Homo sapiens complex locus PTGR1, encoding prostaglandin reductase 1.
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SUMMARY back to top
RefSeq summary
[PTGR1] This gene encodes an enzyme that is involved in the inactivation of the chemotactic factor, leukotriene B4. The encoded protein specifically catalyzes the NADP+ dependent conversion of leukotriene B4 to 12-oxo-leukotriene B4. A pseudogene of this gene is found on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq].

RefSeq annotates 3 representative transcripts (NM included in AceView variants .c, .d and .e), 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 13 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, 2.1 times the average gene in this release. The sequence of this gene is defined by 237 GenBank accessions from 223 cDNA clones, some from leiomios (seen 24 times), liver (22), kidney (19), lung (19), breast carcinoma (13), prostate (8), carcinoid (7) and 65 other tissues. We annotate structural defects or features in 36 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 19 distinct gt-ag introns. Transcription produces 15 different mRNAs, 13 alternatively spliced variants and 2 unspliced forms. There are 2 probable alternative promotors, 5 non overlapping alternative last exons and 5 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 5 cassette exons, overlapping exons with different boundaries, splicing versus retention of one intron.
2 variants were isolated in vivo, despite the fact that they are predicted targets of nonsense mediated mRNA decay (NMD).
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant eAug10).
Function: There are 4 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in processes (leukotriene metabolic process, oxidation reduction, response to toxin). Proteins are expected to have molecular functions (2-alkenal reductase activity, 15-oxoprostaglandin 13-oxidase activity, alcohol dehydrogenase (NAD) activity, binding, oxidoreductase activity, zinc ion binding) and to localize in cytoplasm.
Protein coding potential: 11 spliced and the unspliced mRNAs putatively encode good proteins, altogether 10 different isoforms (6 complete, 3 COOH complete, 1 partial), some containing Zinc-binding dehydrogenase domain [Pfam], a peroxisomal domain [Psort2]. The remaining 3 mRNA variants (2 spliced, 1 unspliced; 2 partial) appear not to encode good proteins.
Isoform PTGR1.bAug10-unspliced is annotated using as Met a Kozak-compatible g..AAGg start, thereby gaining 239 amino acids N-terminal to the first AUG. Finally proteins from this gene may be modulated by acetylation; 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 9, links to other databases and other names
Map: This gene PTGR1 maps on chromosome 9, at 9q31.3 according to Entrez Gene. In AceView, it covers 50.13 kb, from 114362134 to 114312002 (NCBI 37, August 2010), on the reverse strand.
Links to: manual annotations from PhosphoSite, the SNP view, gene overviews from Entrez Gene 22949, 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 PTGR1, RP11-16L21.1, PGR1, ZADH3, LTB4DH, FLJ99229, MGC34943 or LOC22949, fawseyby. It has been described as prostaglandin reductase 1, PRG-1, 15-oxoprostaglandin 13-reductase, leukotriene B4 12-hydroxydehydrogenase, NADP-dependent leukotriene B4 12-hydroxydehydrogenase, zinc binding alcohol dehydrogenase domain containing 3.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Ltb4dh (e= 10-123).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene 2L154 (e=2 10-19).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT-AER (e=2 10-41), AT5G17000 (e=3 10-41), AT5G16990 (e=6 10-41), AT3G03080 (e=10-40), AT1G26320 (e=8 10-39), AT1G65560 (e=6 10-37), AT3G59845 (e=7 10-37), AT5G37980 (e=8 10-36)
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
PTGR1 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 6.21 1.91 213 562 16.4 11.6 6.65 1.78 3.33 6.65 3.57 18.8 30.6 20.2 122 262 18.8 18.8 3.10 18.8 15.3 0.34 70.2 323 18.8 0.96 3.33 7.13 70.2 49.7 4.71 9.41 49.7 161 245 1291 5.04 4.71 4.71 46.3 18.8 199 185 7.64 8.19 11.6 14.3 5.79 10.1 15.3 35.1 10.8 1.45 7.13 15.3 37.6 6.65 13.3 18.8 7.13 23.2 15.3 7.13 2.70 9.41 2.90 92.7 131 8.19 2.19 12.4 8.78 9.41 35.1 10.8 5.79 213 173 4.10 5.79 8.19 6.65 13.3 245 5.04 11.6 10.1 14.3 86.5 30.6 301 245 426 26.6 28.5 17.6 24.8 61.1 6.21 30.6 0.48 0.36 7.64 1.66 1.78 228 8.19 0.34 106 262 20.2 14.3 1291 30.6 80.7 12.4 80.7 4.39 35.1 21.6 4.10 30.6 86.5 30.6 17.6 7.64 80.7 7.64 7.64 75.3 13.3 12.4 23.2 11.6 49.7 15.3 10.8 4.71 14.3 131 397 140 10.1 9.41 17.6 9.41 8.78 0.68 4.71 5.40 32.8 0.68 24.8 10.8 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 PTGR1 5' 3' encoded on minus strand of chromosome 9 from 114,362,134 to 114,312,002 15919 55457 53790 38747 49265 41873 36446 42264 a 30 n b-u 36446 42264 128 115 5432 i 25119 55457 53790 38747 49265 41873 36446 42264 42177 c [NM] 15919 55457 53790 38747 49265 41873 36446 42264 42177 d [NM] 15919 55457 53790 38747 49265 41873 36446 42264 101 e [NM] 15919 55457 53790 125 471 49265 41873 36446 42264 3534 f 15919 55457 109 49265 g 25119 55457 53790 k 36446 42264 3534 5432 h 15919 55457 53790 l 49265 o 42264 128 115 j m-u 1 2kb 0 218 bp exon 2170 bp [gt-ag] intron 58 GenBank accessions 15861 RNA-seq supporting reads 4033 UHR pooled cells 2591 Brain 22 Blood 9045 Neuroblastoma 170 Other (also 14719 Primates bodymap) 116 bp exon 116 bp exon 3049 bp [gt-ag] intron 96 GenBank accessions 55361 RNA-seq supporting reads 16296 UHR pooled cells 7749 Brain 48 Blood 30696 Neuroblastoma 572 Other (also 66766 Primates bodymap) 46 bp exon 1239 bp [gt-ag] intron 93 GenBank accessions 53697 RNA-seq supporting reads 15605 UHR pooled cells 7808 Brain 66 Blood 29670 Neuroblastoma 548 Other (also 13006 Primates bodymap) 57 bp exon 6760 bp [gt-ag] intron 53 GenBank accessions 38694 RNA-seq supporting reads 12199 UHR pooled cells 5514 Brain 53 Blood 20567 Neuroblastoma 361 Other (also 57359 Primates bodymap) 168 bp exon 2408 bp [gt-ag] intron 51 GenBank accessions 49214 RNA-seq supporting reads 15295 UHR pooled cells 6712 Brain 42 Blood 26807 Neuroblastoma 358 Other (also 69164 Primates bodymap) 118 bp exon 4520 bp [gt-ag] intron 72 GenBank accessions 41801 RNA-seq supporting reads 12968 UHR pooled cells 5645 Brain 55 Blood 22737 Neuroblastoma 396 Other (also 35245 Primates bodymap) 156 bp exon 3953 bp [gt-ag] intron 75 GenBank accessions 36371 RNA-seq supporting reads 11701 UHR pooled cells 5021 Brain 49 Blood 19268 Neuroblastoma 332 Other (also 49119 Primates bodymap) 109 bp exon 4524 bp [gt-ag] intron 47 GenBank accessions 42217 RNA-seq supporting reads 14288 UHR pooled cells 5851 Brain 55 Blood 21805 Neuroblastoma 218 Other (also 26274 Primates bodymap) 584 bp exon 3 accessions, some from pericardium (seen once) 584 bp exon 97 bp exon 4334 bp [gt-ag] intron 1 GenBank accession 29 RNA-seq supporting reads 6 UHR pooled cells 3 Brain 20 Neuroblastoma (also 12 Primates bodymap) 292 bp exon 1 accession 292 bp exon 1071 bp exon 1071 bp exon 21 bp uORF 1071 bp exon 1071 bp exon Sequence gap 441 bp 470 bp exon 470 bp exon 12 accessions, some from pooled human melanocyte fetal heart, andpregnant uterus (seen 2 times) bone (once), carcinoid (once) colon (once), kidney (once) 470 bp exon 35 bp exon 35 bp exon 3953 bp [gt-ag] intron 75 GenBank accessions 36371 RNA-seq supporting reads 11701 UHR pooled cells 5021 Brain 49 Blood 19268 Neuroblastoma 332 Other (also 49119 Primates bodymap) 109 bp exon 4524 bp [gt-ag] intron 47 GenBank accessions 42217 RNA-seq supporting reads 14288 UHR pooled cells 5851 Brain 55 Blood 21805 Neuroblastoma 218 Other (also 26274 Primates bodymap) 119 bp exon 4994 bp [gt-ag] intron 3 GenBank accessions 125 RNA-seq supporting reads 30 UHR pooled cells 4 Brain 90 Neuroblastoma 1 Other (also 19 Primates bodymap) 98 bp exon 98 bp exon 736 bp [gt-ag] intron 3 GenBank accessions 112 RNA-seq supporting reads 24 UHR pooled cells 9 Brain 79 Neuroblastoma 106 bp exon 925 bp [gt-ag] intron 9 GenBank accessions 5423 RNA-seq supporting reads 1791 UHR pooled cells 348 Brain 3 Blood 3272 Neuroblastoma 9 Other 1 accession from liver 83 bp exon 93 bp exon 1906 bp [gt-ag] intron 29 GenBank accessions 25090 RNA-seq supporting reads 8047 UHR pooled cells 2929 Brain 32 Blood 13607 Neuroblastoma 475 Other (also 944 Primates bodymap) 116 bp exon 116 bp exon 3049 bp [gt-ag] intron 96 GenBank accessions 55361 RNA-seq supporting reads 16296 UHR pooled cells 7749 Brain 48 Blood 30696 Neuroblastoma 572 Other (also 66766 Primates bodymap) 46 bp exon 1239 bp [gt-ag] intron 93 GenBank accessions 53697 RNA-seq supporting reads 15605 UHR pooled cells 7808 Brain 66 Blood 29670 Neuroblastoma 548 Other (also 13006 Primates bodymap) 57 bp exon 6760 bp [gt-ag] intron 53 GenBank accessions 38694 RNA-seq supporting reads 12199 UHR pooled cells 5514 Brain 53 Blood 20567 Neuroblastoma 361 Other (also 57359 Primates bodymap) 168 bp exon 2408 bp [gt-ag] intron 51 GenBank accessions 49214 RNA-seq supporting reads 15295 UHR pooled cells 6712 Brain 42 Blood 26807 Neuroblastoma 358 Other (also 69164 Primates bodymap) 118 bp exon 4520 bp [gt-ag] intron 72 GenBank accessions 41801 RNA-seq supporting reads 12968 UHR pooled cells 5645 Brain 55 Blood 22737 Neuroblastoma 396 Other (also 35245 Primates bodymap) 156 bp exon 3953 bp [gt-ag] intron 75 GenBank accessions 36371 RNA-seq supporting reads 11701 UHR pooled cells 5021 Brain 49 Blood 19268 Neuroblastoma 332 Other (also 49119 Primates bodymap) 109 bp exon 4524 bp [gt-ag] intron 47 GenBank accessions 42217 RNA-seq supporting reads 14288 UHR pooled cells 5851 Brain 55 Blood 21805 Neuroblastoma 218 Other (also 26274 Primates bodymap) 119 bp exon 6859 bp [gt-ag] intron 26 GenBank accessions 42151 RNA-seq supporting reads 14070 UHR pooled cells 6011 Brain 38 Blood 21837 Neuroblastoma 195 Other (also 76325 Primates bodymap) 267 bp exon 25 accessions, NM_012212.3 some from embryonic stem cells cell lines H1, H7, andh9 (seen 3 times) breast carcinoma (2) skin (2), small intestine (2) squamous cell carcinoma (2) Validated 3' end, 2 accessions 267 bp exon 252 bp exon 2170 bp [gt-ag] intron 58 GenBank accessions 15861 RNA-seq supporting reads 4033 UHR pooled cells 2591 Brain 22 Blood 9045 Neuroblastoma 170 Other (also 14719 Primates bodymap) 116 bp exon 116 bp exon 3049 bp [gt-ag] intron 96 GenBank accessions 55361 RNA-seq supporting reads 16296 UHR pooled cells 7749 Brain 48 Blood 30696 Neuroblastoma 572 Other (also 66766 Primates bodymap) 46 bp exon 1239 bp [gt-ag] intron 93 GenBank accessions 53697 RNA-seq supporting reads 15605 UHR pooled cells 7808 Brain 66 Blood 29670 Neuroblastoma 548 Other (also 13006 Primates bodymap) 57 bp exon 6760 bp [gt-ag] intron 53 GenBank accessions 38694 RNA-seq supporting reads 12199 UHR pooled cells 5514 Brain 53 Blood 20567 Neuroblastoma 361 Other (also 57359 Primates bodymap) 168 bp exon 2408 bp [gt-ag] intron 51 GenBank accessions 49214 RNA-seq supporting reads 15295 UHR pooled cells 6712 Brain 42 Blood 26807 Neuroblastoma 358 Other (also 69164 Primates bodymap) 118 bp exon 4520 bp [gt-ag] intron 72 GenBank accessions 41801 RNA-seq supporting reads 12968 UHR pooled cells 5645 Brain 55 Blood 22737 Neuroblastoma 396 Other (also 35245 Primates bodymap) 156 bp exon 3953 bp [gt-ag] intron 75 GenBank accessions 36371 RNA-seq supporting reads 11701 UHR pooled cells 5021 Brain 49 Blood 19268 Neuroblastoma 332 Other (also 49119 Primates bodymap) 109 bp exon 4524 bp [gt-ag] intron 47 GenBank accessions 42217 RNA-seq supporting reads 14288 UHR pooled cells 5851 Brain 55 Blood 21805 Neuroblastoma 218 Other (also 26274 Primates bodymap) 119 bp exon 6859 bp [gt-ag] intron 26 GenBank accessions 42151 RNA-seq supporting reads 14070 UHR pooled cells 6011 Brain 38 Blood 21837 Neuroblastoma 195 Other (also 76325 Primates bodymap) 267 bp exon 22 accessions, NM_001146108.1 some from liver (seen 12 times) leiomyosarcoma (2), uterus (2) alzheimer cortex (once) kidney (once) Validated 3' end, 9 accessions 267 bp exon 252 bp exon 252 bp exon 162 bp uORF 252 bp exon 2170 bp [gt-ag] intron 58 GenBank accessions 15861 RNA-seq supporting reads 4033 UHR pooled cells 2591 Brain 22 Blood 9045 Neuroblastoma 170 Other (also 14719 Primates bodymap) 116 bp exon 116 bp exon 116 bp exon 3049 bp [gt-ag] intron 96 GenBank accessions 55361 RNA-seq supporting reads 16296 UHR pooled cells 7749 Brain 48 Blood 30696 Neuroblastoma 572 Other (also 66766 Primates bodymap) 46 bp exon 46 bp exon 1239 bp [gt-ag] intron 93 GenBank accessions 53697 RNA-seq supporting reads 15605 UHR pooled cells 7808 Brain 66 Blood 29670 Neuroblastoma 548 Other (also 13006 Primates bodymap) 57 bp exon 57 bp exon 6760 bp [gt-ag] intron 53 GenBank accessions 38694 RNA-seq supporting reads 12199 UHR pooled cells 5514 Brain 53 Blood 20567 Neuroblastoma 361 Other (also 57359 Primates bodymap) 168 bp exon 168 bp exon 2408 bp [gt-ag] intron 51 GenBank accessions 49214 RNA-seq supporting reads 15295 UHR pooled cells 6712 Brain 42 Blood 26807 Neuroblastoma 358 Other (also 69164 Primates bodymap) 118 bp exon 118 bp exon 4520 bp [gt-ag] intron 72 GenBank accessions 41801 RNA-seq supporting reads 12968 UHR pooled cells 5645 Brain 55 Blood 22737 Neuroblastoma 396 Other (also 35245 Primates bodymap) 156 bp exon 156 bp exon 3953 bp [gt-ag] intron 75 GenBank accessions 36371 RNA-seq supporting reads 11701 UHR pooled cells 5021 Brain 49 Blood 19268 Neuroblastoma 332 Other (also 49119 Primates bodymap) 109 bp exon 109 bp exon 4524 bp [gt-ag] intron 47 GenBank accessions 42217 RNA-seq supporting reads 14288 UHR pooled cells 5851 Brain 55 Blood 21805 Neuroblastoma 218 Other (also 26274 Primates bodymap) 119 bp exon 119 bp exon 20291 bp [gt-ag] intron 2 GenBank accessions 99 RNA-seq supporting reads 8 UHR pooled cells 11 Brain 80 Neuroblastoma (also 19 Primates bodymap) 78 bp exon 78 bp exon 79 accessions, NM_001146109.1 some from leiomios (seen 24 times) breast carcinoma (10) pnet (7), kidney (4) liver (4) capped 5' end, 6 accessions 78 bp exon 44 bp exon 2170 bp [gt-ag] intron 58 GenBank accessions 15861 RNA-seq supporting reads 4033 UHR pooled cells 2591 Brain 22 Blood 9045 Neuroblastoma 170 Other (also 14719 Primates bodymap) 116 bp exon 3049 bp [gt-ag] intron 96 GenBank accessions 55361 RNA-seq supporting reads 16296 UHR pooled cells 7749 Brain 48 Blood 30696 Neuroblastoma 572 Other (also 66766 Primates bodymap) 46 bp exon 1239 bp [gt-ag] intron 93 GenBank accessions 53697 RNA-seq supporting reads 15605 UHR pooled cells 7808 Brain 66 Blood 29670 Neuroblastoma 548 Other (also 13006 Primates bodymap) 57 bp exon 3543 bp [gt-ag] intron 4 GenBank accessions 121 RNA-seq supporting reads 30 UHR pooled cells 4 Brain 87 Neuroblastoma 119 bp exon 3098 bp [gt-ag] intron 5 GenBank accessions 466 RNA-seq supporting reads 106 UHR pooled cells 18 Brain 3 Blood 336 Neuroblastoma 3 Other (also 28 Primates bodymap) 168 bp exon 168 bp exon 2408 bp [gt-ag] intron 51 GenBank accessions 49214 RNA-seq supporting reads 15295 UHR pooled cells 6712 Brain 42 Blood 26807 Neuroblastoma 358 Other (also 69164 Primates bodymap) 118 bp exon 4520 bp [gt-ag] intron 72 GenBank accessions 41801 RNA-seq supporting reads 12968 UHR pooled cells 5645 Brain 55 Blood 22737 Neuroblastoma 396 Other (also 35245 Primates bodymap) 156 bp exon 3953 bp [gt-ag] intron 75 GenBank accessions 36371 RNA-seq supporting reads 11701 UHR pooled cells 5021 Brain 49 Blood 19268 Neuroblastoma 332 Other (also 49119 Primates bodymap) 109 bp exon 4524 bp [gt-ag] intron 47 GenBank accessions 42217 RNA-seq supporting reads 14288 UHR pooled cells 5851 Brain 55 Blood 21805 Neuroblastoma 218 Other (also 26274 Primates bodymap) 119 bp exon 5828 bp [gt-ag] intron 8 GenBank accessions 3526 RNA-seq supporting reads 1206 UHR pooled cells 222 Brain 3 Blood 2091 Neuroblastoma 4 Other 1689 bp exon 20 accessions, some from kidney (seen 3 times) hepatocellular carcinoma cell line (2), liver (2) lung (2), pooled human melanocyte fetal heart, andpregnant uterus (2) capped 5' end, 1 accession Validated 3' end, 4 accessions 1689 bp exon 93 bp exon 93 bp exon 2170 bp [gt-ag] intron 58 GenBank accessions 15861 RNA-seq supporting reads 4033 UHR pooled cells 2591 Brain 22 Blood 9045 Neuroblastoma 170 Other (also 14719 Primates bodymap) 116 bp exon 3049 bp [gt-ag] intron 96 GenBank accessions 55361 RNA-seq supporting reads 16296 UHR pooled cells 7749 Brain 48 Blood 30696 Neuroblastoma 572 Other (also 66766 Primates bodymap) 46 bp exon 8056 bp [gt-ag] intron 1 GenBank accession 108 RNA-seq supporting reads 21 UHR pooled cells 7 Brain 80 Neuroblastoma (also 120 Primates bodymap) 168 bp exon 2408 bp [gt-ag] intron 51 GenBank accessions 49214 RNA-seq supporting reads 15295 UHR pooled cells 6712 Brain 42 Blood 26807 Neuroblastoma 358 Other (also 69164 Primates bodymap) 36 bp exon 1 accession from brain 36 bp exon 70 bp exon 1906 bp [gt-ag] intron 29 GenBank accessions 25090 RNA-seq supporting reads 8047 UHR pooled cells 2929 Brain 32 Blood 13607 Neuroblastoma 475 Other (also 944 Primates bodymap) 116 bp exon 116 bp exon 3049 bp [gt-ag] intron 96 GenBank accessions 55361 RNA-seq supporting reads 16296 UHR pooled cells 7749 Brain 48 Blood 30696 Neuroblastoma 572 Other (also 66766 Primates bodymap) 46 bp exon 1239 bp [gt-ag] intron 93 GenBank accessions 53697 RNA-seq supporting reads 15605 UHR pooled cells 7808 Brain 66 Blood 29670 Neuroblastoma 548 Other (also 13006 Primates bodymap) 622 bp exon 4 accessions, some from heart (seen 2 times) 2 pooled tumors (clear cell type) (once) kidney (once), melanotic melanoma (once) skin (once) 622 bp exon 105 bp exon 3953 bp [gt-ag] intron 75 GenBank accessions 36371 RNA-seq supporting reads 11701 UHR pooled cells 5021 Brain 49 Blood 19268 Neuroblastoma 332 Other (also 49119 Primates bodymap) 109 bp exon 4524 bp [gt-ag] intron 47 GenBank accessions 42217 RNA-seq supporting reads 14288 UHR pooled cells 5851 Brain 55 Blood 21805 Neuroblastoma 218 Other (also 26274 Primates bodymap) 119 bp exon 5828 bp [gt-ag] intron 8 GenBank accessions 3526 RNA-seq supporting reads 1206 UHR pooled cells 222 Brain 3 Blood 2091 Neuroblastoma 4 Other 106 bp exon 106 bp exon 925 bp [gt-ag] intron 9 GenBank accessions 5423 RNA-seq supporting reads 1791 UHR pooled cells 348 Brain 3 Blood 3272 Neuroblastoma 9 Other 8 accessions, some from 2 pooled tumors (clear cell type) (seen once) breast carcinoma (once) cell line (once), chondrosarcoma (once) kidney (once) Validated 3' end, 4 accessions 334 bp exon 232 bp exon 232 bp exon 162 bp uORF 232 bp exon 2170 bp [gt-ag] intron 58 GenBank accessions 15861 RNA-seq supporting reads 4033 UHR pooled cells 2591 Brain 22 Blood 9045 Neuroblastoma 170 Other (also 14719 Primates bodymap) 116 bp exon 116 bp exon 116 bp exon 3049 bp [gt-ag] intron 96 GenBank accessions 55361 RNA-seq supporting reads 16296 UHR pooled cells 7749 Brain 48 Blood 30696 Neuroblastoma 572 Other (also 66766 Primates bodymap) 46 bp exon 46 bp exon 1239 bp [gt-ag] intron 93 GenBank accessions 53697 RNA-seq supporting reads 15605 UHR pooled cells 7808 Brain 66 Blood 29670 Neuroblastoma 548 Other (also 13006 Primates bodymap) 1593 bp exon 1593 bp exon 41 accessions, some from lung (seen 9 times) kidney (8), carcinoid (7) brain (3), glioblastoma (pooled) (2) capped 5' end, 3 accessions 1593 bp exon 253 bp exon 253 bp exon 253 bp exon 2408 bp [gt-ag] intron 51 GenBank accessions 49214 RNA-seq supporting reads 15295 UHR pooled cells 6712 Brain 42 Blood 26807 Neuroblastoma 358 Other (also 69164 Primates bodymap) 2 accessions, some from colon (seen once) prostate tumor (once) 53 bp exon 102 bp exon 102 bp exon 4524 bp [gt-ag] intron 47 GenBank accessions 42217 RNA-seq supporting reads 14288 UHR pooled cells 5851 Brain 55 Blood 21805 Neuroblastoma 218 Other (also 26274 Primates bodymap) 119 bp exon 4994 bp [gt-ag] intron 3 GenBank accessions 125 RNA-seq supporting reads 30 UHR pooled cells 4 Brain 90 Neuroblastoma 1 Other (also 19 Primates bodymap) 98 bp exon 98 bp exon 736 bp [gt-ag] intron 3 GenBank accessions 112 RNA-seq supporting reads 24 UHR pooled cells 9 Brain 79 Neuroblastoma 2 accessions, some from alveolar macrophage (seen once) lung (once) Validated 3' end, 2 accessions 437 bp exon 402 bp exon 402 bp exon 2 accessions, some from colon (seen once) head neck (once) 402 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 1572 bp 348 aa 228 bp 297 bp 2kb possibly including promoter 30195 bp 1kb
bAug10-unspliced 1982 bp 343 aa 913 bp 37 bp 18 bp 2kb possibly including promoter 1982 bp 1kb
cAug10 1249 bp 329 aa 103 bp 156 bp 2kb possibly including promoter 36467 bp 1kb
dAug10 1408 bp 329 aa 262 bp 156 bp 2kb possibly including promoter 36890 bp 1kb
eAug10 1219 bp 301 aa 262 bp 51 bp 159 bp 2kb including Promoter 50133 bp 1kb
fAug10 2741 bp 242 aa 542 bp 1665 bp 2kb including Promoter 37073 bp 1kb
gAug10 459 bp 152 aa 2kb 16142 bp 1kb
hAug10 773 bp 118 aa 416 bp 2kb 16003 bp 1kb
iAug10 550 bp 106 aa 227 bp 2kb 15682 bp 1kb
jAug10 756 bp 92 aa 475 bp 2kb 11010 bp 1kb
kAug10 854 bp 70 aa 80 bp 561 bp 2kb probably including promoter 7048 bp 1kb
lAug10 1987 bp 70 aa 242 bp 1532 bp 159 bp 2kb including Promoter 8445 bp 1kb
mAug10-unspliced 402 bp 64 aa 15 bp 192 bp 2kb 402 bp 1kb
nAug10 389 bp 38 aa 272 bp 2kb 4723 bp 1kb
oAug10 306 bp 21 aa 238 bp 2kb 2714 bp 1kb

Gene neighbors and Navigator on chromosome 9q31.3 back to top
ZNF483 C R P C C DNAJC25-GNG10 C I R P R UGCG D C I R P C R C I R P KIAA0368andOR2K2 C R P PTGR1 C R P C9orf29 C R P C9orf84 C R 100kb 0 ZNF483, 79 accessions 6 variants chawpleebu, 98 accessions snawlar, 2 accessions DNAJC25-GNG10, 531 accessions 12 variants timore, 8 accessions, 2 variants UGCG, 433 accessions, 7 variants temore, 10 accessions zuswy, 1 accession swyserby, 1 accession zarpleebu, 1 accession sneysawbu, 1 accession bleego, 2 accessions zarswy, 1 accession sworserby, 1 accession zeypleebu, 1 accession zorpleebu, 4 accessions shyswy, 1 accession bawseyby, 1 accession shoyswy, 1 accession bleyswy, 1 accession dyseyby, 1 accession duseyby, 1 accession storshey, 1 accession chypleebu, 1 accession snylar, 2 accessions fyseyby, 1 accession cheypleebu, 1 accession choypleebu, 1 accession farseyby, 1 accession yamomu, 1 accession forseyby, 1 accession gaseyby, 1 accession shupleebu, 1 accession gerseebu, 1 accession plarswy, 1 accession takuro, 1 accession ployswy, 1 accession goseyby, 1 accession skoswy, 1 accession slyswy, 1 accession flutoyby, 1 accession gerseyby, 3 accessions shawpleebu, 1 accession goyseyby, 3 accessions jeyseebu, 2 accessions joyseebu, 1 accession flotoyby, 3 accessions joseyby, 1 accession sheepleebu, 2 accessions jarseyby, 1 accession swashey, 3 accessions jeeseyby, 1 accession jerseyby, 1 accession sheypleebu, 1 accession jeyseyby, 1 accession shoypleebu, 1 accession blapleebu, 2 accessions blypleebu, 1 accession blupleebu, 1 accession smerswy, 2 accessions kyseyby, 1 accession kawseebu, 1 accession blawpleebu, 1 accession bleepleebu, 2 accessions klytoyby, 1 accession loseebu, 2 accessions keeseyby, 1 accession tumore, 5 accessions snawswy, 1 accession zarreyby, 1 accession bleypleebu, 4 accessions kerseyby, 2 accessions laseyby, 1 accession blorpleebu, 1 accession maseebu, 1 accession museebu, 1 accession kleetoyby, 1 accession sporswy, 1 accession lawseyby, 1 accession lerseyby, 1 accession lorseyby, 1 accession merseebu, 2 accessions moseyby, 3 accessions bloypleebu, 1 accession flypleebu, 1 accession swoshey, 6 accessions mawseyby, 1 accession pyseebu, 1 accession ferswu, 1 accession zopleebu, 1 accession swuserby, 1 accession swerserby, 1 accession sweyserby, 1 accession soteebo, 1 accession nokuro, 1 accession zeeswy, 1 accession swoyserby, 2 accessions sheytoyby, 1 accession byseyby, 2 accessions zoypleebu, 1 accession sweysawbu, 1 accession buseyby, 4 accessions flago, 2 accessions boseyby, 1 accession barseyby, 1 accession berseebu, 2 accessions beeseyby, 1 accession beyseyby, 1 accession remomu, 2 accessions, 2 variants romomu, 2 accessions, 2 variants sarteebo, 1 accession boyseyby, 3 accessions flerswy, 1 accession doseyby, 1 accession dawseyby, 5 accessions dawseebu, 1 accession chopleebu, 1 accession derseebu, 2 accessions charpleebu, 5 accessions dorseyby, 1 accession faseyby, 2 accessions cheepleebu, 2 accessions fuseyby, 2 accessions doyseebu, 3 accessions shapleebu, 3 accessions bleetoyby, 1 accession goseebu, 1 accession feyseyby, 3 accessions shypleebu, 1 accession foyseyby, 1 accession gyseyby, 1 accession guseyby, 1 accession sharpleebu, 1 accession sluswy, 1 accession gawseyby, 2 accessions geeseyby, 2 accessions sleyswy, 1 accession gorseyby, 1 accession slorswy, 1 accession jaseyby, 2 accessions juseyby, 1 accession seeteebo, 1 accession jawseyby, 1 accession shorpleebu, 1 accession smeeswy, 1 accession jorseyby, 1 accession joyseyby, 1 accession blerpleebu, 1 accession kuseyby, 2 accessions karseyby, 1 accession kawseyby, 2 accessions lerseebu, 1 accession keyseyby, 2 accessions korseyby, 1 accession koyseyby, 1 accession lyseyby, 1 accession luseyby, 1 accession loseyby, 1 accession leeseyby, 1 accession leyseyby, 1 accession meeseebu, 1 accession loyseyby, 1 accession maseyby, 1 accession museyby, 1 accession flapleebu, 1 accession borswu, 1 accession gleyplabu, 54 accessions derswu, 1 accession meeseyby, 2 accessions yusuro, 1 accession merseyby, 1 accession spylar, 7 accessions tikuro, 1 accession meyseyby, 2 accessions seyteebo, 1 accession flopleebu, 1 accession poseebu, 1 accession parseebu, 1 accession steeshey, 3 accessions 3 variants KIAA0368andOR2K2, 543 accessions 19 variants PTGR1, 230 accessions 15 variants C9orf29, 14 accessions 5 variants C9orf84, 65 accessions 13 variants glotoyby, 1 accession sutira, 43 accessions 2 variants SUSD1, 110 accessions 9 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               4 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b-u, .c, .d, .e, .f, .g, .h, .i, .j, .k, .l, .m-u, .n, .o Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

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'.

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