Pla2g2a (phospholipase A2 group IIA) - Rat Genome Database

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Gene: Pla2g2a (phospholipase A2 group IIA) Rattus norvegicus
Analyze
Symbol: Pla2g2a
Name: phospholipase A2 group IIA
RGD ID: 620857
Description: Enables calcium-dependent phospholipase A2 activity. Involved in phospholipid metabolic process. Located in perinuclear region of cytoplasm and secretory granule. Human ortholog(s) of this gene implicated in cholecystolithiasis; colorectal cancer; gastroesophageal reflux disease; and human immunodeficiency virus infectious disease. Orthologous to human PLA2G2A (phospholipase A2 group IIA); PARTICIPATES IN glypican signaling pathway; indometacin pharmacodynamics pathway; indometacin pharmacodynamics pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: eted enzyme type IIA phospholipase A2; GIIC sPLA2; group IIA phospholipase A2; phosphatidylcholine 2-acylhydrolase 2A; phospholipase A2, group IIA (platelets, synovial fluid); phospholipase A2, membrane associated; platelet phospholipase A2; sPLA2
RGD Orthologs
Human
Mouse
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25151,076,442 - 151,079,019 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5151,076,442 - 151,079,014 (+)Ensembl
Rnor_6.05157,282,650 - 157,285,295 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5157,282,669 - 157,285,328 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05161,024,039 - 161,026,650 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45157,654,786 - 157,657,360 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15157,664,332 - 157,667,400 (+)NCBI
Celera5149,464,001 - 149,466,577 (+)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
5-aza-2'-deoxycytidine  (ISO)
acetic acid  (ISO)
aflatoxin B1  (ISO)
aflatoxin M1  (ISO)
aldehydo-D-glucosamine  (EXP)
all-trans-retinoic acid  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
anthocyanin  (EXP)
antirheumatic drug  (ISO)
baicalein  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (EXP)
betulinic acid  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
C60 fullerene  (EXP)
cadmium atom  (EXP,ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
chromium(6+)  (ISO)
ciglitazone  (ISO)
cisplatin  (ISO)
clothianidin  (ISO)
colforsin daropate hydrochloride  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
dibenzofuran  (EXP)
dimethyl sulfoxide  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
EC 3.1.1.4 (phospholipase A2) inhibitor  (ISO)
ellagic acid  (ISO)
entinostat  (ISO)
erythromycin A  (ISO)
ethanol  (EXP)
fenvalerate  (EXP)
furan  (EXP)
genistein  (ISO)
ibuprofen  (ISO)
indometacin  (ISO)
kaempferol 3-O-beta-D-galactoside  (ISO)
lead diacetate  (EXP)
lipopolysaccharide  (EXP,ISO)
lycopene  (ISO)
manganese(II) chloride  (EXP)
mangiferin  (ISO)
melittin  (ISO)
methotrexate  (ISO)
mithramycin  (ISO)
N'-Nitrosonornicotine  (EXP)
N-nitrosodiethylamine  (ISO)
nickel atom  (ISO)
nitrofen  (EXP)
olaparib  (EXP)
paclitaxel  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
phenethyl caffeate  (ISO)
phenobarbital  (EXP,ISO)
phenylephrine  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
phosgene  (EXP)
pirinixic acid  (ISO)
prostaglandin E2  (ISO)
quercetagetin  (ISO)
quercetin  (ISO)
rofecoxib  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
scutellarin  (ISO)
simvastatin  (EXP)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
tamoxifen  (ISO)
testosterone  (EXP)
tetracycline  (ISO)
thromboxane A2  (ISO)
thromboxane B2  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
ursodeoxycholic acid  (EXP)
valproic acid  (ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

References

References - curated
1. Abu-Maziad A, etal., Pediatr Res. 2010 Oct;68(4):323-9.
2. Antonio V, etal., Biochem J 2002 Dec 1;368(Pt 2):415-24.
3. Babu A, etal., J Gastrointest Surg. 2009 Dec;13(12):2212-8. Epub 2009 Aug 12.
4. Chen HL, etal., Inhal Toxicol. 2009 Feb;21(4):374-80.
5. Degousee N, etal., J Biol Chem 2001 Nov 23;276(47):43842-9.
6. Fijneman RJ, etal., Cancer Sci. 2008 Nov;99(11):2113-9.
7. Galecki P, etal., J Affect Disord. 2012 May;138(3):360-6. Epub 2012 Feb 12.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. GOA data from the GO Consortium
10. Ishizaki J, etal., Biochem Biophys Res Commun 1989 Aug 15;162(3):1030-6.
11. Kano M, etal., Hepatology. 1998 Aug;28(2):302-13.
12. KEGG
13. Kolko M, etal., J Neurosci Res 2002 Jul 15;69(2):169-77.
14. Komada M, etal., Biochem Biophys Res Commun 1990 May 16;168(3):1059-65.
15. Kuwata H, etal., J Immunol. 2000 Oct 1;165(7):4024-31.
16. Li K, etal., Mol Vis. 2010 Oct 14;16:2084-91.
17. Limou S, etal., Biomed Pharmacother. 2008 Jan;62(1):31-40. Epub 2007 Dec 3.
18. Lopez-Vales R, etal., FASEB J. 2011 Dec;25(12):4240-52. Epub 2011 Aug 25.
19. MacPhee M, etal., Cell 1995 Jun 16;81(6):957-66.
20. MGD data from the GO Consortium
21. NCBI rat LocusLink and RefSeq merged data July 26, 2002
22. OMIM Disease Annotation Pipeline
23. Pipeline to import KEGG annotations from KEGG into RGD
24. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
25. Pipeline to import SMPDB annotations from SMPDB into RGD
26. Ramanadham S, etal., Biochim Biophys Acta. 1998 Feb 23;1390(3):301-12.
27. RGD automated data pipeline
28. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
29. RGD automated import pipeline for gene-chemical interactions
30. Seeds MC, etal., Am J Med Sci. 2011 Dec 14.
31. Titsworth WL, etal., Glia. 2009 Nov 1;57(14):1521-37.
32. Van Schaik RH, etal., Biochim Biophys Acta 1993 Jul 21;1169(1):1-11.
33. Wu F and Chakravarti S, J Immunol. 2007 Nov 15;179(10):6988-7000.
34. Yu J, etal., Inflammation. 2012 Feb;35(1):11-22.
Additional References at PubMed
PMID:2263458   PMID:2400792   PMID:2606907   PMID:2722857   PMID:3235451   PMID:3356705   PMID:3654593   PMID:9032461   PMID:10358193   PMID:12056909   PMID:12782627   PMID:12882648  
PMID:15003994   PMID:15009712   PMID:15255941   PMID:15802623   PMID:15878884   PMID:15927955   PMID:16385482   PMID:16603549   PMID:16807371   PMID:17069818   PMID:17462919   PMID:17475622  
PMID:17908795   PMID:19052818   PMID:19237014   PMID:19375465   PMID:19678934   PMID:19850938   PMID:20086008   PMID:20153419   PMID:21943492   PMID:22093332   PMID:22788969   PMID:22837859  
PMID:23533145   PMID:23580065   PMID:23629656   PMID:25082876   PMID:26162096   PMID:32881777  


Genomics

Comparative Map Data
Pla2g2a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25151,076,442 - 151,079,019 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5151,076,442 - 151,079,014 (+)Ensembl
Rnor_6.05157,282,650 - 157,285,295 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5157,282,669 - 157,285,328 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05161,024,039 - 161,026,650 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45157,654,786 - 157,657,360 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15157,664,332 - 157,667,400 (+)NCBI
Celera5149,464,001 - 149,466,577 (+)NCBICelera
Cytogenetic Map5q36NCBI
PLA2G2A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl119,975,431 - 19,980,416 (-)EnsemblGRCh38hg38GRCh38
GRCh38119,975,431 - 19,980,434 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37120,301,924 - 20,306,927 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36120,174,518 - 20,179,496 (-)NCBINCBI36hg18NCBI36
Build 34120,047,239 - 20,052,215NCBI
Celera118,628,736 - 18,633,743 (-)NCBI
Cytogenetic Map1p36.13NCBI
HuRef118,547,710 - 18,552,716 (-)NCBIHuRef
CHM1_1120,411,642 - 20,416,650 (-)NCBICHM1_1
Pla2g2a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394138,559,168 - 138,562,500 (+)NCBIGRCm39mm39
GRCm39 Ensembl4138,559,168 - 138,562,497 (+)Ensembl
GRCm384138,831,857 - 138,835,189 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4138,831,857 - 138,835,186 (+)EnsemblGRCm38mm10GRCm38
MGSCv374138,387,772 - 138,391,104 (+)NCBIGRCm37mm9NCBIm37
MGSCv364138,103,933 - 138,107,259 (+)NCBImm8
Celera4140,618,192 - 140,621,524 (+)NCBICelera
Cytogenetic Map4D3NCBI
cM Map470.57NCBI
PLA2G2A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1119,973,352 - 19,977,627 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl119,971,084 - 19,977,627 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0118,930,294 - 18,934,563 (-)NCBIMhudiblu_PPA_v0panPan3
Pla2g2a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505840,267,196 - 40,271,190 (-)NCBI
SpeTri2.0NW_0049364746,091,978 - 6,095,961 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PLA2G2A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl678,327,319 - 78,330,699 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1678,327,728 - 78,339,546 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2672,517,061 - 72,556,712 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PLA2G2A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120112,564,414 - 112,569,735 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl20112,565,165 - 112,569,786 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660333,610,631 - 3,615,025 (-)NCBIVero_WHO_p1.0
Pla2g2a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247645,144,549 - 5,152,517 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH141234  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25151,078,784 - 151,078,970 (+)MAPPERmRatBN7.2
Rnor_6.05157,285,060 - 157,285,245NCBIRnor6.0
Rnor_5.05161,026,416 - 161,026,601UniSTSRnor5.0
RGSC_v3.45157,657,129 - 157,657,314UniSTSRGSC3.4
Celera5149,466,343 - 149,466,528UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
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)546711509161317411Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
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)5111416838156416838Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
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)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5143608201161165651Rat
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5143799107158428037Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5144358090157869054Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5144377876161317411Rat
1298090Bp155Blood pressure QTL 1553.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)5151006154161165494Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:124
Count of miRNA genes:93
Interacting mature miRNAs:99
Transcripts:ENSRNOT00000022827
Prediction methods:Microtar, Miranda, Rnahybrid, 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 1
Medium 2 15 30 22 19 22 7 11
Low 28 27 19 19 7 10 57 35 32 7
Below cutoff 1 1 14 2 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_031598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239146 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109379 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC118094 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF365363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY651027 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB772812 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D00523 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM212986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM212987 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220554 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234749 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M25148 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M37127 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X51529 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X52613 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X74364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000022827   ⟹   ENSRNOP00000022827
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5151,076,442 - 151,079,014 (+)Ensembl
Rnor_6.0 Ensembl5157,282,669 - 157,285,328 (+)Ensembl
RefSeq Acc Id: NM_031598   ⟹   NP_113786
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25151,076,442 - 151,079,019 (+)NCBI
Rnor_6.05157,282,718 - 157,285,294 (+)NCBI
Rnor_5.05161,024,039 - 161,026,650 (+)NCBI
RGSC_v3.45157,654,786 - 157,657,360 (+)RGD
Celera5149,464,001 - 149,466,577 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006239146   ⟹   XP_006239208
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25151,076,447 - 151,079,019 (+)NCBI
Rnor_6.05157,282,650 - 157,285,295 (+)NCBI
Rnor_5.05161,024,039 - 161,026,650 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039109379   ⟹   XP_038965307
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25151,077,089 - 151,079,019 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_113786   ⟸   NM_031598
- Peptide Label: precursor
- UniProtKB: P14423 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006239208   ⟸   XM_006239146
- Peptide Label: isoform X1
- UniProtKB: P14423 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022827   ⟸   ENSRNOT00000022827
RefSeq Acc Id: XP_038965307   ⟸   XM_039109379
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13694194
Promoter ID:EPDNEW_R4719
Type:multiple initiation site
Name:Pla2g2a_1
Description:phospholipase A2 group IIA
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_6.05157,282,718 - 157,282,778EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
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:620857 AgrOrtholog
Ensembl Genes ENSRNOG00000016945 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000022827 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000022827 UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.90.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro PLipase_A2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLipase_A2_Asp_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLipase_A2_dom UniProtKB/Swiss-Prot
  PLipase_A2_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLipase_A2_His_AS UniProtKB/Swiss-Prot
KEGG Report rno:29692 UniProtKB/Swiss-Prot
NCBI Gene 29692 ENTREZGENE
PANTHER PTHR11716 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Phospholip_A2_1 UniProtKB/Swiss-Prot
PharmGKB PLA2G2A RGD
PhenoGen Pla2g2a PhenoGen
PRINTS PHPHLIPASEA2 UniProtKB/Swiss-Prot
PROSITE PA2_ASP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PA2_HIS UniProtKB/Swiss-Prot
SMART PA2c UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48619 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B6VNU1_RAT UniProtKB/TrEMBL
  B6VNU2_RAT UniProtKB/TrEMBL
  P14423 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-30 Pla2g2a  phospholipase A2 group IIA  Pla2g2a  phospholipase A2, group IIA (platelets, synovial fluid)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Pla2g2a  phospholipase A2, group IIA (platelets, synovial fluid)      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Pla2g2a  phospholipase A2, group IIA (platelets, synovial fluid)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease mediates the pathogenesis of various inflammatory diseases, including sepsis and rheumatoid arthritis; found in atherosclerotic plaques 628361
gene_expression expressed in platelets and synovial fluid 70574
gene_expression synthesized and secreted in large amounts by smooth muscle cells (SMCs) when stimulated 628361
gene_function hydolyzes the acyl group at the sn-2 position of phospholipids present in lipoproteins and cell membranes forming non-esterified fatty acids and lysophospholipids 628361
gene_pathway Ras/Ets pathway is involved in the induction by IL-1b 628361
gene_product highly basic protein 70574
gene_regulation mRNA and cellular and extracellular protein levels were stimulated by interleukin-1beta (IL-1b) in cardiomyocytes; extracellular activity was also enhanced 70-fold 70574
gene_regulation p38 MAPK activity is required for IL-1b induction of expression and release 70574
gene_regulation induced by agents that increase intracellular cAMP, including forskolin and inflammatory cytokines like IL-1 b or TNFa 628361
gene_transcript distal region bearing a CAAT/enhancer binding protein (C/EBP)-responsive element (-242 to -223) was sufficient for cAMP/protein kinase A-mediated promoter activation and the activation of the promoter by IL-1b requires activation of an Ets-responsive elem 628361
gene_transcript 500bp region upstream of the transcription start site mediates activation by synergistically acting cAMP and IL-1b 628361