Ptafr (platelet-activating factor receptor) - Rat Genome Database
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Gene: Ptafr (platelet-activating factor receptor) Rattus norvegicus
Analyze
Symbol: Ptafr
Name: platelet-activating factor receptor
RGD ID: 61897
Description: Exhibits mitogen-activated protein kinase binding activity and platelet activating factor receptor activity. Involved in several processes, including positive regulation of transport; regulation of blood vessel diameter; and regulation of gene expression. Localizes to plasma membrane. Used to study several diseases, including acute kidney failure; neutropenia; perinatal necrotizing enterocolitis; pleurisy; and transient cerebral ischemia. Biomarker of conjunctivitis; sciatic neuropathy; and transient cerebral ischemia. Orthologous to human PTAFR (platelet activating factor receptor); PARTICIPATES IN calcium/calcium-mediated signaling pathway; Staphylococcus aureus infection pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2-acetyl-1-alkyl-sn-glycero-3-phosphocholine; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: PAF-R; PAFr
Orthologs:
Homo sapiens (human) : PTAFR (platelet activating factor receptor)  HGNC  Alliance
Mus musculus (house mouse) : Ptafr (platelet-activating factor receptor)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Ptafr (platelet activating factor receptor)
Pan paniscus (bonobo/pygmy chimpanzee) : PTAFR (platelet activating factor receptor)
Canis lupus familiaris (dog) : PTAFR (platelet activating factor receptor)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Ptafr (platelet activating factor receptor)
Sus scrofa (pig) : PTAFR (platelet activating factor receptor)
Chlorocebus sabaeus (African green monkey) : PTAFR (platelet activating factor receptor)
Heterocephalus glaber (naked mole-rat) : Ptafr (platelet activating factor receptor)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.05150,746,284 - 150,775,675 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5150,754,021 - 150,775,672 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05154,414,542 - 154,443,798 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45152,565,687 - 152,587,342 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15152,575,728 - 152,597,381 (-)NCBI
Celera5143,199,712 - 143,221,168 (+)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cellular response to 2-O-acetyl-1-O-hexadecyl-sn-glycero-3-phosphocholine  (IEP)
cellular response to cAMP  (IEP)
cellular response to fatty acid  (IEP)
cellular response to gravity  (IEP)
chemotaxis  (IEA)
G protein-coupled purinergic nucleotide receptor signaling pathway  (IEA)
G protein-coupled receptor signaling pathway  (IBA,IMP,ISO)
inflammatory response  (ISO)
inositol trisphosphate biosynthetic process  (ISO)
lipopolysaccharide-mediated signaling pathway  (IEA)
negative regulation of blood pressure  (IMP)
obsolete positive regulation of blood vessel diameter  (IMP)
parturition  (IMP)
phosphatidylinositol-mediated signaling  (ISO)
positive regulation of cellular extravasation  (IMP)
positive regulation of gastro-intestinal system smooth muscle contraction  (IMP)
positive regulation of inositol phosphate biosynthetic process  (IDA)
positive regulation of interleukin-6 production  (IMP)
positive regulation of leukocyte cell-cell adhesion  (IMP)
positive regulation of leukocyte tethering or rolling  (IMP)
positive regulation of maternal process involved in parturition  (IMP)
positive regulation of neutrophil degranulation  (IMP)
positive regulation of phospholipase C activity  (IDA)
positive regulation of sensory perception of pain  (IMP)
positive regulation of smooth muscle cell proliferation  (IMP)
positive regulation of smooth muscle contraction  (IMP)
positive regulation of transcytosis  (IMP)
positive regulation of translation  (IMP)
positive regulation of tumor necrosis factor production  (IMP)
positive regulation of vasoconstriction  (IMP)
positive regulation of voltage-gated chloride channel activity  (IDA)
regulation of transcription by RNA polymerase II  (IMP)
response to 2-O-acetyl-1-O-hexadecyl-sn-glycero-3-phosphocholine  (IEP)
response to dexamethasone  (IEP)
response to lipopolysaccharide  (IEP,ISO)
response to organophosphorus  (IEP)
response to symbiotic bacterium  (IEP)
transcytosis  (IMP)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Beauchamp MH, etal., Invest Ophthalmol Vis Sci. 2002 Oct;43(10):3327-37.
2. Bito H, etal., Eur J Biochem 1994 Apr 1;221(1):211-8.
3. Borges CM, etal., J Leukoc Biol. 2000 Apr;67(4):515-9.
4. Carlson SA, etal., J Biol Chem. 1996 Sep 20;271(38):23146-53.
5. Carlson SA, etal., Mol Pharmacol. 1998 Mar;53(3):451-8.
6. Chao W, etal., J Biol Chem. 1990 Oct 15;265(29):17576-83.
7. Doebber TW, etal., J Immunol. 1986 Jun 15;136(12):4659-68.
8. Dubois C, etal., J Immunol. 1989 Aug 1;143(3):964-70.
9. Fletcher JR, etal., Ann Surg. 1990 Mar;211(3):312-6.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. GOA data from the GO Consortium
12. Handley DA, etal., Immunopharmacology. 1986 Aug;12(1):11-6.
13. Hruby ZW, etal., Arch Immunol Ther Exp (Warsz). 1991;39(5-6):575-86.
14. Hu WM and Man RY, Br J Pharmacol. 1991 Dec;104(4):773-5.
15. Ichinowatari G, etal., Eur J Pharmacol. 2002 Jan 11;434(3):187-96.
16. Jesus-Morais CM, etal., Planta Med. 2000 Apr;66(3):211-6.
17. Ji RL, etal., World J Gastroenterol. 2011 May 7;17(17):2241-7. doi: 10.3748/wjg.v17.i17.2241.
18. Karasawa A, etal., Methods Find Exp Clin Pharmacol. 1990 May;12(4):231-7.
19. Kassuya CA, etal., Eur J Pharmacol. 2006 Sep 28;546(1-3):182-8. Epub 2006 Jul 22.
20. Kim YH, etal., J Lipid Res. 2013 Oct;54(10):2678-86. doi: 10.1194/jlr.M037176. Epub 2013 Aug 2.
21. Kumei Y, etal., Ann N Y Acad Sci. 2004 Dec;1030:116-20.
22. Lu J, etal., Pediatr Res. 2007 Apr;61(4):427-32.
23. Man RY and Kinnaird AA, Br J Pharmacol. 1995 Nov;116(5):2359-64.
24. Marotta DM, etal., Biochem Pharmacol. 2009 Apr 1;77(7):1223-35.
25. Martins MA, etal., Eur J Pharmacol. 1993 Jun 11;237(1):17-22.
26. MGD data from the GO Consortium
27. Mizuno S, etal., Dig Dis Sci. 2001 Jun;46(6):1299-304.
28. Nakao A, etal., Am J Physiol. 1997 Sep;273(3 Pt 2):F445-50.
29. Nakasaki T, etal., Prostaglandins Other Lipid Mediat. 1999 Aug;58(1):29-41.
30. NCBI rat LocusLink and RefSeq merged data July 26, 2002
31. Okubo M, etal., Mol Pain. 2012 Feb 2;8:8. doi: 10.1186/1744-8069-8-8.
32. Pipeline to import KEGG annotations from KEGG into RGD
33. Ponpipom MM, etal., Biochem Biophys Res Commun. 1988 Feb 15;150(3):1213-20.
34. Predescu D, etal., Eur J Cell Biol. 1996 Jan;69(1):86-98.
35. Raisanen A, etal., Transpl Int. 1993;6(5):251-7.
36. RGD automated data pipeline
37. RGD automated import pipeline for gene-chemical interactions
38. Ring A, etal., J Clin Invest. 1998 Jul 15;102(2):347-60.
39. Schmidt H, etal., J Surg Res. 1996 Jan;60(1):29-35.
40. Souza DG, etal., Br J Pharmacol. 2000 Dec;131(8):1800-8.
41. Souza DG, etal., Br J Pharmacol. 2003 Jun;139(4):733-40.
42. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
43. Sun D and Gilboe DD, J Neurochem. 1994 May;62(5):1929-38.
44. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
45. Tolins JP, etal., J Lab Clin Med. 1989 Mar;113(3):316-24.
46. Vergnolle N J Immunol. 1999 Nov 1;163(9):5064-9.
47. Wang H, etal., Biochem J. 1997 Mar 1;322 ( Pt 2):603-8.
48. Wang H, etal., Immunology. 1999 Jul;97(3):447-54.
49. Yamano M, etal., Naunyn Schmiedebergs Arch Pharmacol. 1998 Aug;358(2):253-63.
50. Yoshikawa D, etal., Eur J Pharmacol. 1998 Jan 26;342(2-3):241-5.
51. Zhang X, etal., Neurochem Res. 2007 Mar;32(3):451-6.
52. Zhu YP, etal., Biol Reprod. 1991 Jan;44(1):39-42.
53. Zinchuk O, etal., Mol Vis. 2005 Feb 9;11:114-23.
Additional References at PubMed
PMID:1281995   PMID:1374385   PMID:1656963   PMID:1657923   PMID:9013981   PMID:14742561   PMID:15489334   PMID:16920964   PMID:17589953   PMID:18186558   PMID:21298035   PMID:21391918  


Genomics

Comparative Map Data
Ptafr
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.05150,746,284 - 150,775,675 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5150,754,021 - 150,775,672 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05154,414,542 - 154,443,798 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45152,565,687 - 152,587,342 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15152,575,728 - 152,597,381 (-)NCBI
Celera5143,199,712 - 143,221,168 (+)NCBICelera
Cytogenetic Map5q36NCBI
PTAFR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl128,147,166 - 28,193,936 (-)EnsemblGRCh38hg38GRCh38
GRCh38128,147,166 - 28,193,856 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37128,473,677 - 28,520,447 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36128,348,425 - 28,375,778 (-)NCBINCBI36hg18NCBI36
Build 34128,160,005 - 28,187,333NCBI
Celera126,869,321 - 26,916,090 (-)NCBI
Cytogenetic Map1p35.3NCBI
HuRef126,730,992 - 26,777,615 (-)NCBIHuRef
CHM1_1128,589,192 - 28,635,951 (-)NCBICHM1_1
Ptafr
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394132,291,378 - 132,309,994 (+)NCBI
GRCm384132,564,067 - 132,582,683 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4132,564,067 - 132,582,683 (+)EnsemblGRCm38mm10GRCm38
MGSCv374132,119,982 - 132,136,781 (+)NCBIGRCm37mm9NCBIm37
MGSCv364131,836,143 - 131,852,942 (+)NCBImm8
Celera4130,724,940 - 130,741,731 (+)NCBICelera
Cytogenetic Map4D2.3NCBI
cM Map465.56NCBI
Ptafr
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554527,311,901 - 7,312,929 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554527,309,854 - 7,345,579 (-)NCBIChiLan1.0ChiLan1.0
PTAFR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1128,447,178 - 28,474,623 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl128,447,833 - 28,448,861 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0127,405,880 - 27,436,184 (-)NCBIMhudiblu_PPA_v0panPan3
PTAFR
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl272,225,386 - 72,256,352 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1272,225,386 - 72,256,353 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ptafr
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647412,333,905 - 12,337,140 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTAFR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl685,235,390 - 85,272,333 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1685,235,390 - 85,272,360 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2684,789,514 - 84,851,193 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PTAFR
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl20104,657,179 - 104,658,207 (+)Ensembl
ChlSab1.120104,627,591 - 104,658,840 (+)NCBI
Ptafr
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476411,996,454 - 12,025,751 (-)NCBI

Position Markers
RH128779  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05150,775,411 - 150,775,630NCBIRnor6.0
Rnor_5.05154,443,534 - 154,443,753UniSTSRnor5.0
RGSC_v3.45152,565,732 - 152,565,951UniSTSRGSC3.4
Celera5143,220,904 - 143,221,123UniSTS
Cytogenetic Map5q36UniSTS
RH 3.4 Map5965.51UniSTS
UniSTS:144285  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05150,772,744 - 150,773,278NCBIRnor6.0
Rnor_5.05154,440,867 - 154,441,401UniSTSRnor5.0
RGSC_v3.45152,568,084 - 152,568,618UniSTSRGSC3.4
Celera5143,218,237 - 143,218,771UniSTS
Cytogenetic Map5q36UniSTS
UniSTS:484979  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05150,772,440 - 150,773,849NCBIRnor6.0
Rnor_5.05154,440,563 - 154,441,972UniSTSRnor5.0
RGSC_v3.45152,567,513 - 152,568,922UniSTSRGSC3.4
Celera5143,217,933 - 143,219,342UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5149568588167739697Rat
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5149832180164807402Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5142309061173707219Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5134502140157212422Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132551937173707219Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5149029982173687766Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5114140832159140832Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5142307322173707219Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)5100723739153577831Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5136354114173707219Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5138154677172402610Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)584963058173504662Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5128687766173687766Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133943857173707219Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5114140832159140832Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133943857173707219Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5125455818157225114Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5134197905173707219Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)547745646167946134Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5107119214152119214Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5150340838164298744Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)571552569157225114Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5111278451156278451Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5112279412157279412Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540777918154732375Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)5102945579154732228Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5150360936167946134Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)561612600168109659Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5116767924161767924Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136640731173707219Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5134712342173707219Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5116767924161767924Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5116767924161767924Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5116767924161767924Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5134712342173707219Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5112279412157279412Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5112279412157279412Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5112279412157279412Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5112279412157279412Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5131077716173707219Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:686
Count of miRNA genes:281
Interacting mature miRNAs:369
Transcripts:ENSRNOT00000017687
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 11 5 1
Low 1 43 57 41 8 41 8 11 70 35 30 10 8
Below cutoff 4 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017687   ⟹   ENSRNOP00000017687
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl5150,754,021 - 150,775,672 (+)Ensembl
RefSeq Acc Id: NM_053321   ⟹   NP_445773
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05150,754,021 - 150,775,675 (+)NCBI
Rnor_5.05154,414,542 - 154,443,798 (+)NCBI
RGSC_v3.45152,565,687 - 152,587,342 (-)RGD
Celera5143,199,712 - 143,221,168 (+)RGD
Sequence:
RefSeq Acc Id: XM_006239063   ⟹   XP_006239125
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05150,746,284 - 150,775,675 (+)NCBI
Rnor_5.05154,414,542 - 154,443,798 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006239064   ⟹   XP_006239126
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05150,765,465 - 150,775,675 (+)NCBI
Rnor_5.05154,414,542 - 154,443,798 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_445773   ⟸   NM_053321
- UniProtKB: P46002 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006239125   ⟸   XM_006239063
- Peptide Label: isoform X1
- UniProtKB: P46002 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006239126   ⟸   XM_006239064
- Peptide Label: isoform X1
- UniProtKB: P46002 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000017687   ⟸   ENSRNOT00000017687

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13694099
Promoter ID:EPDNEW_R4624
Type:multiple initiation site
Name:Ptafr_1
Description:platelet-activating factor receptor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05150,753,983 - 150,754,043EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61897 AgrOrtholog
Ensembl Genes ENSRNOG00000013231 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000017687 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000017687 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7097307 IMAGE-MGC_LOAD
InterPro GPCR_Rhodpsn UniProtKB/Swiss-Prot
  GPCR_Rhodpsn_7TM UniProtKB/Swiss-Prot
  PAF_rcpt UniProtKB/Swiss-Prot
KEGG Report rno:58949 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91594 IMAGE-MGC_LOAD
NCBI Gene 58949 ENTREZGENE
Pfam 7tm_1 UniProtKB/Swiss-Prot
PhenoGen Ptafr PhenoGen
PRINTS GPCRRHODOPSN UniProtKB/Swiss-Prot
  PAFRECEPTOR UniProtKB/Swiss-Prot
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/Swiss-Prot
  G_PROTEIN_RECEP_F1_2 UniProtKB/Swiss-Prot
TIGR TC215610
UniGene Rn.10137 ENTREZGENE
UniProt P46002 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Ptafr  platelet-activating factor receptor       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference