Atp2a2 (ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2) - Rat Genome Database

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Gene: Atp2a2 (ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2) Rattus norvegicus
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Symbol: Atp2a2
Name: ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2
RGD ID: 2174
Description: Enables several functions, including ATP binding activity; P-type calcium transporter activity involved in regulation of cardiac muscle cell membrane potential; and lutropin-choriogonadotropic hormone receptor binding activity. Involved in several processes, including calcium ion transport; regulation of cardiac muscle cell membrane potential; and regulation of cardiac muscle contraction. Located in several cellular components, including apical ectoplasmic specialization; perinuclear region of cytoplasm; and sarcoplasmic reticulum. Is extrinsic component of cytoplasmic side of plasma membrane. Part of protein-containing complex. Used to study abdominal obesity-metabolic syndrome 1; congestive heart failure; and type 2 diabetes mellitus. Biomarker of euthyroid sick syndrome; heart disease; hypothyroidism; pulmonary hypertension; and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in acrokeratosis verruciformis; essential hypertension; keratosis follicularis; and pulmonary hypertension. Orthologous to human ATP2A2 (ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2); PARTICIPATES IN acebutolol pharmacodynamics pathway; adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway; amiodarone pharmacodynamics pathway; INTERACTS WITH (+)-pilocarpine; (R)-noradrenaline; 1-[(2,3,4-trimethoxyphenyl)methyl]piperazine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: ATPase, Ca++ transporting, cardiac muscle, slow twitch 2; ATPase, Ca++ transporting, slow twitch 2; calcium pump 2; calcium-transporting ATPase sarcoplasmic reticulum type, slow twitch skeletal muscle isoform; endoplasmic reticulum class 1/2 Ca(2+) ATPase; sarco(endo)plasmic reticulum Ca(2+)-dependent ATPase 2; sarcoplasmic/endoplasmic reticulum calcium ATPase 2; Serca2; SercaII; SR Ca(2+)-ATPase 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: QTLs:   Calcic1  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21234,072,710 - 34,122,142 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl1239,553,903 - 39,603,326 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01239,553,903 - 39,603,326 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01241,434,651 - 41,482,924 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41235,266,600 - 35,316,237 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11235,129,987 - 35,179,584 (+)NCBI
Celera1235,744,606 - 35,793,364 (+)NCBICelera
Cytogenetic Map12q16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
(R)-lipoic acid  (ISO)
(R)-noradrenaline  (EXP,ISO)
(S)-amphetamine  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-[(2,3,4-trimethoxyphenyl)methyl]piperazine  (EXP)
17alpha-ethynylestradiol  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2,6-dinitrotoluene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3,3',5-triiodo-L-thyronine  (EXP)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (ISO)
all-trans-retinoic acid  (ISO)
alloxan  (EXP)
alpha-pinene  (ISO)
amiodarone  (EXP)
ammonium acetate  (EXP)
ammonium chloride  (EXP)
Aroclor 1254  (ISO)
arsenous acid  (ISO)
astragaloside IV  (EXP)
atrazine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
beta-D-glucosamine  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Brodifacoum  (EXP)
butan-1-ol  (ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
candesartan  (EXP)
Candesartan cilexetil  (EXP)
capsaicin  (EXP)
carbon nanotube  (ISO)
carvedilol  (EXP)
chloropicrin  (ISO)
chlorpyrifos  (EXP)
choline  (ISO)
chrysene  (ISO)
cilostazol  (EXP)
cisplatin  (EXP)
clofibrate  (EXP)
cobalt dichloride  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
delta-tocotrienol  (ISO)
Deoxycorticosterone acetate  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
dieldrin  (EXP)
dioxygen  (EXP)
diuron  (EXP)
doxorubicin  (EXP,ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
ethanol  (ISO)
fenofibrate  (EXP)
fluoxetine  (EXP)
folic acid  (ISO)
fructose  (ISO)
furan  (EXP)
genistein  (EXP)
gentamycin  (EXP)
glafenine  (EXP)
Goe 6976  (EXP)
hexadecanoic acid  (ISO)
hydrogen peroxide  (EXP,ISO)
indinavir  (ISO)
indometacin  (ISO)
isoprenaline  (EXP)
L-methionine  (ISO)
lamivudine  (ISO)
leflunomide  (ISO)
lipoic acid  (ISO)
lipopolysaccharide  (ISO)
lithium atom  (EXP)
lithium hydride  (EXP)
lycopene  (ISO)
metformin  (EXP)
methamphetamine  (EXP)
methotrexate  (ISO)
methoxychlor  (EXP)
methylseleninic acid  (ISO)
metoprolol  (EXP)
N-acetyl-L-cysteine  (EXP,ISO)
nickel dichloride  (ISO)
ochratoxin A  (EXP,ISO)
ozone  (EXP,ISO)
paclitaxel  (EXP)
paracetamol  (ISO)
paraquat  (EXP,ISO)
PCB138  (EXP)
perfluorooctanoic acid  (EXP)
phenobarbital  (ISO)
phenylephrine  (EXP,ISO)
phlorizin  (ISO)
phorbol 13-acetate 12-myristate  (EXP)
pirinixic acid  (ISO)
piroxicam  (ISO)
potassium dichromate  (ISO)
prazosin  (EXP)
procymidone  (EXP)
progesterone  (EXP)
propiconazole  (ISO)
quercetin  (ISO)
razoxane  (EXP)
resveratrol  (EXP,ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
sarpogrelate  (EXP)
silicon dioxide  (ISO)
simvastatin  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium chloride  (EXP)
staurosporine  (EXP)
streptozocin  (EXP,ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
tetramethylpyrazine  (ISO)
tetraphene  (ISO)
thapsigargin  (EXP,ISO)
titanium dioxide  (ISO)
torcetrapib  (ISO)
tributylstannane  (ISO)
trichloroacetic acid  (EXP)
trichloroethene  (EXP,ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zidovudine  (ISO)
zinc oxide  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
autophagosome assembly  (ISO,ISS)
autophagosome membrane docking  (ISO,ISS)
calcium ion import into sarcoplasmic reticulum  (IDA)
calcium ion transmembrane transport  (IBA,IDA,ISO)
calcium ion transport  (IDA)
calcium ion transport from cytosol to endoplasmic reticulum  (ISO)
cardiac muscle hypertrophy in response to stress  (ISO)
cellular calcium ion homeostasis  (IBA,ISO)
cellular response to heat  (IEP)
cellular response to oxidative stress  (ISO)
endoplasmic reticulum calcium ion homeostasis  (ISO)
ER-nucleus signaling pathway  (ISO)
ion transmembrane transport  (IBA)
mitochondrion-endoplasmic reticulum membrane tethering  (ISO,ISS)
negative regulation of heart contraction  (ISO)
negative regulation of receptor binding  (ISO)
organelle localization by membrane tethering  (ISO,ISS)
organelle organization  (ISO)
positive regulation of endoplasmic reticulum calcium ion concentration  (ISO)
regulation of calcium ion-dependent exocytosis of neurotransmitter  (ISO)
regulation of cardiac muscle cell action potential involved in regulation of contraction  (IDA)
regulation of cardiac muscle cell membrane potential  (IDA)
regulation of cardiac muscle contraction by calcium ion signaling  (IBA,IDA,ISO)
regulation of muscle contraction  (TAS)
regulation of the force of heart contraction  (ISO)
relaxation of cardiac muscle  (IDA,ISO)
response to endoplasmic reticulum stress  (IEP)
response to lipopolysaccharide  (IEP)
response to peptide hormone  (IDA)
sarcoplasmic reticulum calcium ion transport  (IDA,ISO)
skeletal muscle contraction  (IEP)
T-tubule organization  (ISO)
transition between fast and slow fiber  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
acebutolol pharmacodynamics pathway  (ISO)
adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway  (ISO)
Alzheimer's disease pathway  (IEA)
amiodarone pharmacodynamics pathway  (ISO)
amlodipine pharmacodynamics pathway  (ISO)
arrhythmogenic right ventricular cardiomyopathy pathway  (IEA)
atenolol pharmacodynamics pathway  (ISO)
betaxolol pharmacodynamics pathway  (ISO)
bisoprolol pharmacodynamics pathway  (ISO)
bupranolol drug pathway  (ISO)
bupranolol pharmacodynamics pathway  (ISO)
calcium transport pathway  (ISO)
calcium/calcium-mediated signaling pathway  (IEA,ISO)
carvedilol pharmacodynamics pathway  (ISO)
dilated cardiomyopathy pathway  (IEA)
diltiazem pharmacodynamics pathway  (ISO)
disopyramide pharmacodynamics pathway  (ISO)
dobutamine pharmacodynamics pathway  (ISO)
esmolol pharmacodynamics pathway  (ISO)
flecainde pharmacodynamics pathway  (ISO)
fosphenytoin pharmacodynamics pathway  (ISO)
hypertrophic cardiomyopathy pathway  (IEA)
ibutilide pharmacodynamics pathway  (ISO)
isoprenaline pharmacodynamics pathway  (ISO)
isradipine pharmacodynamics pathway  (ISO)
levobunolol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
metoprolol pharmacodynamics pathway  (ISO)
mexiletine pharmacodynamics pathway  (ISO)
nadolol pharmacodynamics pathway  (ISO)
nebivolol pharmacodynamics pathway  (ISO)
nifedipine pharmacodynamics pathway  (ISO)
nimodipine pharmacodynamics pathway  (ISO)
nisoldipine pharmacodynamics pathway  (ISO)
nitrendipine pharmacodynamics pathway  (ISO)
penbutolol pharmacodynamics pathway  (ISO)
phenytoin pharmacodynamics pathway  (ISO)
pindolol pharmacodynamics pathway  (ISO)
procainamide pharmacodynamics pathway  (ISO)
propranolol pharmacodynamics pathway  (ISO)
quinidine pharmacodynamics pathway  (ISO)
sotalol pharmacodynamics pathway  (ISO)
timolol pharmacodynamics pathway  (ISO)
verapamil pharmacodynamics pathway  (ISO)

References

References - curated
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34. Pipeline to import KEGG annotations from KEGG into RGD
35. Pipeline to import SMPDB annotations from SMPDB into RGD
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37. RGD automated import pipeline for gene-chemical interactions
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Additional References at PubMed
PMID:8889548   PMID:9038922   PMID:9887021   PMID:10555147   PMID:10587333   PMID:11402072   PMID:12481932   PMID:12606313   PMID:12659846   PMID:12756243   PMID:12773312   PMID:12804600  
PMID:13129932   PMID:14561754   PMID:14575311   PMID:14593108   PMID:14747299   PMID:14749390   PMID:15191357   PMID:15201701   PMID:15528241   PMID:15670758   PMID:15670840   PMID:15677742  
PMID:15766574   PMID:16081076   PMID:16081870   PMID:16087130   PMID:16113063   PMID:16185075   PMID:16402920   PMID:16407245   PMID:16517946   PMID:16648178   PMID:16786169   PMID:17131044  
PMID:17287366   PMID:17482761   PMID:17516033   PMID:17717121   PMID:18006556   PMID:18068335   PMID:18408128   PMID:18456736   PMID:18562801   PMID:18581135   PMID:18612190   PMID:18836677  
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PMID:29476059   PMID:29947686   PMID:30188326   PMID:30717322   PMID:30721562   PMID:31373602   PMID:31409881   PMID:32353354   PMID:32704072   PMID:33130073  


Genomics

Candidate Gene Status
Atp2a2 is a candidate Gene for QTL Calcic1
Atp2a2 is a candidate Gene for QTL Calcic2
Comparative Map Data
Atp2a2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21234,072,710 - 34,122,142 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl1239,553,903 - 39,603,326 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01239,553,903 - 39,603,326 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01241,434,651 - 41,482,924 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41235,266,600 - 35,316,237 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11235,129,987 - 35,179,584 (+)NCBI
Celera1235,744,606 - 35,793,364 (+)NCBICelera
Cytogenetic Map12q16NCBI
ATP2A2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl12110,280,756 - 110,351,093 (+)EnsemblGRCh38hg38GRCh38
GRCh3812110,281,247 - 110,351,093 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3712110,719,052 - 110,788,898 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3612109,203,815 - 109,273,278 (+)NCBINCBI36hg18NCBI36
Build 3412109,182,151 - 109,251,615NCBI
Celera12110,344,773 - 110,414,642 (+)NCBI
Cytogenetic Map12q24.11NCBI
HuRef12107,737,670 - 107,807,502 (+)NCBIHuRef
CHM1_112110,686,837 - 110,756,707 (+)NCBICHM1_1
Atp2a2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395122,591,576 - 122,640,288 (-)NCBIGRCm39mm39
GRCm39 Ensembl5122,591,576 - 122,640,288 (-)Ensembl
GRCm385122,453,513 - 122,502,225 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5122,453,513 - 122,502,225 (-)EnsemblGRCm38mm10GRCm38
MGSCv375122,903,522 - 122,952,234 (-)NCBIGRCm37mm9NCBIm37
MGSCv365122,714,131 - 122,762,512 (-)NCBImm8
Celera5119,532,083 - 119,580,718 (-)NCBICelera
Cytogenetic Map5FNCBI
cM Map562.38NCBI
Atp2a2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554827,233,336 - 7,295,754 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554827,233,336 - 7,295,754 (+)NCBIChiLan1.0ChiLan1.0
ATP2A2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112111,249,039 - 111,316,532 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12111,246,508 - 111,311,923 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v012107,857,009 - 107,924,938 (+)NCBIMhudiblu_PPA_v0panPan3
ATP2A2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1268,148,181 - 8,209,392 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl268,148,236 - 8,209,388 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha268,312,735 - 8,373,567 (+)NCBI
ROS_Cfam_1.0268,406,466 - 8,467,508 (+)NCBI
UMICH_Zoey_3.1268,366,182 - 8,427,199 (+)NCBI
UNSW_CanFamBas_1.0268,424,775 - 8,485,590 (+)NCBI
UU_Cfam_GSD_1.0268,381,368 - 8,442,436 (+)NCBI
Atp2a2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118156,121,831 - 156,178,459 (-)NCBI
SpeTri2.0NW_0049365583,300,941 - 3,357,595 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATP2A2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1431,674,757 - 31,744,973 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11431,674,659 - 31,744,981 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21433,446,619 - 33,491,489 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Sscrofa10.21433,642,897 - 33,670,781 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ATP2A2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111105,522,175 - 105,590,291 (+)NCBI
ChlSab1.1 Ensembl11105,522,157 - 105,590,958 (+)Ensembl
Vero_WHO_p1.0NW_023666037139,532,362 - 139,600,791 (-)NCBI
Atp2a2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474721,509,360 - 21,567,424 (-)NCBI

Position Markers
D12S2026  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21234,121,779 - 34,122,116 (+)MAPPERmRatBN7.2
Rnor_6.01239,602,964 - 39,603,300NCBIRnor6.0
Rnor_5.01241,482,562 - 41,482,898UniSTSRnor5.0
RGSC_v3.41235,315,875 - 35,316,211UniSTSRGSC3.4
Celera1235,793,002 - 35,793,338UniSTS
Cytogenetic Map12q16UniSTS
G15902  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21234,118,867 - 34,119,059 (+)MAPPERmRatBN7.2
Rnor_6.01239,600,052 - 39,600,243NCBIRnor6.0
Rnor_5.01241,479,650 - 41,479,841UniSTSRnor5.0
RGSC_v3.41235,312,963 - 35,313,154UniSTSRGSC3.4
Celera1235,790,090 - 35,790,281UniSTS
Cytogenetic Map12q16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)1215081045150810Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1215081045150810Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)1249257845492578Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12247568747475687Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12251344247513442Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12251344247513442Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12421005149210051Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6922362652716770Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922363052716770Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12978983452716770Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121312721150320041Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121441977552716770Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)121502198652716770Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121571460941291738Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121590890052716770Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121590890052716770Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121718558044098244Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121834247752716770Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121834247752716770Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121872904352716770Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121875259352716770Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101875259352716770Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)122265070245946937Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122265070248598906Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)122265070252716770Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122265072141291738Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)122287629743799153Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)122490659052716770Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122609884552716770Rat
70169Eae13Experimental allergic encephalomyelitis QTL 130.032nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)122719024042196641Rat
8693658Alc33Alcohol consumption QTL 332.10.68drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)122911360949560679Rat
8693635Alc28Alcohol consumption QTL 282.70.439drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)122911360950757185Rat
1556747Calcic1Intracellular calcium level QTL 13.6platelet calcium amount (VT:0010500)platelet intracellular calcium level (CMO:0000922)123172356547433663Rat
1300175Cm5Cardiac mass QTL 53.78heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)123172356551955754Rat
1600386Calcic2Intracellular calcium level QTL 20.001platelet physiology trait (VT:0005464)platelet intracellular calcium level (CMO:0000922)123172356552716770Rat
1331787Rf41Renal function QTL 412.998kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)123172368845946802Rat
631829Alc6Alcohol consumption QTL 64.7consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)123228978243305579Rat
1300162Bp188Blood pressure QTL 1883.19arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123752188451955754Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1064
Count of miRNA genes:349
Interacting mature miRNAs:486
Transcripts:ENSRNOT00000001738, ENSRNOT00000024347
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 33
Medium 3 16 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001110139 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001110823 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_027839 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA900747 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC104314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF031937 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF043106 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BE119640 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BM387097 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK355798 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK356436 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK356454 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK357706 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK358684 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO404645 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EV765256 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223340 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J04022 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J04023 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J04024 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JC583798 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M25267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X15635 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000001738   ⟹   ENSRNOP00000001738
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1239,553,903 - 39,603,326 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000024347   ⟹   ENSRNOP00000024347
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1239,554,171 - 39,601,778 (+)Ensembl
RefSeq Acc Id: NM_001110139   ⟹   NP_001103609
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,072,710 - 34,122,142 (+)NCBI
Rnor_6.01239,553,903 - 39,603,326 (+)NCBI
Rnor_5.01241,434,651 - 41,482,924 (+)NCBI
RGSC_v3.41235,266,600 - 35,316,237 (+)RGD
Celera1235,744,606 - 35,793,364 (+)RGD
Sequence:
RefSeq Acc Id: NM_001110823   ⟹   NP_001104293
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,072,710 - 34,119,226 (+)NCBI
Rnor_6.01239,553,903 - 39,600,410 (+)NCBI
Rnor_5.01241,434,651 - 41,482,924 (+)NCBI
RGSC_v3.41235,266,600 - 35,316,237 (+)RGD
Celera1235,744,606 - 35,790,448 (+)NCBI
Sequence:
RefSeq Acc Id: NR_027839
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,072,710 - 34,122,142 (+)NCBI
Rnor_6.01239,553,903 - 39,603,326 (+)NCBI
Rnor_5.01241,434,651 - 41,482,924 (+)NCBI
RGSC_v3.41235,266,600 - 35,316,237 (+)RGD
Celera1235,744,606 - 35,793,364 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001103609   ⟸   NM_001110139
- Peptide Label: isoform a
- UniProtKB: P11507 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001104293   ⟸   NM_001110823
- Peptide Label: isoform b
- UniProtKB: P11507 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000024347   ⟸   ENSRNOT00000024347
RefSeq Acc Id: ENSRNOP00000001738   ⟸   ENSRNOT00000001738

Transcriptome

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

Promoters
RGD ID:13698642
Promoter ID:EPDNEW_R9166
Type:initiation region
Name:Atp2a2_1
Description:ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R9167  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01239,553,907 - 39,553,967EPDNEW
RGD ID:13698643
Promoter ID:EPDNEW_R9167
Type:initiation region
Name:Atp2a2_2
Description:ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R9166  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01239,554,336 - 39,554,396EPDNEW

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2174 AgrOrtholog
Ensembl Genes ENSRNOG00000001285 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000001738 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000024347 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000001738 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000024347 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.1110.10 UniProtKB/Swiss-Prot
  3.40.50.1000 UniProtKB/Swiss-Prot
InterPro ATPase_P-typ_cation-transptr_C UniProtKB/Swiss-Prot
  ATPase_P-typ_cation-transptr_N UniProtKB/Swiss-Prot
  ATPase_P-typ_cyto_dom_N UniProtKB/Swiss-Prot
  ATPase_P-typ_P_site UniProtKB/Swiss-Prot
  ATPase_P-typ_TM_dom_sf UniProtKB/Swiss-Prot
  ATPase_P-typ_transduc_dom_A_sf UniProtKB/Swiss-Prot
  HAD-like_sf UniProtKB/Swiss-Prot
  HAD_sf UniProtKB/Swiss-Prot
  P-type_ATPase_IIA UniProtKB/Swiss-Prot
  P_typ_ATPase UniProtKB/Swiss-Prot
  P_typ_ATPase_HD_dom UniProtKB/Swiss-Prot
KEGG Report rno:29693 UniProtKB/Swiss-Prot
NCBI Gene 29693 ENTREZGENE
Pfam Cation_ATPase_C UniProtKB/Swiss-Prot
  Cation_ATPase_N UniProtKB/Swiss-Prot
PharmGKB ATP2A2 RGD
PhenoGen Atp2a2 PhenoGen
PRINTS HATPASE UniProtKB/Swiss-Prot
PROSITE ATPASE_E1_E2 UniProtKB/Swiss-Prot
SMART Cation_ATPase_N UniProtKB/Swiss-Prot
Superfamily-SCOP SSF56784 UniProtKB/Swiss-Prot
  SSF81653 UniProtKB/Swiss-Prot
  SSF81660 UniProtKB/Swiss-Prot
  SSF81665 UniProtKB/Swiss-Prot
TIGRFAMs ATPase-IIA1_Ca UniProtKB/Swiss-Prot
  ATPase_P-type UniProtKB/Swiss-Prot
UniProt AT2A2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary P11508 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Atp2a2  ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2  Atp2a2  ATPase, Ca++ transporting, cardiac muscle, slow twitch 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Atp2a2  ATPase, Ca++ transporting, cardiac muscle, slow twitch 2    ATPase, Ca++ transporting, cardiac muscle, slow twitch 2   Symbol and Name status set to approved 625702 APPROVED
2003-04-14 Atp2a2  ATPase, Ca++ transporting, cardiac muscle, slow twitch 2   SercaII  sarco(endo)plasmic reticulum Ca(2+)-dependent ATPase 2  Data Merged 628472 PENDING
2002-06-10 SercaII  sarco(endo)plasmic reticulum Ca(2+)-dependent ATPase 2      Symbol and Name status set to approved 70586 APPROVED
2002-06-10 Atp2a2  ATPase, Ca++ transporting, cardiac muscle, slow twitch 2       Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in heart atria and ventricles 631306
gene_expression expressed in slow skeletal muscle 69761
gene_function transports calcium into the sarcoplasmic reticulum from the cytoplasm 68726
gene_function transports calcium into the sarcoplasmic reticulum from the cytoplasm 70642
gene_process plays a critical role in the contractile ability in cardiac myocytes 68726
gene_process plays a critical role in the contractile ability in cardiac myocytes 70642
gene_process involved in calcium cycling in the heart 631306
gene_process involved in sequestering calcium in endoplasmic reticulum stores in dental enamel-forming cells 1298687
gene_regulation expression induced by activation of ATF6 transcription factor and calcium depletion 70642
gene_regulation may be regulated by phospholamban 631306
gene_regulation expression level is responsive to thyroid hormone(T3)with atria demonstrating the largest change in protein content 631306