Atp7a (ATPase copper transporting alpha) - Rat Genome Database

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Gene: Atp7a (ATPase copper transporting alpha) Rattus norvegicus
Analyze
Symbol: Atp7a
Name: ATPase copper transporting alpha
RGD ID: 2179
Description: Exhibits chaperone binding activity and small GTPase binding activity. Involved in several processes, including cellular response to metal ion; gland development; and regulation of cation transmembrane transport. Localizes to several cellular components, including basolateral plasma membrane; brush border membrane; and cytoplasmic vesicle. Biomarker of Alzheimer's disease; Wilson disease; congenital diaphragmatic hernia; and iron deficiency anemia. Human ortholog(s) of this gene implicated in Menkes disease; X-linked distal spinal muscular atrophy 3; cutis laxa; and occipital horn syndrome. Orthologous to human ATP7A (ATPase copper transporting alpha); PARTICIPATES IN cisplatin drug pathway; INTERACTS WITH 1,2-dimethylhydrazine; 2,2,2-tetramine; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: ATPase Cu++ transporting alpha polypeptide (Menkes syndrome); ATPase, Cu++ transporting, alpha polypeptide; ATPase, Cu++ transporting, alpha polypeptide (Menkes syndrome); copper pump 1; copper-transporting ATPase 1; menkes disease-associated protein homolog; Mnk
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X71,094,144 - 71,201,550 (+)NCBI
Rnor_6.0 EnsemblX77,076,106 - 77,193,644 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X77,076,085 - 77,193,644 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X56,198,947 - 56,313,382 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X94,192,540 - 94,249,776 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X94,265,972 - 94,323,206 (+)NCBI
CeleraX72,450,404 - 72,510,070 (+)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1'-azobis(N,N-dimethylformamide)  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1,4-dithiothreitol  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2,2-tetramine  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-hydroxypropanoic acid  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acetylcholine  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
ATP  (ISO)
atrazine  (ISO)
bathocuproine disulfonic acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
brefeldin A  (ISO)
butanal  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (ISO)
carboplatin  (ISO)
chloroprene  (EXP)
chromium(6+)  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) chloride  (EXP,ISO)
copper(II) sulfate  (ISO)
CU-O LINKAGE  (ISO)
cycloheximide  (EXP)
cyclosporin A  (ISO)
D-penicillamine  (ISO)
decabromodiphenyl ether  (EXP)
desferrioxamine B  (EXP)
dextran sulfate  (ISO)
dibutyl phthalate  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
folic acid  (ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
irinotecan  (ISO)
iron atom  (EXP,ISO)
iron(0)  (EXP,ISO)
ketamine  (EXP)
L-1,4-dithiothreitol  (ISO)
lead diacetate  (EXP)
lipopolysaccharide  (ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
manganese(II) chloride  (EXP)
melanins  (ISO)
methapyrilene  (ISO)
methimazole  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
mithramycin  (EXP)
mitoxantrone  (ISO)
monensin A  (ISO)
N-ethylmaleimide  (ISO)
neocuproine  (ISO)
nitrofen  (EXP)
omeprazole  (ISO)
oxaliplatin  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
platinum  (ISO)
platinum(0)  (ISO)
potassium chromate  (ISO)
pyrrolidine dithiocarbamate  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
satraplatin  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver monochloride  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
streptozocin  (ISO)
succimer  (ISO)
superoxide  (ISO)
tetrachloromethane  (ISO)
tetrathiomolybdate(2-)  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (EXP,ISO)
vincristine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
ATP metabolic process  (ISO)
blood vessel development  (ISO)
blood vessel remodeling  (ISO)
cartilage development  (ISO)
catecholamine metabolic process  (ISO)
cellular copper ion homeostasis  (IBA,ISO,ISS)
cellular response to amino acid stimulus  (IMP)
cellular response to antibiotic  (IEP)
cellular response to cadmium ion  (IEP)
cellular response to cobalt ion  (IEP)
cellular response to copper ion  (IDA,IEP)
cellular response to hypoxia  (IEP)
cellular response to iron ion  (IEP)
cellular response to lead ion  (IEP)
cellular response to platelet-derived growth factor stimulus  (IMP)
central nervous system neuron development  (ISO)
cerebellar Purkinje cell differentiation  (ISO)
collagen fibril organization  (ISO)
copper ion export  (IBA,IMP,ISO,ISS)
copper ion import  (ISO)
copper ion transport  (IEA,ISO)
dendrite morphogenesis  (ISO)
detoxification of copper ion  (ISO)
dopamine metabolic process  (ISO)
elastic fiber assembly  (ISO)
elastin biosynthetic process  (ISO)
epinephrine metabolic process  (ISO)
extracellular matrix organization  (ISO)
female pregnancy  (IEP)
hair follicle morphogenesis  (ISO)
hindlimb morphogenesis  (ISO)
in utero embryonic development  (IEP)
lactation  (IEP)
liver development  (IEP)
locomotory behavior  (ISO)
lung alveolus development  (ISO)
mitochondrion organization  (ISO)
negative regulation of catecholamine metabolic process  (ISO)
negative regulation of iron ion transmembrane transport  (IMP)
negative regulation of neuron apoptotic process  (ISO)
neuron projection morphogenesis  (ISO)
norepinephrine biosynthetic process  (ISO)
norepinephrine metabolic process  (ISO)
peptidyl-lysine modification  (ISO)
pigmentation  (ISO)
positive regulation of catalytic activity  (ISO)
positive regulation of cell size  (IMP)
positive regulation of cytochrome-c oxidase activity  (ISO)
positive regulation of epithelial cell proliferation  (IMP)
positive regulation of lamellipodium assembly  (IMP)
positive regulation of melanin biosynthetic process  (ISO,ISS)
positive regulation of monophenol monooxygenase activity  (ISO,ISS)
positive regulation of oxidoreductase activity  (ISO)
positive regulation of response to wounding  (IMP)
positive regulation of superoxide dismutase activity  (ISO)
positive regulation of vascular associated smooth muscle cell migration  (IMP)
pyramidal neuron development  (ISO)
regulation of cytochrome-c oxidase activity  (IMP)
regulation of gene expression  (IMP,ISO)
regulation of oxidative phosphorylation  (ISO)
release of cytochrome c from mitochondria  (ISO)
removal of superoxide radicals  (ISO)
response to copper ion  (IDA,IEP)
response to iron(III) ion  (IEP)
response to lead ion  (IEP)
response to manganese ion  (IDA,IEP)
response to zinc ion  (IEP)
serotonin metabolic process  (ISO)
skin development  (ISO)
T-helper cell differentiation  (ISO)
tryptophan metabolic process  (ISO)
tyrosine metabolic process  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Ashino T, etal., Circ Res. 2010 Sep 17;107(6):787-99. doi: 10.1161/CIRCRESAHA.110.225334. Epub 2010 Jul 29.
2. Babich PS, etal., Bull Exp Biol Med. 2009 Aug;148(2):217-22.
3. Bauerly KA, etal., Am J Physiol Gastrointest Liver Physiol. 2005 May;288(5):G1007-14. Epub 2004 Dec 9.
4. Bonnemaison ML, etal., J Biol Chem. 2015 Aug 28;290(35):21264-79. doi: 10.1074/jbc.M115.641027. Epub 2015 Jul 13.
5. Cao Z, etal., Int J Clin Exp Pathol. 2015 Oct 1;8(10):12829-36. eCollection 2015.
6. Chou DK, etal., Toxicol Sci. 2007 Sep;99(1):267-76. Epub 2007 Jun 20.
7. Collins JF Biol Res. 2006;39(1):25-37.
8. Collins JF, etal., Am J Physiol Gastrointest Liver Physiol. 2005 May;288(5):G964-71. Epub 2005 Jan 6.
9. Collins JF, etal., Am J Physiol Gastrointest Liver Physiol. 2009 Oct;297(4):G695-707. doi: 10.1152/ajpgi.00203.2009. Epub 2009 Aug 13.
10. D'Amico F, etal., Acta Histochem. 2005;107(5):373-8. Epub 2005 Sep 23.
11. Das S, etal., Am J Hum Genet. 1995 Mar;56(3):570-6.
12. Desai V, etal., Clin Genet. 2011 Feb;79(2):176-82. doi: 10.1111/j.1399-0004.2010.01451.x.
13. Fu X, etal., Toxicol Sci. 2014 Jun;139(2):432-51. doi: 10.1093/toxsci/kfu048. Epub 2014 Mar 10.
14. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
15. GOA data from the GO Consortium
16. Grimes A, etal., Hum Mol Genet. 1997 Jul;6(7):1037-42.
17. Gulec S and Collins JF, J Nutr. 2014 Jan;144(1):12-9. doi: 10.3945/jn.113.183160. Epub 2013 Oct 30.
18. Gulec S and Collins JF, J Trace Elem Med Biol. 2014 Oct;28(4):459-64. doi: 10.1016/j.jtemb.2014.07.010. Epub 2014 Aug 4.
19. Gulec S and Collins JF, PLoS One. 2013 Jun 11;8(6):e66010. doi: 10.1371/journal.pone.0066010. Print 2013.
20. Han M, etal., J Neurochem. 2016 Jun 22. doi: 10.1111/jnc.13717.
21. Ip V, etal., Mol Pain. 2010 Sep 13;6:53. doi: 10.1186/1744-8069-6-53.
22. Kaler SG, etal., Nat Genet. 1994 Oct;8(2):195-202.
23. Kelleher SL and Lonnerdal B, Am J Physiol Regul Integr Comp Physiol. 2006 Oct;291(4):R1181-91. Epub 2006 Jun 1.
24. Kelleher SL and Lonnerdal B, J Nutr. 2003 Jul;133(7):2141-8.
25. Kennerson ML, etal., Am J Hum Genet. 2010 Mar 12;86(3):343-52. doi: 10.1016/j.ajhg.2010.01.027. Epub 2010 Feb 18.
26. Kohno T, etal., Arterioscler Thromb Vasc Biol. 2013 Apr;33(4):805-13. doi: 10.1161/ATVBAHA.112.300862. Epub 2013 Jan 24.
27. Lenartowicz M, etal., Biometals. 2015 Feb;28(1):51-9. doi: 10.1007/s10534-014-9802-z. Epub 2014 Oct 28.
28. MGD data from the GO Consortium
29. Mogensen M, etal., Orphanet J Rare Dis. 2011 Nov 10;6:73. doi: 10.1186/1750-1172-6-73.
30. Moizard MP, etal., Clin Genet. 2011 Mar;79(3):243-53. doi: 10.1111/j.1399-0004.2010.01461.x.
31. Moller LB, etal., Am J Hum Genet 2000 Apr;66(4):1211-20. Epub 2000 Mar 17.
32. Monnot AD, etal., Exp Biol Med (Maywood). 2012 Mar;237(3):327-33. doi: 10.1258/ebm.2011.011170.
33. NCBI rat LocusLink and RefSeq merged data July 26, 2002
34. Nyasae L, etal., Am J Physiol Gastrointest Liver Physiol. 2006 Dec 7;.
35. OMIM Disease Annotation Pipeline
36. Perez-Siles G, etal., Metallomics. 2016 Jun 13.
37. 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.
38. Qi M and Byers PH, Hum Mol Genet. 1998 Mar;7(3):465-9.
39. Qian Y, etal., Mol Cell Biochem 1998 Apr;181(1-2):49-61.
40. Ravia JJ, etal., J Biol Chem. 2005 Oct 28;280(43):36221-7. Epub 2005 Aug 4.
41. RGD automated data pipeline
42. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
43. RGD automated import pipeline for gene-chemical interactions
44. RGD comprehensive gene curation
45. Sancho-Martinez SM, etal., Pharmacol Ther. 2012 Oct;136(1):35-55. doi: 10.1016/j.pharmthera.2012.07.003. Epub 2012 Jul 14.
46. Schlief ML, etal., J Neurosci. 2005 Jan 5;25(1):239-46.
47. Steveson TC, etal., Endocrinology. 2003 Jan;144(1):188-200.
48. Takahashi T, etal., Pediatr Surg Int. 2015 Jan;31(1):31-5. doi: 10.1007/s00383-014-3620-9. Epub 2014 Oct 16.
49. Tchaparian EH, etal., Arch Biochem Biophys. 2000 Jul 1;379(1):71-7.
50. Xie L and Collins JF, Am J Physiol Cell Physiol. 2011 Jun;300(6):C1298-305. doi: 10.1152/ajpcell.00023.2011. Epub 2011 Feb 23.
51. Xie L and Collins JF, Am J Physiol Cell Physiol. 2013 Feb 1;304(3):C257-62. doi: 10.1152/ajpcell.00336.2012. Epub 2012 Nov 21.
52. Xie L and Collins JF, J Biol Chem. 2013 Aug 16;288(33):23943-52. doi: 10.1074/jbc.M113.489500. Epub 2013 Jun 28.
53. Yamaguchi Y, etal., Biochem J 1994 Jul 1;301 ( Pt 1):1-4.
54. Zhang S, etal., Cardiovasc Diabetol. 2014 Jun 14;13:100. doi: 10.1186/1475-2840-13-100.
55. Zhao H, etal., Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi. 2014 Nov;32(11):819-22.
56. Zheng G, etal., Toxicol Lett. 2014 Feb 10;225(1):110-8. doi: 10.1016/j.toxlet.2013.11.034. Epub 2013 Dec 6.
Additional References at PubMed
PMID:14140   PMID:17511   PMID:20889   PMID:27591   PMID:187892   PMID:564942   PMID:571898   PMID:573617   PMID:573619   PMID:937819   PMID:1115218   PMID:1752214  
PMID:1779648   PMID:2288383   PMID:2473662   PMID:3385878   PMID:3674914   PMID:4147174   PMID:4405722   PMID:4561716   PMID:4670054   PMID:4808708   PMID:4858102   PMID:6542992  
PMID:6685755   PMID:7197928   PMID:7509170   PMID:7688531   PMID:7769737   PMID:7873696   PMID:8009964   PMID:8025644   PMID:8096378   PMID:8174230   PMID:8434133   PMID:8550574  
PMID:8640230   PMID:8895222   PMID:8943055   PMID:9321757   PMID:9686356   PMID:9817923   PMID:10098864   PMID:10332039   PMID:10497213   PMID:10567439   PMID:10632785   PMID:11092760  
PMID:11214319   PMID:11311799   PMID:11391006   PMID:12812980   PMID:14572476   PMID:15035611   PMID:15634671   PMID:15670166   PMID:16338116   PMID:16371425   PMID:16397091   PMID:16641100  
PMID:17003121   PMID:19946888   PMID:22130675   PMID:22579041   PMID:30257103  


Genomics

Comparative Map Data
Atp7a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X71,094,144 - 71,201,550 (+)NCBI
Rnor_6.0 EnsemblX77,076,106 - 77,193,644 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X77,076,085 - 77,193,644 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X56,198,947 - 56,313,382 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X94,192,540 - 94,249,776 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X94,265,972 - 94,323,206 (+)NCBI
CeleraX72,450,404 - 72,510,070 (+)NCBICelera
Cytogenetic MapXq22NCBI
ATP7A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX77,910,656 - 78,050,395 (+)EnsemblGRCh38hg38GRCh38
GRCh38X77,910,693 - 78,050,395 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X77,166,190 - 77,305,892 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X77,052,876 - 77,192,208 (+)NCBINCBI36hg18NCBI36
Build 34X76,972,343 - 77,111,584NCBI
CeleraX77,407,059 - 77,546,975 (+)NCBI
Cytogenetic MapXq21.1NCBI
HuRefX70,752,187 - 70,892,316 (+)NCBIHuRef
CHM1_1X77,058,841 - 77,198,586 (+)NCBICHM1_1
Atp7a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X105,070,830 - 105,171,766 (+)NCBIGRCm39mm39
GRCm39 EnsemblX105,070,882 - 105,168,532 (+)Ensembl
GRCm38X106,027,224 - 106,128,161 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX106,027,276 - 106,124,926 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X103,222,615 - 103,323,499 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X102,230,036 - 102,327,636 (+)NCBImm8
CeleraX92,880,992 - 92,982,185 (+)NCBICelera
Cytogenetic MapXDNCBI
cM MapX47.36NCBI
Atp7a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555571,355,397 - 1,515,393 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555571,355,471 - 1,515,725 (+)NCBIChiLan1.0ChiLan1.0
ATP7A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X77,205,579 - 77,342,762 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX77,255,312 - 77,342,756 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X67,093,675 - 67,231,318 (+)NCBIMhudiblu_PPA_v0panPan3
ATP7A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X60,203,336 - 60,356,525 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX60,203,270 - 60,352,869 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX51,216,457 - 51,369,626 (+)NCBI
ROS_Cfam_1.0X61,442,067 - 61,595,242 (+)NCBI
UMICH_Zoey_3.1X59,148,063 - 59,301,397 (+)NCBI
UNSW_CanFamBas_1.0X60,758,474 - 60,911,162 (+)NCBI
UU_Cfam_GSD_1.0X60,346,304 - 60,499,464 (+)NCBI
Atp7a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X42,009,558 - 42,154,264 (-)NCBI
SpeTri2.0NW_0049366832,874,022 - 2,936,214 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATP7A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX61,972,874 - 62,110,058 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X61,972,544 - 62,110,058 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X70,891,299 - 71,026,996 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ATP7A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X66,843,519 - 66,985,655 (+)NCBI
ChlSab1.1 EnsemblX66,843,558 - 66,985,709 (+)Ensembl
Atp7a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248362,804,349 - 3,058,125 (-)NCBI

Position Markers
DXWox23  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X71,160,291 - 71,160,568 (+)MAPPER
Rnor_6.0X77,142,228 - 77,142,504NCBIRnor6.0
Rnor_5.0X56,265,346 - 56,265,622UniSTSRnor5.0
RGSC_v3.4X94,214,857 - 94,215,133UniSTSRGSC3.4
CeleraX72,472,721 - 72,472,997UniSTS
Cytogenetic MapXq31UniSTS
Atp7a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X71,163,343 - 71,163,869 (+)MAPPER
Rnor_6.0X77,145,280 - 77,145,805NCBIRnor6.0
Rnor_5.0X56,268,398 - 56,268,923UniSTSRnor5.0
RGSC_v3.4X94,217,909 - 94,218,434UniSTSRGSC3.4
CeleraX72,475,773 - 72,476,298UniSTS
Cytogenetic MapXq31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X70352120127888215Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:50
Interacting mature miRNAs:52
Transcripts:ENSRNOT00000065388
Prediction methods:Miranda, Pita, 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 17 4 14 4 1 1 21 29 9 1
Low 3 42 37 34 5 34 7 9 74 14 11 2 7
Below cutoff 1 3 3 3 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_052803 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256995 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773334 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099486 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099487 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099488 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC130061 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY011398 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ817345 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ817347 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ817348 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229589 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU131267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU131268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU131269 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L28172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U59245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000080141   ⟹   ENSRNOP00000071625
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX77,119,911 - 77,190,449 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000085227   ⟹   ENSRNOP00000073682
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX77,143,892 - 77,146,290 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089381   ⟹   ENSRNOP00000071914
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX77,076,151 - 77,136,010 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091527   ⟹   ENSRNOP00000073176
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX77,076,106 - 77,193,644 (+)Ensembl
RefSeq Acc Id: NM_052803   ⟹   NP_434690
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X71,137,973 - 71,198,354 (+)NCBI
Rnor_6.0X77,119,911 - 77,190,449 (+)NCBI
Rnor_5.0X56,198,947 - 56,313,382 (+)NCBI
RGSC_v3.4X94,192,540 - 94,249,776 (+)RGD
CeleraX72,450,404 - 72,510,070 (+)RGD
Sequence:
RefSeq Acc Id: XM_006256995   ⟹   XP_006257057
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X71,094,145 - 71,201,550 (+)NCBI
Rnor_6.0X77,076,085 - 77,193,644 (+)NCBI
Rnor_5.0X56,198,947 - 56,313,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256997   ⟹   XP_006257059
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X71,094,145 - 71,201,550 (+)NCBI
Rnor_6.0X77,076,085 - 77,193,644 (+)NCBI
Rnor_5.0X56,198,947 - 56,313,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008773334   ⟹   XP_008771556
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X77,102,654 - 77,193,644 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099486   ⟹   XP_038955414
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X71,094,145 - 71,201,550 (+)NCBI
RefSeq Acc Id: XM_039099487   ⟹   XP_038955415
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X71,094,144 - 71,201,550 (+)NCBI
RefSeq Acc Id: XM_039099488   ⟹   XP_038955416
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X71,094,145 - 71,198,139 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_434690   ⟸   NM_052803
- UniProtKB: P70705 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006257057   ⟸   XM_006256995
- Peptide Label: isoform X1
- UniProtKB: P70705 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006257059   ⟸   XM_006256997
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008771556   ⟸   XM_008773334
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000071625   ⟸   ENSRNOT00000080141
RefSeq Acc Id: ENSRNOP00000073682   ⟸   ENSRNOT00000085227
RefSeq Acc Id: ENSRNOP00000071914   ⟸   ENSRNOT00000089381
RefSeq Acc Id: ENSRNOP00000073176   ⟸   ENSRNOT00000091527
RefSeq Acc Id: XP_038955415   ⟸   XM_039099487
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955414   ⟸   XM_039099486
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955416   ⟸   XM_039099488
- Peptide Label: isoform X4
Protein Domains
HMA

Transcriptome

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

Promoters
RGD ID:13701903
Promoter ID:EPDNEW_R12424
Type:multiple initiation site
Name:Atp7a_1
Description:ATPase copper transporting alpha
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_6.0X77,076,161 - 77,076,221EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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 (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
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)
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
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 (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 (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)
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
WKY/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
WKY/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
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (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
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:2179 AgrOrtholog
Ensembl Genes ENSRNOG00000061367 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000071625 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000071914 UniProtKB/TrEMBL
  ENSRNOP00000073176 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000073682 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000080141 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000085227 UniProtKB/TrEMBL
  ENSRNOT00000089381 UniProtKB/TrEMBL
  ENSRNOT00000091527 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.1110.10 UniProtKB/Swiss-Prot
InterPro 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
  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
  P_typ_ATPase UniProtKB/Swiss-Prot
  P_typ_ATPase_HD_dom UniProtKB/Swiss-Prot
KEGG Report rno:24941 UniProtKB/Swiss-Prot
NCBI Gene 24941 ENTREZGENE
Pfam HMA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB ATP7A RGD
PhenoGen Atp7a PhenoGen
PROSITE ATPASE_E1_E2 UniProtKB/Swiss-Prot
  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
  SSF81653 UniProtKB/Swiss-Prot
  SSF81665 UniProtKB/Swiss-Prot
TIGRFAMs ATPase-IB_hvy UniProtKB/Swiss-Prot
  ATPase_P-type UniProtKB/Swiss-Prot
  TIGR00003 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A096MJU5_RAT UniProtKB/TrEMBL
  ATP7A_RAT UniProtKB/Swiss-Prot
  D1GCS2_RAT UniProtKB/TrEMBL
  D1GCS3_RAT UniProtKB/TrEMBL
  D1MCF1_RAT UniProtKB/TrEMBL
  D1MCF3_RAT UniProtKB/TrEMBL
  P70705 ENTREZGENE
  Q99NX2_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Atp7a  ATPase copper transporting alpha  Atp7a  ATPase, Cu++ transporting, alpha polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Atp7a  ATPase, Cu++ transporting, alpha polypeptide    ATPase, Cu++ transporting, alpha polypeptide (Menkes syndrome)  Name updated 625702 APPROVED
2002-06-10 Atp7a  ATPase, Cu++ transporting, alpha polypeptide (Menkes syndrome)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains has six metal binding sites 631784
gene_homology has 98% identity to mouse protein 631784
gene_protein 1492 amino acids 631784