Atp2b1 (ATPase plasma membrane Ca2+ transporting 1) - Rat Genome Database

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Gene: Atp2b1 (ATPase plasma membrane Ca2+ transporting 1) Rattus norvegicus
Analyze
Symbol: Atp2b1
Name: ATPase plasma membrane Ca2+ transporting 1
RGD ID: 621303
Description: Enables PDZ domain binding activity. Involved in several processes, including calcium ion export; cellular response to lipid; and response to cold. Located in several cellular components, including basolateral plasma membrane; dendritic spine membrane; and neuronal cell body membrane. Is active in GABA-ergic synapse and glutamatergic synapse. Is integral component of presynaptic active zone membrane. Biomarker of hypertension. Orthologous to human ATP2B1 (ATPase plasma membrane Ca2+ transporting 1); PARTICIPATES IN calcium transport pathway; calcium/calcium-mediated signaling pathway; INTERACTS WITH 1,2-dimethylhydrazine; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: ATPase, Ca++ transporting, plasma membrane 1; plasma membrane calcium ATPase; plasma membrane calcium pump; plasma membrane calcium-transporting ATPase 1; Pmca1; Pmca1a; Pmca1b; Pmca1c
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Atp2b1em2Mcwi  
Genetic Models: SS-Atp2b1em2Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2733,735,595 - 33,845,226 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl733,735,871 - 33,843,295 (+)Ensembl
Rnor_6.0741,114,606 - 41,223,138 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl741,114,697 - 41,220,579 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0741,153,926 - 41,262,537 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4736,493,661 - 36,600,280 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1736,513,931 - 36,620,551 (+)NCBI
Celera730,753,051 - 30,859,194 (+)NCBICelera
Cytogenetic Map7q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3-dimethoxynaphthalene-1,4-dione  (ISO)
2,6-dinitrotoluene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
4-tert-Octylphenol  (EXP)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
aminoguanidine  (EXP)
antimony(0)  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bucladesine  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calciol  (ISO)
calcitriol  (EXP,ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
chromium atom  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (EXP,ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP)
diethylstilbestrol  (EXP)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
disulfiram  (EXP)
diuron  (EXP)
endosulfan  (EXP)
Enterolactone  (ISO)
ethanol  (EXP,ISO)
gallic acid  (ISO)
gentamycin  (EXP)
gold atom  (ISO)
gold(0)  (ISO)
irinotecan  (EXP)
isoflavones  (ISO)
ivermectin  (ISO)
lycopene  (ISO)
medroxyprogesterone acetate  (ISO)
melphalan  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
miconazole  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodimethylamine  (ISO)
oxaliplatin  (EXP)
p-tert-Amylphenol  (EXP)
paracetamol  (ISO)
PCB138  (EXP)
perfluorononanoic acid  (ISO)
phenobarbital  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
serpentine asbestos  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
streptozocin  (ISO)
succimer  (ISO)
sunitinib  (ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (ISO)
tetrahydropalmatine  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
triptonide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
tungsten  (ISO)
valproic acid  (EXP,ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
vinclozolin  (EXP)
zinc oxide  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Armbrecht HJ, etal., Biochim Biophys Acta. 1994 Oct 12;1195(1):110-4.
2. Bhargava A, etal., J Neurosci. 2000 May 1;20(9):3129-38.
3. Boyken J, etal., Neuron. 2013 Apr 24;78(2):285-97. doi: 10.1016/j.neuron.2013.02.027.
4. Brandt P and Neve RL, J Neurochem. 1992 Oct;59(4):1566-9.
5. Brini M and Carafoli E, Physiol Rev. 2009 Oct;89(4):1341-78. doi: 10.1152/physrev.00032.2008.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Glendenning P, etal., J Bone Miner Res. 2001 Mar;16(3):525-34.
8. GOA data from the GO Consortium
9. Grati M, etal., J Cell Sci. 2006 Jul 15;119(Pt 14):2995-3007. Epub 2006 Jun 27.
10. Husain M, etal., Am J Physiol. 1997 Jun;272(6 Pt 1):C1947-59.
11. Jiang L, etal., J Neurochem. 2007 Jul;102(2):378-88.
12. Kenyon KA, etal., J Comp Neurol. 2010 Aug 15;518(16):3169-83. doi: 10.1002/cne.22409.
13. MGD data from the GO Consortium
14. NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. Pipeline to import KEGG annotations from KEGG into RGD
16. Post H, etal., Prostate. 2008 Jul 1;68(10):1076-85.
17. Renteria RC, etal., Vis Neurosci. 2005 May-Jun;22(3):263-74.
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. Sgambato-Faure V, etal., Biochem Biophys Res Commun. 2006 May 5;343(2):630-7. Epub 2006 Mar 15.
21. Shull GE and Greeb J, J Biol Chem 1988 Jun 25;263(18):8646-57.
22. Zhang GH, etal., Zhonghua Yi Xue Za Zhi. 2009 Nov 3;89(40):2862-6.
Additional References at PubMed
PMID:8428948   PMID:10858669   PMID:14593108   PMID:16956963   PMID:17938178   PMID:18029012   PMID:18058007   PMID:19292454   PMID:19653992   PMID:19946888   PMID:20458337   PMID:20553254  
PMID:22311909   PMID:22713297   PMID:22871113   PMID:23460639   PMID:24378673   PMID:24805951   PMID:26392310   PMID:28827723   PMID:29104511   PMID:29476059   PMID:29950683   PMID:30053369  
PMID:30190470  


Genomics

Comparative Map Data
Atp2b1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2733,735,595 - 33,845,226 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl733,735,871 - 33,843,295 (+)Ensembl
Rnor_6.0741,114,606 - 41,223,138 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl741,114,697 - 41,220,579 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0741,153,926 - 41,262,537 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4736,493,661 - 36,600,280 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1736,513,931 - 36,620,551 (+)NCBI
Celera730,753,051 - 30,859,194 (+)NCBICelera
Cytogenetic Map7q13NCBI
ATP2B1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1289,588,049 - 89,709,300 (-)EnsemblGRCh38hg38GRCh38
GRCh381289,588,049 - 89,709,366 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371289,981,826 - 90,103,143 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361288,505,957 - 88,573,975 (-)NCBINCBI36hg18NCBI36
Build 341288,484,295 - 88,552,312NCBI
Celera1289,653,490 - 89,721,509 (-)NCBI
Cytogenetic Map12q21.33NCBI
HuRef1287,047,680 - 87,115,698 (-)NCBIHuRef
CHM1_11289,946,885 - 90,014,891 (-)NCBICHM1_1
Atp2b1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391098,750,243 - 98,862,005 (+)NCBIGRCm39mm39
GRCm39 Ensembl1098,750,268 - 98,862,005 (+)Ensembl
GRCm381098,914,630 - 99,026,143 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1098,914,406 - 99,026,143 (+)EnsemblGRCm38mm10GRCm38
MGSCv371098,377,786 - 98,488,777 (+)NCBIGRCm37mm9NCBIm37
MGSCv361098,344,858 - 98,453,480 (+)NCBImm8
Celera10100,886,627 - 100,998,171 (+)NCBICelera
Cytogenetic Map10C3NCBI
Atp2b1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540526,872,379 - 26,932,703 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540526,872,379 - 26,932,270 (-)NCBIChiLan1.0ChiLan1.0
ATP2B1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11290,427,560 - 90,495,320 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1290,427,560 - 90,495,320 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01287,107,900 - 87,229,514 (-)NCBIMhudiblu_PPA_v0panPan3
ATP2B1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11530,547,009 - 30,674,094 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1530,547,015 - 30,616,429 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1531,001,748 - 31,071,230 (-)NCBI
ROS_Cfam_1.01531,191,421 - 31,320,135 (-)NCBI
UMICH_Zoey_3.11530,496,017 - 30,565,441 (-)NCBI
UNSW_CanFamBas_1.01530,557,909 - 30,627,319 (-)NCBI
UU_Cfam_GSD_1.01530,851,958 - 30,921,528 (-)NCBI
Atp2b1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494529,604,363 - 29,710,134 (+)NCBI
SpeTri2.0NW_0049365076,525,302 - 6,631,003 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATP2B1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl592,935,694 - 93,061,446 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1592,935,688 - 93,061,406 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2597,597,062 - 97,709,794 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ATP2B1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11184,985,957 - 85,053,923 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1184,989,169 - 85,103,957 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037160,096,429 - 160,215,991 (+)NCBIVero_WHO_p1.0
Atp2b1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475016,990,288 - 17,103,279 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH144662  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2733,835,721 - 33,835,927 (+)MAPPERmRatBN7.2
Rnor_6.0741,214,071 - 41,214,276NCBIRnor6.0
Rnor_5.0741,253,241 - 41,253,446UniSTSRnor5.0
RGSC_v3.4736,593,772 - 36,593,977UniSTSRGSC3.4
Celera730,852,686 - 30,852,891UniSTS
RH 3.4 Map7279.7UniSTS
Cytogenetic Map7q13UniSTS
BF387281  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2733,788,039 - 33,788,212 (+)MAPPERmRatBN7.2
Rnor_6.0741,166,391 - 41,166,563NCBIRnor6.0
Rnor_5.0741,205,561 - 41,205,733UniSTSRnor5.0
RGSC_v3.4736,546,092 - 36,546,264UniSTSRGSC3.4
Celera730,805,006 - 30,805,178UniSTS
RH 3.4 Map7277.0UniSTS
Cytogenetic Map7q13UniSTS
RH140668  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2733,788,997 - 33,789,200 (+)MAPPERmRatBN7.2
Rnor_6.0741,167,349 - 41,167,551NCBIRnor6.0
Rnor_5.0741,206,519 - 41,206,721UniSTSRnor5.0
RGSC_v3.4736,547,050 - 36,547,252UniSTSRGSC3.4
Celera730,805,964 - 30,806,166UniSTS
RH 3.4 Map7277.3UniSTS
Cytogenetic Map7q13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)71903280735526300Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)71965431749753746Rat
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)71965431749753746Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72673740163902784Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)72940968353612950Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat


Genetic Models
This gene Atp2b1 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:220
Count of miRNA genes:141
Interacting mature miRNAs:156
Transcripts:ENSRNOT00000005450, ENSRNOT00000005491, ENSRNOT00000041354, ENSRNOT00000066174
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 41 54 38 19 38 8 10 74 35 34 11 8
Low 2 3 3 3 1 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053311 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006241294 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006241295 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006241296 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078600 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078601 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078602 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF076783 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212562 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212633 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227803 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229411 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230212 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232405 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J03753 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L04739 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000041354   ⟹   ENSRNOP00000040092
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl733,735,879 - 33,843,041 (+)Ensembl
Rnor_6.0 Ensembl741,114,697 - 41,220,579 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000066174   ⟹   ENSRNOP00000059397
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl733,735,871 - 33,843,295 (+)Ensembl
Rnor_6.0 Ensembl741,115,154 - 41,220,344 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000119758   ⟹   ENSRNOP00000090086
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl733,735,879 - 33,843,041 (+)Ensembl
RefSeq Acc Id: NM_053311   ⟹   NP_445763
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2733,735,975 - 33,842,229 (+)NCBI
Rnor_6.0741,114,697 - 41,220,579 (+)NCBI
Rnor_5.0741,153,926 - 41,262,537 (+)NCBI
RGSC_v3.4736,493,661 - 36,600,280 (+)RGD
Celera730,753,051 - 30,859,194 (+)RGD
Sequence:
RefSeq Acc Id: XM_006241294   ⟹   XP_006241356
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2733,735,596 - 33,845,226 (+)NCBI
Rnor_6.0741,114,606 - 41,223,138 (+)NCBI
Rnor_5.0741,153,926 - 41,262,537 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006241296   ⟹   XP_006241358
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2733,735,597 - 33,845,226 (+)NCBI
Rnor_6.0741,114,606 - 41,223,138 (+)NCBI
Rnor_5.0741,153,926 - 41,262,537 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039078600   ⟹   XP_038934528
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2733,735,595 - 33,845,226 (+)NCBI
RefSeq Acc Id: XM_039078601   ⟹   XP_038934529
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2733,736,361 - 33,845,226 (+)NCBI
RefSeq Acc Id: XM_039078602   ⟹   XP_038934530
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2733,736,793 - 33,845,226 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_445763   ⟸   NM_053311
- UniProtKB: P11505 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006241356   ⟸   XM_006241294
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006241358   ⟸   XM_006241296
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000040092   ⟸   ENSRNOT00000041354
RefSeq Acc Id: ENSRNOP00000059397   ⟸   ENSRNOT00000066174
RefSeq Acc Id: XP_038934528   ⟸   XM_039078600
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934529   ⟸   XM_039078601
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934530   ⟸   XM_039078602
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000090086   ⟸   ENSRNOT00000119758

Transcriptome

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

Promoters
RGD ID:13695171
Promoter ID:EPDNEW_R5696
Type:initiation region
Name:Atp2b1_2
Description:ATPase plasma membrane Ca2+ transporting 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R5697  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0741,114,631 - 41,114,691EPDNEW
RGD ID:13695188
Promoter ID:EPDNEW_R5697
Type:multiple initiation site
Name:Atp2b1_1
Description:ATPase plasma membrane Ca2+ transporting 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R5696  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0741,115,081 - 41,115,141EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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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:621303 AgrOrtholog
Ensembl Genes ENSRNOG00000004026 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000040092 UniProtKB/Swiss-Prot
  ENSRNOP00000059397 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000041354 UniProtKB/Swiss-Prot
  ENSRNOT00000066174 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.1110.10 UniProtKB/Swiss-Prot
  3.40.50.1000 UniProtKB/Swiss-Prot
InterPro ATP2B1 UniProtKB/Swiss-Prot
  ATP_Ca_trans_C UniProtKB/Swiss-Prot
  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_IIB UniProtKB/Swiss-Prot
  P_typ_ATPase UniProtKB/Swiss-Prot
  P_typ_ATPase_HD_dom UniProtKB/Swiss-Prot
KEGG Report rno:29598 UniProtKB/Swiss-Prot
NCBI Gene 29598 ENTREZGENE
PANTHER PTHR24093:SF245 UniProtKB/Swiss-Prot
Pfam ATP_Ca_trans_C UniProtKB/Swiss-Prot
  Cation_ATPase_C UniProtKB/Swiss-Prot
  Cation_ATPase_N UniProtKB/Swiss-Prot
PhenoGen Atp2b1 PhenoGen
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-IIB_Ca UniProtKB/Swiss-Prot
  ATPase_P-type UniProtKB/Swiss-Prot
UniProt AT2B1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q63442 UniProtKB/Swiss-Prot
  Q9R1L7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Atp2b1  ATPase, Ca++ transporting, plasma membrane 1      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Atp2b1  ATPase, Ca++ transporting, plasma membrane 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_protein 1,176 amino acids; 129.5 kDa 631720