression quantiles None Weak 1 2 3 4 5 6 7 8 10 20 This gene All genes log2 distributions RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
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          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene PTGS2 5' 3' encoded on minus strand of chromosome 1 from 186,649,554 to 186,640,919 4941 7848 9411 9703 8191 8000 9749 a [NM] 4941 7848 9411 12 8191 8000 9749 b 4941 7848 9411 9703 8191 8000 9749 c 4941 7848 34 f d e-u g-u h-u 1 2kb 0 184 bp exon 184 bp exon 800 bp [gt-ag] intron 56 GenBank accessions 4885 RNA-seq supporting reads 889 UHR pooled cells 373 Brain 1795 Blood 1815 Neuroblastoma 13 Other (also 465 Primates bodymap) 117 bp exon 120 bp [gt-ag] intron 57 GenBank accessions 7791 RNA-seq supporting reads 986 UHR pooled cells 390 Brain 4648 Blood 1716 Neuroblastoma 51 Other (also 1884 Primates bodymap) 144 bp exon 653 bp [gt-ag] intron 55 GenBank accessions 9356 RNA-seq supporting reads 1483 UHR pooled cells 560 Brain 5021 Blood 2215 Neuroblastoma 77 Other (also 1851 Primates bodymap) 144 bp exon 430 bp [gt-ag] intron 24 GenBank accessions 9679 RNA-seq supporting reads 1234 UHR pooled cells 463 Brain 6008 Blood 1910 Neuroblastoma 64 Other (also 1431 Primates bodymap) 182 bp exon 732 bp [gt-ag] intron 21 GenBank accessions 8170 RNA-seq supporting reads 1051 UHR pooled cells 440 Brain 4881 Blood 1722 Neuroblastoma 76 Other (also 1873 Primates bodymap) 84 bp exon 119 bp [gt-ag] intron 18 GenBank accessions 7982 RNA-seq supporting reads 1272 UHR pooled cells 502 Brain 4316 Blood 1780 Neuroblastoma 112 Other (also 1748 Primates bodymap) 247 bp exon 282 bp [gt-ag] intron 17 GenBank accessions 11067 RNA-seq supporting reads 1866 UHR pooled cells 751 Brain 5534 Blood 2765 Neuroblastoma 151 Other (also 2397 Primates bodymap) 287 bp exon 501 bp [gt-ag] intron 19 GenBank accessions 9730 RNA-seq supporting reads 1786 UHR pooled cells 697 Brain 4882 Blood 2277 Neuroblastoma 88 Other (also 2725 Primates bodymap) 148 bp exon 486 bp [gt-ag] intron 20 GenBank accessions 9840 RNA-seq supporting reads 1726 UHR pooled cells 606 Brain 5241 Blood 2170 Neuroblastoma 97 Other (also 1739 Primates bodymap) 2950 bp exon 112 accessions, NM_000963.2 some from coronary artery (seen 11 times) islets of langerhans (5) lung (5), pancreas (5) prostate (5) capped 5' end, 37 accessions Validated 3' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 3 accessions 2950 bp exon 52 bp exon 800 bp [gt-ag] intron 56 GenBank accessions 4885 RNA-seq supporting reads 889 UHR pooled cells 373 Brain 1795 Blood 1815 Neuroblastoma 13 Other (also 465 Primates bodymap) 117 bp exon 120 bp [gt-ag] intron 57 GenBank accessions 7791 RNA-seq supporting reads 986 UHR pooled cells 390 Brain 4648 Blood 1716 Neuroblastoma 51 Other (also 1884 Primates bodymap) 144 bp exon 653 bp [gt-ag] intron 55 GenBank accessions 9356 RNA-seq supporting reads 1483 UHR pooled cells 560 Brain 5021 Blood 2215 Neuroblastoma 77 Other (also 1851 Primates bodymap) 144 bp exon 144 bp exon 540 bp [gt-ag] intron 1 GenBank accession 11 RNA-seq supporting reads 10 Blood 1 Neuroblastoma (also 1 Primates bodymap) 72 bp exon 732 bp [gt-ag] intron 21 GenBank accessions 8170 RNA-seq supporting reads 1051 UHR pooled cells 440 Brain 4881 Blood 1722 Neuroblastoma 76 Other (also 1873 Primates bodymap) 84 bp exon 119 bp [gt-ag] intron 18 GenBank accessions 7982 RNA-seq supporting reads 1272 UHR pooled cells 502 Brain 4316 Blood 1780 Neuroblastoma 112 Other (also 1748 Primates bodymap) 247 bp exon 282 bp [gt-ag] intron 17 GenBank accessions 11067 RNA-seq supporting reads 1866 UHR pooled cells 751 Brain 5534 Blood 2765 Neuroblastoma 151 Other (also 2397 Primates bodymap) 287 bp exon 501 bp [gt-ag] intron 19 GenBank accessions 9730 RNA-seq supporting reads 1786 UHR pooled cells 697 Brain 4882 Blood 2277 Neuroblastoma 88 Other (also 2725 Primates bodymap) 148 bp exon 486 bp [gt-ag] intron 20 GenBank accessions 9840 RNA-seq supporting reads 1726 UHR pooled cells 606 Brain 5241 Blood 2170 Neuroblastoma 97 Other (also 1739 Primates bodymap) 1 accession from peripheral blood Validated 3' end, 1 accession 410 bp exon 156 bp exon 156 bp exon 800 bp [gt-ag] intron 56 GenBank accessions 4885 RNA-seq supporting reads 889 UHR pooled cells 373 Brain 1795 Blood 1815 Neuroblastoma 13 Other (also 465 Primates bodymap) 117 bp exon 120 bp [gt-ag] intron 57 GenBank accessions 7791 RNA-seq supporting reads 986 UHR pooled cells 390 Brain 4648 Blood 1716 Neuroblastoma 51 Other (also 1884 Primates bodymap) 144 bp exon 653 bp [gt-ag] intron 55 GenBank accessions 9356 RNA-seq supporting reads 1483 UHR pooled cells 560 Brain 5021 Blood 2215 Neuroblastoma 77 Other (also 1851 Primates bodymap) 144 bp exon 430 bp [gt-ag] intron 24 GenBank accessions 9679 RNA-seq supporting reads 1234 UHR pooled cells 463 Brain 6008 Blood 1910 Neuroblastoma 64 Other (also 1431 Primates bodymap) 182 bp exon 732 bp [gt-ag] intron 21 GenBank accessions 8170 RNA-seq supporting reads 1051 UHR pooled cells 440 Brain 4881 Blood 1722 Neuroblastoma 76 Other (also 1873 Primates bodymap) 84 bp exon 119 bp [gt-ag] intron 18 GenBank accessions 7982 RNA-seq supporting reads 1272 UHR pooled cells 502 Brain 4316 Blood 1780 Neuroblastoma 112 Other (also 1748 Primates bodymap) 816 bp exon 816 bp exon 501 bp [gt-ag] intron 19 GenBank accessions 9730 RNA-seq supporting reads 1786 UHR pooled cells 697 Brain 4882 Blood 2277 Neuroblastoma 88 Other (also 2725 Primates bodymap) 148 bp exon 486 bp [gt-ag] intron 20 GenBank accessions 9840 RNA-seq supporting reads 1726 UHR pooled cells 606 Brain 5241 Blood 2170 Neuroblastoma 97 Other (also 1739 Primates bodymap) 67 accessions, some from lung (seen 7 times) prostate (7), breast carcinoma (5) coronary artery (4), left pelvis (4) 2971 bp exon 184 bp exon 184 bp exon 800 bp [gt-ag] intron 56 GenBank accessions 4885 RNA-seq supporting reads 889 UHR pooled cells 373 Brain 1795 Blood 1815 Neuroblastoma 13 Other (also 465 Primates bodymap) 117 bp exon 120 bp [gt-ag] intron 57 GenBank accessions 7791 RNA-seq supporting reads 986 UHR pooled cells 390 Brain 4648 Blood 1716 Neuroblastoma 51 Other (also 1884 Primates bodymap) 144 bp exon 657 bp [gt-ag] intron 1 GenBank accession 33 RNA-seq supporting reads 4 UHR pooled cells 3 Brain 21 Blood 5 Neuroblastoma (also 3 Primates bodymap) 131 bp exon 1 accession capped 5' end, 1 accession 131 bp exon 621 bp exon 621 bp exon 57 bp uORF 621 bp exon 621 bp exon 486 bp [gt-ag] intron 20 GenBank accessions 9840 RNA-seq supporting reads 1726 UHR pooled cells 606 Brain 5241 Blood 2170 Neuroblastoma 97 Other (also 1739 Primates bodymap) 423 bp exon 423 bp exon 2 accessions, some from human skeletal muscle (seen once) sympathetic trunk (once) 423 bp exon 654 bp exon 1 accession from prostate 654 bp exon 581 bp exon 581 bp exon 2 accessions, some from spleen (seen once) capped 5' end, 2 accessions 581 bp exon 531 bp exon 531 bp exon 1 accession capped 5' end, 1 accession 531 bp exon Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aAug10 4487 bp 604 aa 132 bp 2540 bp 2kb including Promoter 8610 bp 1kb
bAug10 1705 bp 451 aa 349 bp 2kb possibly including promoter 5938 bp 1kb
cAug10 4762 bp 373 aa 3638 bp 2kb 8603 bp 1kb
dAug10 1044 bp 161 aa 545 bp 13 bp 54 bp 2kb possibly including promoter 1530 bp 1kb
eAug10-unspliced 654 bp 137 aa 240 bp 2kb 654 bp 1kb
fAug10 576 bp 107 aa 132 bp 120 bp 2kb including Promoter 2153 bp 1kb
gAug10-unspliced 581 bp 65 aa 132 bp 251 bp 2kb including Promoter 581 bp 1kb
hAug10-unspliced 531 bp 73 aa 12 bp 297 bp 2kb including Promoter 531 bp 1kb

Gene neighbors and Navigator on chromosome 1q25.2-q25.3 back to top
PRG4 D C R P C1orf27 D C R P OCLM D P C PLA2G4A D C I R P R D C I R P TPR D C I R P PDC D C I R P PTGS2 100kb 0 HMCN1, 73 accessions, 6 variants PRG4, 234 accessions, 9 variants C1orf27, 228 accessions 10 variants OCLM, 18 accessions, 2 variants sporlarbu, 1 accession PLA2G4A, 48 accessions 2 variants nosayo, 3 accessions, 2 variants gleevoybo, 1 accession kikamo, 1 accession sneykeybo, 1 accession derjoybu, 1 accession spukeybo, 1 accession jarjoybu, 1 accession jerjoybu, 2 accessions spalarbu, 1 accession gurybo, 3 accessions gleeweebo, 1 accession keyjoybu, 1 accession plokley, 1 accession sperlarbu, 1 accession kakuyo, 1 accession sparkeybo, 1 accession nesayo, 2 accessions, 2 variants siruro, 2 accessions stalarbu, 2 accessions stolarbu, 3 accessions gorybo, 1 accession kukamo, 1 accession sterlarbu, 1 accession korjoybu, 1 accession storlarbu, 1 accession stoylarbu, 1 accession plawkley, 1 accession gleyweebo, 1 accession glorweebo, 1 accession swolarbu, 1 accession globu, 7 accessions pleekley, 11 accessions swarlarbu, 1 accession goler, 1 accession sweelarbu, 2 accessions sworlarbu, 1 accession gloyweebo, 1 accession balawbu, 2 accessions lorjoybu, 1 accession klyweebo, 1 accession sporkeybo, 1 accession klarweebo, 1 accession plorkley, 6 accessions bolawbu, 1 accession barlawbu, 1 accession bawlawbu, 2 accessions tarjoybu, 1 accession beelawbu, 3 accessions kleeweebo, 2 accessions klerweebo, 1 accession stykeybo, 1 accession beylawbu, 1 accession borlawbu, 1 accession smeelarbu, 1 accession smerlarbu, 2 accessions sokuyo, 1 accession smoylarbu, 2 accessions gyrybo, 1 accession glarweebo, 1 accession glawweebo, 1 accession spokeybo, 1 accession foler, 1 accession spawlarbu, 2 accessions speelarbu, 2 accessions speylarbu, 2 accessions spoylarbu, 1 accession spawkeybo, 1 accession stularbu, 1 accession starlarbu, 1 accession stawlarbu, 1 accession glerweebo, 1 accession steelarbu, 1 accession guler, 1 accession swularbu, 2 accessions leyjoybu, 1 accession swawlarbu, 2 accessions swerlarbu, 1 accession sweylarbu, 1 accession swoylarbu, 2 accessions klaweebo, 2 accessions bulawbu, 1 accession kluweebo, 1 accession meejoybu, 1 accession kloweebo, 1 accession garler, 2 accessions klawweebo, 1 accession sojoybu, 1 accession stokeybo, 2 accessions glervoybo, 1 accession TPR, 518 accessions, 18 variants PDC, 18 accessions, 2 variants PTGS2, 188 accessions 8 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               1165 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e-u, .f, .g-u, .h-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !