Atp7b (ATPase copper transporting beta) - Rat Genome Database

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Gene: Atp7b (ATPase copper transporting beta) Rattus norvegicus
Analyze
Symbol: Atp7b
Name: ATPase copper transporting beta
RGD ID: 2180
Description: Enables copper ion binding activity; copper ion transmembrane transporter activity; and zinc ion binding activity. Involved in several processes, including cellular response to metal ion; copper ion export; and lactation. Located in several cellular components, including basolateral plasma membrane; bicellular tight junction; and trans-Golgi network. Used to study Wilson disease; hepatitis; hepatocellular carcinoma; liver carcinoma; and renal adenoma. Human ortholog(s) of this gene implicated in Wilson disease. Orthologous to human ATP7B (ATPase copper transporting beta); PARTICIPATES IN cisplatin drug pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: ATPase Cu++ transporting beta polypeptide (same as Wilson disease); ATPase, Cu++ transporting, beta polypeptide; ATPase, Cu++ transporting, beta polypeptide (same as Wilson disease); copper pump 2; copper-transporting ATPase 2; Hts; PINA; PINA gene, promoter; pineal night-specific ATPase; Wd; wilson disease-associated protein homolog
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Atp7bhts  
Genetic Models: LEC/Tj LEC/Hok WKAH.LEC-Atp7bhts/Tj
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21669,952,286 - 70,024,404 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1669,951,778 - 70,023,636 (+)Ensembl
Rnor_6.01674,865,516 - 74,944,935 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1674,865,516 - 74,945,286 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01674,495,179 - 74,575,822 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41674,607,988 - 74,680,080 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11674,608,239 - 74,679,614 (+)NCBI
Celera1667,837,288 - 67,908,140 (+)NCBICelera
RH 3.4 Map16664.21RGD
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
1,1'-azobis(N,N-dimethylformamide)  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,6-dinitrotoluene  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
ammonium chloride  (EXP,ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
ATP  (ISO)
bathocuproine disulfonic acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
beta-hexachlorocyclohexane  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP)
brefeldin A  (ISO)
buta-1,3-diene  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
carboplatin  (ISO)
chloroprene  (ISO)
cholesterol  (EXP)
cisplatin  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) chloride  (EXP,ISO)
copper(II) sulfate  (ISO)
CU-O LINKAGE  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
D-penicillamine  (ISO)
decabromodiphenyl ether  (EXP)
dichlorine  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ferroheme b  (ISO)
folic acid  (ISO)
genistein  (EXP)
glutathione  (ISO)
glycidol  (EXP)
glycine betaine  (ISO)
GW 4064  (ISO)
heme b  (ISO)
hydrogen peroxide  (ISO)
iron atom  (EXP)
iron(0)  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
luteolin  (EXP)
magnesium atom  (ISO)
malonaldehyde  (EXP)
manganese atom  (EXP,ISO)
manganese(0)  (EXP,ISO)
manganese(II) chloride  (EXP)
menadione  (ISO)
methapyrilene  (ISO)
methoxychlor  (EXP)
methylmercury chloride  (ISO)
monosodium L-glutamate  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nitrofen  (EXP)
nocodazole  (ISO)
oxaliplatin  (ISO)
ozone  (EXP)
paracetamol  (ISO)
pentachlorophenol  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
platinum  (ISO)
platinum(0)  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
protoporphyrin  (ISO)
quercetin  (EXP,ISO)
S-adenosyl-L-homocysteine  (ISO)
S-adenosyl-L-methioninate  (ISO)
S-adenosyl-L-methionine  (ISO)
satraplatin  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
streptozocin  (EXP)
tetrachloromethane  (EXP)
tetrathiomolybdate(2-)  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
triclosan  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zinc acetate  (ISO)
zinc atom  (ISO)
zinc dichloride  (ISO)
zinc sulfate  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Aida T, etal., Gynecol Oncol. 2005 Apr;97(1):41-5.
2. Bauerly KA, etal., Am J Physiol Gastrointest Liver Physiol. 2005 May;288(5):G1007-14. Epub 2004 Dec 9.
3. Boerboom D, etal., Cancer Res. 2006 Feb 15;66(4):1964-73.
4. Borjigin J, etal., J Neurosci. 1999 Feb 1;19(3):1018-26.
5. Fu X, etal., Toxicol Sci. 2014 Jun;139(2):432-51. doi: 10.1093/toxsci/kfu048. Epub 2014 Mar 10.
6. Fujiyoshi J, etal., Sci Rep. 2019 Feb 7;9(1):1535. doi: 10.1038/s41598-018-38275-y.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Guo Y, etal., Am J Physiol Gastrointest Liver Physiol. 2005 Nov;289(5):G904-16. Epub 2005 Jun 30.
9. Hernandez S, etal., Gastroenterology. 2008 Apr;134(4):1215-23. Epub 2008 Jan 17.
10. Kanzaki A, etal., Jpn J Cancer Res. 2002 Jan;93(1):70-7.
11. Kelleher SL and Lonnerdal B, Am J Physiol Regul Integr Comp Physiol. 2006 Oct;291(4):R1181-91. Epub 2006 Jun 1.
12. Kelleher SL and Lonnerdal B, J Nutr. 2003 Jul;133(7):2141-8.
13. Kose H, etal., Genomics. 2007 Jun;89(6):673-7. doi: 10.1016/j.ygeno.2007.03.001. Epub 2007 Apr 16.
14. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
15. Levy E, etal., Life Sci. 2007 Mar 27;80(16):1472-83. Epub 2007 Jan 20.
16. Li Y, etal., J Clin Invest. 1991 May;87(5):1858-61. doi: 10.1172/JCI115208.
17. Masuda R, etal., Lab Anim. 1988 Apr;22(2):166-9. doi: 10.1258/002367788780864402.
18. Meng Y, etal., Biochim Biophys Acta 2004 Nov 5;1690(3):208-19.
19. Merle U, etal., Scand J Gastroenterol. 2006 Aug;41(8):974-82. doi: 10.1080/00365520600554790.
20. MGD data from the GO Consortium
21. Minami T, etal., Jpn J Cancer Res 2001 Aug;92(8):841-7.
22. Mori M, etal., Am J Pathol. 1994 Jan;144(1):200-4.
23. Nakayama K, etal., Int J Cancer. 2002 Oct 10;101(5):488-95.
24. NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. Okayasu T, etal., Pediatr Res. 1992 Mar;31(3):253-7. doi: 10.1203/00006450-199203000-00011.
26. OMIM Disease Annotation Pipeline
27. Platonova NA, etal., J Trace Elem Med Biol. 2017 Sep;43:126-134. doi: 10.1016/j.jtemb.2016.12.013. Epub 2017 Jan 3.
28. RGD automated data pipeline
29. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
30. RGD automated import pipeline for gene-chemical interactions
31. Sancho-Martinez SM, etal., Pharmacol Ther. 2012 Oct;136(1):35-55. doi: 10.1016/j.pharmthera.2012.07.003. Epub 2012 Jul 14.
32. Sasaki N, etal., Biochem Biophys Res Commun 1994 Jul 15;202(1):512-8.
33. Schmitt F, etal., PLoS One. 2013 Dec 17;8(12):e82323. doi: 10.1371/journal.pone.0082323. eCollection 2013.
34. Sánchez-Monteagudo A, etal., Clin Genet. 2020 Feb 11. doi: 10.1111/cge.13719.
35. Tsay MJ, etal., Biochim Biophys Acta. 2004 Jan 20;1688(1):78-85.
36. Wu J, etal., Nat Genet 1994 Aug;7(4):541-5.
37. Yamaguchi Y, etal., Biochem J 1994 Jul 1;301 ( Pt 1):1-4.
38. Yoshida MC, etal., J Hered 1987 Nov-Dec;78(6):361-5.
Additional References at PubMed
PMID:1588441   PMID:2845190   PMID:6863890   PMID:8040371   PMID:8257436   PMID:9392450   PMID:9465110   PMID:9484715   PMID:9837819   PMID:10441329   PMID:11085952   PMID:11237756  
PMID:12029094   PMID:12572677   PMID:14709553   PMID:15205462   PMID:15269005   PMID:15634671   PMID:15681833   PMID:15950762   PMID:16436657   PMID:16472602   PMID:16567646   PMID:16939419  
PMID:16964378   PMID:17987273   PMID:18637198   PMID:19946888   PMID:20836889   PMID:22130675   PMID:25378584   PMID:26004889  


Genomics

Comparative Map Data
Atp7b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21669,952,286 - 70,024,404 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1669,951,778 - 70,023,636 (+)Ensembl
Rnor_6.01674,865,516 - 74,944,935 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1674,865,516 - 74,945,286 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01674,495,179 - 74,575,822 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41674,607,988 - 74,680,080 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11674,608,239 - 74,679,614 (+)NCBI
Celera1667,837,288 - 67,908,140 (+)NCBICelera
RH 3.4 Map16664.21RGD
Cytogenetic Map16q12.5NCBI
ATP7B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1351,930,436 - 52,012,125 (-)EnsemblGRCh38hg38GRCh38
GRCh381351,932,669 - 52,012,130 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371352,506,805 - 52,585,586 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361351,404,806 - 51,483,631 (-)NCBINCBI36hg18NCBI36
Build 341351,404,805 - 51,483,631NCBI
Celera1333,555,444 - 33,634,269 (-)NCBI
Cytogenetic Map13q14.3NCBI
HuRef1333,295,317 - 33,374,147 (-)NCBIHuRef
CHM1_11352,473,433 - 52,553,190 (-)NCBICHM1_1
Atp7b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39822,482,799 - 22,550,632 (-)NCBIGRCm39mm39
GRCm39 Ensembl822,482,801 - 22,550,321 (-)Ensembl
GRCm38821,992,783 - 22,060,074 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl821,992,785 - 22,060,305 (-)EnsemblGRCm38mm10GRCm38
MGSCv37823,104,820 - 23,170,546 (-)NCBIGRCm37mm9NCBIm37
MGSCv36823,459,893 - 23,525,619 (-)NCBImm8
Celera823,490,671 - 23,556,555 (-)NCBICelera
Cytogenetic Map8A2NCBI
cM Map810.78NCBI
Atp7b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554315,229,126 - 5,269,616 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554315,228,395 - 5,297,120 (-)NCBIChiLan1.0ChiLan1.0
ATP7B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11351,808,491 - 51,888,488 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1351,810,555 - 51,851,839 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01333,063,698 - 33,144,528 (-)NCBIMhudiblu_PPA_v0panPan3
ATP7B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.122162,474 - 225,599 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl22191,888 - 225,266 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha22227,530 - 260,908 (+)NCBI
ROS_Cfam_1.022144,381 - 208,578 (+)NCBI
UMICH_Zoey_3.12295,838 - 129,431 (+)NCBI
UNSW_CanFamBas_1.022145,387 - 179,042 (+)NCBI
UU_Cfam_GSD_1.022163,429 - 197,022 (+)NCBI
Atp7b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945161,210,231 - 161,278,988 (-)NCBI
SpeTri2.0NW_0049365654,694,294 - 4,763,661 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATP7B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11115,892,549 - 15,942,070 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21116,218,277 - 16,263,614 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ATP7B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1329,817,712 - 29,899,302 (-)NCBI
ChlSab1.1 Ensembl329,816,860 - 29,899,077 (-)Ensembl
Vero_WHO_p1.0NW_02366605713,915,907 - 13,997,411 (+)NCBI
Atp7b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247482,112,574 - 2,183,994 (+)NCBI

Position Markers
RH94694  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21670,022,578 - 70,022,768 (+)MAPPERmRatBN7.2
Rnor_6.01674,943,878 - 74,944,067NCBIRnor6.0
Rnor_5.01674,573,744 - 74,573,933UniSTSRnor5.0
RGSC_v3.41674,679,023 - 74,679,212UniSTSRGSC3.4
Celera1667,907,083 - 67,907,272UniSTS
RH 3.4 Map16664.21UniSTS
Cytogenetic Map16q12.2-q12.4UniSTS
Atp7b  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21669,987,114 - 69,987,972 (+)MAPPERmRatBN7.2
Rnor_6.01674,906,171 - 74,907,028NCBIRnor6.0
Rnor_5.01674,535,834 - 74,536,691UniSTSRnor5.0
RGSC_v3.41674,643,520 - 74,644,377UniSTSRGSC3.4
Celera1667,872,111 - 67,872,968UniSTS
Cytogenetic Map16q12.2-q12.4UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162515279370152793Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165571108783402471Rat
1298527Arunc2Aerobic running capacity QTL 22.9exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)166853271675029966Rat


Genetic Models
This gene Atp7b is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:356
Count of miRNA genes:198
Interacting mature miRNAs:229
Transcripts:ENSRNOT00000058072
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
Medium 1 2 41 41 3 41 1
Low 2 29 7 10 74 35 39 11
Below cutoff 12 9 6 8 9 1 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000058072   ⟹   ENSRNOP00000054880
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1669,986,513 - 70,023,636 (+)Ensembl
Rnor_6.0 Ensembl1674,865,516 - 74,944,935 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089265   ⟹   ENSRNOP00000069905
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1669,973,188 - 70,023,636 (+)Ensembl
Rnor_6.0 Ensembl1674,886,719 - 74,945,286 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109904   ⟹   ENSRNOP00000094594
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1669,951,778 - 70,023,636 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000118838   ⟹   ENSRNOP00000086033
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1669,952,286 - 70,023,636 (+)Ensembl
RefSeq Acc Id: NM_012511   ⟹   NP_036643
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21669,952,286 - 70,023,636 (+)NCBI
Rnor_6.01674,865,516 - 74,944,935 (+)NCBI
Rnor_5.01674,495,179 - 74,575,822 (+)NCBI
RGSC_v3.41674,607,988 - 74,680,080 (+)RGD
Celera1667,837,288 - 67,908,140 (+)RGD
Sequence:
RefSeq Acc Id: XM_017599991   ⟹   XP_017455480
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21669,972,856 - 70,024,404 (+)NCBI
Rnor_6.01674,886,737 - 74,944,934 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039094191   ⟹   XP_038950119
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21669,996,812 - 70,023,295 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036643   ⟸   NM_012511
- UniProtKB: Q9QUG4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455480   ⟸   XM_017599991
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JWJ5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000054880   ⟸   ENSRNOT00000058072
RefSeq Acc Id: ENSRNOP00000069905   ⟸   ENSRNOT00000089265
RefSeq Acc Id: XP_038950119   ⟸   XM_039094191
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000094594   ⟸   ENSRNOT00000109904
RefSeq Acc Id: ENSRNOP00000086033   ⟸   ENSRNOT00000118838
Protein Domains
HMA

Transcriptome

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

Promoters
RGD ID:13700195
Promoter ID:EPDNEW_R10719
Type:initiation region
Name:Atp7b_1
Description:ATPase copper transporting beta
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01674,865,497 - 74,865,557EPDNEW

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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
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
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)
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)
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
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
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)
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
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)
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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
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)
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)
SS/JrHsdMcwi (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
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2180 AgrOrtholog
Ensembl Genes ENSRNOG00000012878 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000054880 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069905 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000058072 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000089265 UniProtKB/TrEMBL
Gene3D-CATH 3.40.1110.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro ATPase_P-typ_cyto_dom_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-typ_P_site UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-typ_TM_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-typ_transduc_dom_A_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HAD-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Heavy-metal-associated_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMA_Cu_ion-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMA_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMA_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-typ_ATPase_IB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P_typ_ATPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P_typ_ATPase_HD_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24218 UniProtKB/TrEMBL
NCBI Gene 24218 ENTREZGENE
Pfam HMA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB ATP7B RGD
PhenoGen Atp7b PhenoGen
PROSITE ATPASE_E1_E2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMA_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMA_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF55008 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56784 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF81653 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF81665 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs ATPase-IB_hvy UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TIGR00003 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JWJ5 ENTREZGENE, UniProtKB/TrEMBL
  ATP7B_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q9QUG4 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary Q63676 UniProtKB/Swiss-Prot
  Q9JLY3 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Atp7b  ATPase copper transporting beta  Atp7b  ATPase, Cu++ transporting, beta polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Atp7b  ATPase, Cu++ transporting, beta polypeptide    ATPase, Cu++ transporting, beta polypeptide (same as Wilson disease)  Name updated 625702 APPROVED
2002-06-10 Atp7b  ATPase, Cu++ transporting, beta polypeptide (same as Wilson disease)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease deletion of 900 bp of the coding region at the 3' end results in the rat model for Wilson disease 631728
gene_function copper transport ATPase 631728
gene_process necessary component of copper transport pathway 631728