Pla2g2a (phospholipase A2 group IIA)

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Gene: Pla2g2a (phospholipase A2 group IIA) Rattus norvegicus

Analyze

Symbol:

Pla2g2a

Name:

phospholipase A2 group IIA

RGD ID:

620857

Description:

Exhibits calcium-dependent phospholipase A2 activity. Involved in phospholipid metabolic process. Localizes to 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 ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	PLA2G2A (phospholipase A2 group IIA)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Pla2g2a (phospholipase A2, group IIA (platelets, synovial fluid))	HGNC	Inparanoid, Panther, Ensembl
Pan paniscus (bonobo/pygmy chimpanzee):	PLA2G2A (phospholipase A2 group IIA)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pla2g2a (phospholipase A2 group IIA)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PLA2G2A (phospholipase A2 group IIA)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	PLA2G2A (phospholipase A2 group IIA)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Pla2g2a (phospholipase A2 group IIA)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	PLA2G2A (phospholipase A2 group IIA)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Pla2g2a (phospholipase A2, group IIA (platelets, synovial fluid))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	C07E3.9	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OMA\|PhylomeDB)
Caenorhabditis elegans (roundworm):	C03H5.4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OMA)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	151,076,442 - 151,079,019 (+)	NCBI
Rnor_6.0 Ensembl	5	157,282,669 - 157,285,328 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	157,282,650 - 157,285,295 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	161,024,039 - 161,026,650 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	157,654,786 - 157,657,360 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	157,664,332 - 157,667,400 (+)	NCBI
Celera	5	149,464,001 - 149,466,577 (+)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Acute Lung Injury (IEP)

Adrenal Insufficiency (IEP)

adult respiratory distress syndrome (ISO)

allergic conjunctivitis (ISO)

atherosclerosis (ISO)

cholecystolithiasis (ISO)

colitis (ISO)

colorectal cancer (ISO)

Colorectal Neoplasms (ISO)

endometriosis (ISO)

gastroesophageal reflux disease (ISO)

human immunodeficiency virus infectious disease (ISO)

Intestinal Neoplasms (ISO)

mental depression (ISO)

Myocardial Ischemia (ISO)

Neonatal Sepsis (ISO)

Reperfusion Injury (ISO)

Spinal Cord Injuries (IEP,ISO)

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)

olaparib (EXP)

paclitaxel (EXP)

panobinostat (ISO)

paracetamol (ISO)

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)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

arachidonic acid secretion (IEA)

cytolysis (IEA)

defense response to Gram-positive bacterium (ISO,ISS)

inflammatory response (IEA)

intestinal stem cell homeostasis (ISS)

lipid catabolic process (TAS)

phosphatidic acid metabolic process (ISO)

phosphatidylcholine metabolic process (ISO,ISS)

phosphatidylethanolamine metabolic process (ISO,ISS)

phospholipid metabolic process (IBA,IDA,ISO)

positive regulation of ERK1 and ERK2 cascade (ISO)

regulation of neutrophil activation (ISO,ISS)

Cellular Component

endoplasmic reticulum (IEA,ISO)

extracellular space (ISO)

mitochondrial outer membrane (IEA)

perinuclear region of cytoplasm (IDA)

plasma membrane (IEA)

secretory granule (IDA)

Molecular Function

calcium ion binding (IBA)

calcium-dependent phospholipase A2 activity (IBA,IDA,ISO)

phospholipase A2 activity (ISO,TAS)

phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine) (IEA)

phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine) (IEA)

phospholipid binding (IBA,ISO)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

alpha-linolenic acid metabolic pathway (IEA)

arachidonic acid metabolic pathway (IEA)

ether lipid metabolic pathway (IEA)

Fc epsilon receptor mediated signaling pathway (IEA)

glutamate signaling pathway (IEA)

glycerophospholipid metabolic pathway (IEA)

glypican signaling pathway (ISO)

gonadotropin-releasing hormone signaling pathway (IEA)

indometacin pharmacodynamics pathway (ISO)

linoleic acid metabolic pathway (IEA)

long term depression (IEA)

mitogen activated protein kinase signaling pathway (IEA)

toxoplasmosis pathway (IEA)

vascular endothelial growth factor signaling pathway (IEA)

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

Genomics

Comparative Map Data

Pla2g2a
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	151,076,442 - 151,079,019 (+)	NCBI
Rnor_6.0 Ensembl	5	157,282,669 - 157,285,328 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	157,282,650 - 157,285,295 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	161,024,039 - 161,026,650 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	157,654,786 - 157,657,360 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	157,664,332 - 157,667,400 (+)	NCBI
Celera	5	149,464,001 - 149,466,577 (+)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

PLA2G2A
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	1	19,975,431 - 19,980,416 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	19,975,431 - 19,980,434 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	20,301,924 - 20,306,927 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	20,174,518 - 20,179,496 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	1	20,047,239 - 20,052,215	NCBI
Celera	1	18,628,736 - 18,633,743 (-)	NCBI
Cytogenetic Map	1	p36.13	NCBI
HuRef	1	18,547,710 - 18,552,716 (-)	NCBI		HuRef
CHM1_1	1	20,411,642 - 20,416,650 (-)	NCBI		CHM1_1

Pla2g2a
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	138,559,168 - 138,562,500 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	4	138,559,168 - 138,562,497 (+)	Ensembl
GRCm38	4	138,831,857 - 138,835,189 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	138,831,857 - 138,835,186 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	138,387,772 - 138,391,104 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	4	138,103,933 - 138,107,259 (+)	NCBI			mm8
Celera	4	140,618,192 - 140,621,524 (+)	NCBI		Celera
Cytogenetic Map	4	D3	NCBI
cM Map	4	70.57	NCBI

PLA2G2A
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	1	19,973,352 - 19,977,627 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	19,971,084 - 19,977,627 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	18,930,294 - 18,934,563 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

Pla2g2a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405058	40,267,196 - 40,271,190 (-)	NCBI
SpeTri2.0	NW_004936474	6,091,978 - 6,095,961 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PLA2G2A
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	78,327,319 - 78,330,699 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	78,327,728 - 78,339,546 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	72,517,061 - 72,556,712 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PLA2G2A
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	20	112,564,414 - 112,569,735 (+)	NCBI
ChlSab1.1 Ensembl	20	112,565,165 - 112,569,786 (+)	Ensembl

Pla2g2a
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624764	5,144,549 - 5,152,517 (-)	NCBI

Position Markers

RH141234

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	157,285,060 - 157,285,245	NCBI	Rnor6.0
Rnor_5.0	5	161,026,416 - 161,026,601	UniSTS	Rnor5.0
RGSC_v3.4	5	157,657,129 - 157,657,314	UniSTS	RGSC3.4
Celera	5	149,466,343 - 149,466,528	UniSTS
Cytogenetic Map	5	q36	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1578766	Tcas11	Tongue tumor susceptibility QTL 11	4.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	5	47745646	167946134	Rat
61393	Bp7	Blood pressure QTL 7	4.5	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	61612600	168109659	Rat
1302790	Scl20	Serum cholesterol level QTL 20	6.4	0.0001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	84963058	173504662	Rat
1298089	Scl14	Serum cholesterol level QTL 14	5.8	0.0004	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	114140832	159140832	Rat
1598847	Cm62	Cardiac mass QTL 62	3.4		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	114140832	159140832	Rat
8552960	Pigfal15	Plasma insulin-like growth factor 1 level QTL 15			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	116767924	161767924	Rat
8694198	Abfw3	Abdominal fat weight QTL 3	16.13	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	5	116767924	161767924	Rat
8694389	Bw160	Body weight QTL 160	6.17	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	5	116767924	161767924	Rat
8694441	Bw169	Body weight QTL 169	17.61	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	5	116767924	161767924	Rat
1641920	Colcs1	Colorectal carcinoma susceptibility QTL 1	2.99	0.0055	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	5	128687766	173687766	Rat
10053720	Scort26	Serum corticosterone level QTL 26	2.06	0.0147	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	131077716	173707219	Rat
724525	Bp147	Blood pressure QTL 147	4.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	132551937	173707219	Rat
1598819	Bp292	Blood pressure QTL 292	4.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	133943857	173707219	Rat
1598861	Cm64	Cardiac mass QTL 64	2.9		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	133943857	173707219	Rat
634349	Bp139	Blood pressure QTL 139		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	134197905	173707219	Rat
8552908	Pigfal4	Plasma insulin-like growth factor 1 level QTL 4	6.6		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	134712342	173707219	Rat
8694169	Bw148	Body weight QTL 148	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	134712342	173707219	Rat
738018	Anxrr4	Anxiety related response QTL 4	5.1		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	5	136354114	173707219	Rat
7794791	Mcs33	Mammary carcinoma susceptibility QTL 33	1.93		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	5	136640731	173707219	Rat
631505	Bp103	Blood pressure QTL 103	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	138154677	172402610	Rat
631562	Apr2	Acute phase response QTL 2	3.7		blood murinoglobulin 1 amount (VT:0010597)	plasma murinoglobulin 1 level (CMO:0001931)	5	142307322	173707219	Rat
61444	Strs2	Sensitivity to stroke QTL 2	4.7		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	5	142309061	173707219	Rat
1331721	Bp210	Blood pressure QTL 210	3.413		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	5	149029982	173687766	Rat
2302369	Scl60	Serum cholesterol level QTL 60	3.13		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	149568588	167739697	Rat
631263	Cm24	Cardiac mass QTL 24	3.5		heart mass (VT:0007028)	heart left ventricle weight to body weight ratio (CMO:0000530)	5	149832180	164807402	Rat
1300119	Bp180	Blood pressure QTL 180	3.82		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	5	150340838	164298744	Rat
2313096	Bmd78	Bone mineral density QTL 78	3.1	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	5	150360936	167946134	Rat
1298090	Bp155	Blood pressure QTL 155	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	5	157212422	167739539	Rat

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

View RNA-SEQ Expression Data

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 Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	5	157,282,669 - 157,285,328 (+)	Ensembl

RefSeq Acc Id:

NM_031598 ⟹ NP_113786

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	151,076,442 - 151,079,019 (+)	NCBI
Rnor_6.0	5	157,282,718 - 157,285,294 (+)	NCBI
Rnor_5.0	5	161,024,039 - 161,026,650 (+)	NCBI
RGSC_v3.4	5	157,654,786 - 157,657,360 (+)	RGD
Celera	5	149,464,001 - 149,466,577 (+)	NCBI

Sequence:

show sequence

AAGGCAGGCCCTTGAACAAGAAGCCATACCACCATCCCATCCAAGAGAGCTGACAGCATGAAGG
TCCTCCTGTTGCTAGCAGTTGTGATCATGGCCTTTGGCTCAATTCAGGTCCAGGGGAGCCTTCT
GGAGTTTGGGCAAATGATTCTGTTTAAGACAGGAAAGAGAGCTGATGTTAGCTATGGCTTCTAC
GGTTGCCATTGTGGTGTGGGTGGCAGAGGATCCCCCAAGGATGCCACAGATTGGTGCTGTGTGA
CTCATGACTGTTGTTACAACCGTCTGGAGAAACGTGGATGTGGCACAAAGTTTCTGACCTACAA
GTTCTCCTACCGAGGGGGCCAAATCTCCTGCTCTACAAACCAGGACTCCTGCCGGAAACAGCTG
TGCCAGTGCGATAAAGCTGCCGCTGAATGTTTTGCCCGGAACAAGAAAAGCTACAGTTTAAAGT
ACCAGTTCTACCCCAACAAGTTTTGCAAAGGGAAGACGCCCAGTTGCTGAAAGAGACATCTTCT
GAAACATCCAGACATCCTCTAACACCTCTCCTAGCCCAACCAAGTTCCCCAGTGATCAAGAAAA
CACCCCTCTCCAACCCTAGAAGCAGGCGGGCCCTTCTGTCTTCACCCAGAAGGAGCCGCTGAAG
CCTGATCTTTCCCCAACACTCCACAGCCTTGGATCCGCCCACTTTTCCCTTGGCATCCAACTTC
CTGCTGCGTAGTACCTAAGAGGGTCCTGAGAGGCTCTCGCAAGTAAAGCAATTCATCAACAAAA
AAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006239146 ⟹ XP_006239208

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	151,076,447 - 151,079,019 (+)	NCBI
Rnor_6.0	5	157,282,650 - 157,285,295 (+)	NCBI
Rnor_5.0	5	161,024,039 - 161,026,650 (+)	NCBI

Sequence:

show sequence

GTGGCTCTCCGATCCCCAGCCCTGCAGAGGGAAGAGCTATTTAAGAGCATTGGGAGTACAGGAA
AAACAAGGCAGGCCCTTGAACAAGAAGCCATACCACCATCCCATCCAAGAGAACGAGTCCCAGG
AGGACTAGAGGAAGTGCAGGGGTGGTCCCATCACCACATCATTCCTGTGTGAGGGACAGTTCCA
CGGAGCCAGGAGGGACAAGAGAGCTGACAGCATGAAGGTCCTCCTGTTGCTAGCAGTTGTGATC
ATGGCCTTTGGCTCAATTCAGGTCCAGGGGAGCCTTCTGGAGTTTGGGCAAATGATTCTGTTTA
AGACAGGAAAGAGAGCTGATGTTAGCTATGGCTTCTACGGTTGCCATTGTGGTGTGGGTGGCAG
AGGATCCCCCAAGGATGCCACAGATTGGTGCTGTGTGACTCATGACTGTTGTTACAACCGTCTG
GAGAAACGTGGATGTGGCACAAAGTTTCTGACCTACAAGTTCTCCTACCGAGGGGGCCAAATCT
CCTGCTCTACAAACCAGGACTCCTGCCGGAAACAGCTGTGCCAGTGCGATAAAGCTGCCGCTGA
ATGTTTTGCCCGGAACAAGAAAAGCTACAGTTTAAAGTACCAGTTCTACCCCAACAAGTTTTGC
AAAGGGAAGACGCCCAGTTGCTGAAAGAGACATCTTCTGAAACATCCAGACATCCTCTAACACC
TCTCCTAGCCCAACCAAGTTCCCCAGTGATCAAGAAAACACCCCTCTCCAACCCTAGAAGCAGG
CGGGCCCTTCTGTCTTCACCCAGAAGGAGCCGCTGAAGCCTGATCTTTCCCCAACACTCCACAG
CCTTGGATCCGCCCACTTTTCCCTTGGCATCCAACTTCCTGCTGCGTAGTACCTAAGAGGGTCC
TGAGAGGCTCTCGCAAGTAAAGCAATTCATCAACAAC

hide sequence

RefSeq Acc Id:

XM_039109379 ⟹ XP_038965307

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	151,077,089 - 151,079,019 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_113786	(Get FASTA)	NCBI Sequence Viewer
	XP_006239208	(Get FASTA)	NCBI Sequence Viewer
	XP_038965307	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA41223	(Get FASTA)	NCBI Sequence Viewer
	AAA41920	(Get FASTA)	NCBI Sequence Viewer
	AAK52061	(Get FASTA)	NCBI Sequence Viewer
	AAT68713	(Get FASTA)	NCBI Sequence Viewer
	BAA00410	(Get FASTA)	NCBI Sequence Viewer
	CAA35909	(Get FASTA)	NCBI Sequence Viewer
	CAR82344	(Get FASTA)	NCBI Sequence Viewer
	CAR82345	(Get FASTA)	NCBI Sequence Viewer
	EDL80890	(Get FASTA)	NCBI Sequence Viewer
	EDL80891	(Get FASTA)	NCBI Sequence Viewer
	P14423	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_113786 ⟸ NM_031598
- Peptide Label:	precursor
- UniProtKB:	P14423 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MKVLLLLAVVIMAFGSIQVQGSLLEFGQMILFKTGKRADVSYGFYGCHCGVGGRGSPKDATDWC CVTHDCCYNRLEKRGCGTKFLTYKFSYRGGQISCSTNQDSCRKQLCQCDKAAAECFARNKKSYS LKYQFYPNKFCKGKTPSC hide sequence

RefSeq Acc Id:	XP_006239208 ⟸ XM_006239146
- Peptide Label:	isoform X1
- UniProtKB:	P14423 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MKVLLLLAVVIMAFGSIQVQGSLLEFGQMILFKTGKRADVSYGFYGCHCGVGGRGSPKDATDWC CVTHDCCYNRLEKRGCGTKFLTYKFSYRGGQISCSTNQDSCRKQLCQCDKAAAECFARNKKSYS LKYQFYPNKFCKGKTPSC hide 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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	5	157,282,718 - 157,282,778	EPDNEW

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

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620857	AgrOrtholog
Ensembl Genes	ENSRNOG00000016945	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000022827	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000022827	ENTREZGENE, 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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)

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Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)