Ppp2ca (protein phosphatase 2 catalytic subunit alpha) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Ppp2ca (protein phosphatase 2 catalytic subunit alpha) Rattus norvegicus
Analyze
Symbol: Ppp2ca
Name: protein phosphatase 2 catalytic subunit alpha
RGD ID: 3380
Description: Exhibits several functions, including beta-2 adrenergic receptor binding activity; enzyme binding activity; and ion channel binding activity. Involved in several processes, including cellular response to hormone stimulus; negative regulation of ion transport; and regulation of protein metabolic process. Localizes to several cellular components, including postsynaptic density; protein phosphatase type 2A complex; and terminal bouton. Biomarker of type 2 diabetes mellitus. Orthologous to human PPP2CA (protein phosphatase 2 catalytic subunit alpha); PARTICIPATES IN adenosine monophosphate-activated protein kinase (AMPK) signaling pathway; ataxia telangiectasia-mutated (ATM) signaling pathway; dopamine signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC103694903; PP2A-alpha; Pp2a1; Protein phosphatase 2 (formerly 2A) catalytic subunit alpha isoform; protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform; protein phosphatase 2, catalytic subunit, alpha isoform; protein phosphatase 2, catalytic subunit, alpha isozyme; protein phosphatase 2a, catalytic subunit, alpha isoform; protein phosphatase-2A-alpha; serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
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
mRatBN7.21036,358,110 - 36,377,864 (+)NCBI
Rnor_6.0 Ensembl1037,535,871 - 37,554,664 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01037,534,449 - 37,554,861 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01037,324,233 - 37,343,985 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41037,621,256 - 37,641,008 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11037,627,685 - 37,647,436 (+)NCBI
Celera1035,713,154 - 35,732,937 (+)NCBICelera
Cytogenetic Map10q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-methyl-6-(phenylethynyl)pyridine  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
5-azacytidine  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (ISO)
cadmium dichloride  (EXP,ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
camptothecin  (ISO)
choline  (ISO)
clofibric acid  (EXP)
clozapine  (EXP)
cocaine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
curcumin  (ISO)
dehydroepiandrosterone  (EXP)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibutyl phthalate  (ISO)
dichlorine  (EXP)
dicrotophos  (ISO)
dobutamine  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP)
endosulfan  (EXP)
Estragole  (EXP)
ethanol  (EXP,ISO)
flutamide  (EXP)
folic acid  (ISO)
fumonisin B1  (EXP)
gentamycin  (EXP)
haloperidol  (EXP)
hydrogen peroxide  (EXP,ISO)
hydroquinone  (ISO)
imipramine  (EXP)
ionomycin  (ISO)
isoprenaline  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP)
lead(0)  (EXP)
lead(2+)  (EXP)
lipopolysaccharide  (ISO)
methylmercury chloride  (ISO)
microcystin-LR  (EXP,ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-nitrosodiethylamine  (EXP)
nickel dichloride  (ISO)
okadaic acid  (EXP,ISO)
ozone  (EXP)
paracetamol  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
progesterone  (EXP)
razoxane  (EXP)
resveratrol  (ISO)
SB 431542  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
streptozocin  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (ISO)
theophylline  (ISO)
toluene  (EXP)
trichloroethene  (ISO)
uranium atom  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Arif M, etal., Proc Natl Acad Sci U S A. 2014 Jan 21;111(3):1144-9. doi: 10.1073/pnas.1322614111. Epub 2014 Jan 6.
2. Arnaud L, etal., FEBS Lett. 2011 Sep 2;585(17):2653-9. doi: 10.1016/j.febslet.2011.07.020. Epub 2011 Jul 28.
3. Arora DK, etal., Endocrinology. 2014 Feb;155(2):380-91. doi: 10.1210/en.2013-1773. Epub 2013 Nov 21.
4. Bhatti S, etal., Cell Mol Life Sci. 2011 Sep;68(18):2977-3006. doi: 10.1007/s00018-011-0683-9. Epub 2011 May 2.
5. Bishop JD, etal., J Endocrinol. 2006 Aug;190(2):307-12.
6. Chan PM, etal., J Biol Chem. 2008 Sep 5;283(36):24949-61. doi: 10.1074/jbc.M801728200. Epub 2008 Jun 27.
7. Chan SF and Sucher NJ, J Neurosci. 2001 Oct 15;21(20):7985-92.
8. Chen S, etal., J Biol Chem. 2008 Apr 18;283(16):10513-21. doi: 10.1074/jbc.M709852200. Epub 2008 Feb 1.
9. Chim SS, etal., J Cell Biochem 2000 Jun 12;78(4):533-40.
10. Cho IS, etal., PLoS One. 2012;7(4):e34860. doi: 10.1371/journal.pone.0034860. Epub 2012 Apr 3.
11. Davare MA, etal., J Biol Chem. 2000 Dec 15;275(50):39710-7.
12. Galbo T, etal., PLoS One. 2011;6(11):e27424. doi: 10.1371/journal.pone.0027424. Epub 2011 Nov 7.
13. Goedert M, etal., J Neurochem. 2000 Nov;75(5):2155-62.
14. Gong CX, etal., Brain Res. 2000 Jan 24;853(2):299-309.
15. Hall DD, etal., Biochemistry. 2006 Mar 14;45(10):3448-59.
16. Hardie DG, etal., Trends Biochem Sci. 2011 Sep;36(9):470-7. doi: 10.1016/j.tibs.2011.06.004. Epub 2011 Jul 23.
17. Heller FA, etal., Pediatr Res. 1998 Jan;43(1):68-76.
18. Hellwinkel OJ, etal., BJU Int. 2008 Jun;101(11):1454-60. Epub 2008 Mar 11.
19. Ishida A, etal., Br J Pharmacol. 2008 Jun;154(4):729-40. doi: 10.1038/bjp.2008.127. Epub 2008 May 5.
20. Jangati GR, etal., Biochem Biophys Res Commun. 2006 Sep 22;348(2):649-52. doi: 10.1016/j.bbrc.2006.07.100. Epub 2006 Jul 28.
21. Kitagawa Y, etal., Biochim Biophys Acta 1988 Nov 10;951(1):123-9.
22. Kloeker S, etal., Biochem J. 1997 Oct 15;327 ( Pt 2):481-6.
23. Kolupaeva V, etal., PLoS One. 2008;3(10):e3447. doi: 10.1371/journal.pone.0003447. Epub 2008 Oct 17.
24. Krankel N, etal., Mol Genet Metab. 2003 Sep-Oct;80(1-2):262-71.
25. Levallet G, etal., J Endocrinol. 2008 Apr;197(1):45-54. doi: 10.1677/JOE-07-0497.
26. Li D, etal., J Neurosci. 2005 Feb 23;25(8):1914-23.
27. Liangpunsakul S, etal., Am J Physiol Gastrointest Liver Physiol. 2008 Dec;295(6):G1173-81. doi: 10.1152/ajpgi.90349.2008. Epub 2008 Oct 2.
28. Liangpunsakul S, etal., Am J Physiol Gastrointest Liver Physiol. 2010 Jun;298(6):G1004-12. doi: 10.1152/ajpgi.00482.2009. Epub 2010 Mar 11.
29. Lin TB, etal., J Pineal Res. 2016 Apr;60(3):263-76. doi: 10.1111/jpi.12307. Epub 2016 Jan 29.
30. Marasa BS, etal., Am J Physiol Cell Physiol. 2008 May;294(5):C1277-87. doi: 10.1152/ajpcell.90635.2007. Epub 2008 Mar 5.
31. MGD data from the GO Consortium
32. Nagao M, etal., Princess Takamatsu Symp. 1989;20:177-84.
33. Nakashima A, etal., FEBS Lett. 2013 Sep 17;587(18):2924-9. doi: 10.1016/j.febslet.2013.07.027. Epub 2013 Jul 24.
34. NCBI rat LocusLink and RefSeq merged data July 26, 2002
35. Nien WL, etal., Mol Cell Endocrinol. 2007 Jan 15;263(1-2):10-7. Epub 2006 Nov 2.
36. O'Malley PG, etal., Biochem J. 2005 Sep 15;390(Pt 3):665-73.
37. Pallottini V, etal., Mech Ageing Dev. 2007 Nov-Dec;128(11-12):688-95. Epub 2007 Oct 16.
38. Panier S and Durocher D, Nat Rev Mol Cell Biol. 2013 Oct;14(10):661-72. doi: 10.1038/nrm3659. Epub 2013 Sep 4.
39. Pipeline to import KEGG annotations from KEGG into RGD
40. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
41. Rahman A, etal., Neurotoxicology. 2012 Jun;33(3):370-83. doi: 10.1016/j.neuro.2012.02.014. Epub 2012 Mar 1.
42. Ramamoorthy S, etal., Biochem Biophys Res Commun. 2010 Jan 15;391(3):1517-21. doi: 10.1016/j.bbrc.2009.12.110. Epub 2009 Dec 24.
43. RGD automated data pipeline
44. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
45. RGD automated import pipeline for gene-chemical interactions
46. Seshacharyulu P, etal., Cancer Lett. 2013 Jul 10;335(1):9-18. doi: 10.1016/j.canlet.2013.02.036. Epub 2013 Feb 20.
47. Shi K, etal., Biochem Biophys Res Commun. 2007 Nov 23;363(3):626-32. Epub 2007 Sep 17.
48. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
49. Tamasi V, etal., Mol Pharmacol. 2008 Mar;73(3):968-76. Epub 2007 Dec 13.
50. Ugi S, etal., Mol Cell Biol 2002 Apr;22(7):2375-87.
51. Van Kanegan MJ and Strack S, Mol Cell Biol. 2009 Feb;29(3):662-74. doi: 10.1128/MCB.01242-08. Epub 2008 Nov 24.
52. Wang D, etal., FASEB J. 2010 Sep;24(9):3511-21. doi: 10.1096/fj.10-156661. Epub 2010 Apr 15.
53. Wheat WH, etal., Mol Cell Biol. 1994 Sep;14(9):5881-90.
54. Yger M and Girault JA, Front Behav Neurosci. 2011 Sep 8;5:56. doi: 10.3389/fnbeh.2011.00056. eCollection 2011.
55. Yoo SJ, etal., J Cell Biochem. 2008 Sep 1;105(1):290-300. doi: 10.1002/jcb.21830.
56. Zhu LQ, etal., J Neurosci. 2010 Mar 10;30(10):3839-48. doi: 10.1523/JNEUROSCI.5174-09.2010.
Additional References at PubMed
PMID:2174876   PMID:2554255   PMID:2554256   PMID:9770493   PMID:9847399   PMID:9882488   PMID:9920888   PMID:10781942   PMID:11590243   PMID:12606433   PMID:12885400   PMID:15194871  
PMID:15489334   PMID:15661743   PMID:15865439   PMID:16030137   PMID:16123140   PMID:16129692   PMID:16258073   PMID:16420440   PMID:16549018   PMID:16717086   PMID:16754670   PMID:16822951  
PMID:17055435   PMID:17158207   PMID:17174897   PMID:17255109   PMID:17259072   PMID:18084284   PMID:18388891   PMID:18550542   PMID:18835920   PMID:20017541   PMID:20080667   PMID:20106966  
PMID:20458337   PMID:20485545   PMID:20684275   PMID:21080067   PMID:21257729   PMID:22031698   PMID:22082260   PMID:22242112   PMID:22892311   PMID:22892312   PMID:23020770   PMID:23716589  
PMID:23840384   PMID:24475092   PMID:24625528   PMID:25007834   PMID:25038454   PMID:25869568   PMID:26316108   PMID:26378614   PMID:27459928   PMID:27572322   PMID:28442576   PMID:30595372  
PMID:30611118   PMID:31974600  


Genomics

Comparative Map Data
Ppp2ca
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21036,358,110 - 36,377,864 (+)NCBI
Rnor_6.0 Ensembl1037,535,871 - 37,554,664 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01037,534,449 - 37,554,861 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01037,324,233 - 37,343,985 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41037,621,256 - 37,641,008 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11037,627,685 - 37,647,436 (+)NCBI
Celera1035,713,154 - 35,732,937 (+)NCBICelera
Cytogenetic Map10q22NCBI
PPP2CA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5134,194,332 - 134,226,073 (-)EnsemblGRCh38hg38GRCh38
GRCh385134,194,332 - 134,226,073 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh375133,530,023 - 133,561,764 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365133,560,047 - 133,589,849 (-)NCBINCBI36hg18NCBI36
Build 345133,560,046 - 133,589,849NCBI
Celera5129,655,849 - 129,685,663 (-)NCBI
Cytogenetic Map5q31.1NCBI
HuRef5128,717,117 - 128,746,747 (-)NCBIHuRef
CHM1_15132,964,711 - 132,994,524 (-)NCBICHM1_1
Ppp2ca
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391151,989,651 - 52,013,576 (+)NCBIGRCm39mm39
GRCm39 Ensembl1151,989,508 - 52,018,605 (+)Ensembl
GRCm381152,098,824 - 52,122,749 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1152,098,681 - 52,127,778 (+)EnsemblGRCm38mm10GRCm38
MGSCv371151,912,326 - 51,936,251 (+)NCBIGRCm37mm9NCBIm37
MGSCv361151,942,247 - 51,966,172 (+)NCBImm8
Celera1156,667,217 - 56,691,076 (+)NCBICelera
Cytogenetic Map11B1.3NCBI
Ppp2ca
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554085,433,268 - 5,460,361 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554085,435,117 - 5,460,361 (-)NCBIChiLan1.0ChiLan1.0
PPP2CA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15135,751,964 - 135,761,395 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5135,751,958 - 135,765,786 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05129,599,606 - 129,629,312 (-)NCBIMhudiblu_PPA_v0panPan3
PPP2CA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11122,388,327 - 22,410,052 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1122,385,257 - 22,410,052 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1121,134,537 - 21,156,029 (-)NCBI
ROS_Cfam_1.01123,189,481 - 23,211,243 (-)NCBI
UMICH_Zoey_3.11121,889,485 - 21,911,229 (-)NCBI
UNSW_CanFamBas_1.01121,754,643 - 21,776,444 (-)NCBI
UU_Cfam_GSD_1.01122,397,162 - 22,418,841 (-)NCBI
Ppp2ca
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213114,028,481 - 114,052,523 (+)NCBI
SpeTri2.0NW_0049366471,031,118 - 1,055,961 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PPP2CA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2136,494,541 - 136,522,646 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12136,497,780 - 136,522,630 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22142,095,024 - 142,123,724 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PPP2CA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12336,999,110 - 37,028,916 (-)NCBI
ChlSab1.1 Ensembl2336,997,078 - 37,029,280 (-)Ensembl
Vero_WHO_p1.0NW_02366603440,904,228 - 40,936,193 (+)NCBI
Ppp2ca
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473338,012,694 - 38,033,745 (+)NCBI

Position Markers
RH127380  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21182,279,884 - 82,280,069 (+)MAPPER
mRatBN7.21036,377,586 - 36,377,771 (+)MAPPER
mRatBN7.21036,377,586 - 36,377,771 (-)MAPPER
mRatBN7.21182,279,884 - 82,280,069 (-)MAPPER
Rnor_6.01186,422,634 - 86,422,818NCBIRnor6.0
Rnor_6.01037,535,201 - 37,535,385NCBIRnor6.0
Rnor_5.01189,523,373 - 89,523,557UniSTSRnor5.0
Rnor_5.01037,343,708 - 37,343,892UniSTSRnor5.0
RGSC_v3.41037,640,731 - 37,640,915UniSTSRGSC3.4
RGSC_v3.41184,271,502 - 84,271,686UniSTSRGSC3.4
Celera1181,056,435 - 81,056,619UniSTS
Celera1035,732,660 - 35,732,844UniSTS
Cytogenetic Map10q22UniSTS
PMC22838P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21182,278,463 - 82,278,570 (+)MAPPER
mRatBN7.21036,358,300 - 36,358,407 (+)MAPPER
mRatBN7.21036,358,300 - 36,358,407 (-)MAPPER
mRatBN7.21182,278,463 - 82,278,570 (-)MAPPER
Rnor_6.01186,421,213 - 86,421,319NCBIRnor6.0
Rnor_6.01037,554,564 - 37,554,670NCBIRnor6.0
Rnor_5.01189,521,952 - 89,522,058UniSTSRnor5.0
Rnor_5.01037,324,424 - 37,324,530UniSTSRnor5.0
RGSC_v3.41037,621,447 - 37,621,553UniSTSRGSC3.4
RGSC_v3.41184,270,081 - 84,270,187UniSTSRGSC3.4
Celera1181,056,065 - 81,056,171UniSTS
Celera1035,713,345 - 35,713,451UniSTS
Cytogenetic Map10q22UniSTS
Ppp2ca  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21182,278,604 - 82,279,072 (+)MAPPER
Rnor_6.01186,421,354 - 86,421,821NCBIRnor6.0
Rnor_5.01189,522,093 - 89,522,560UniSTSRnor5.0
RGSC_v3.41184,270,222 - 84,270,689UniSTSRGSC3.4
Cytogenetic Map10q22UniSTS
Ppp2ca  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21036,373,858 - 36,373,905 (+)MAPPER
mRatBN7.21182,279,039 - 82,279,090 (+)MAPPER
Rnor_6.01186,421,789 - 86,421,839NCBIRnor6.0
Rnor_5.01189,522,528 - 89,522,578UniSTSRnor5.0
RGSC_v3.41184,270,657 - 84,270,707UniSTSRGSC3.4
Cytogenetic Map10q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138594330Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142669970Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)10144902893Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1076442166221621Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10587753664401490Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10622909575983805Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10642907599492409Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10752145052521450Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109841807108540162Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101263951357639513Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101263951357639513Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101263951357639513Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101482789492423564Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014827894107857673Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014827894110992275Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101537547462469074Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101646873661468736Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11712154262121542Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11712154262121542Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101824639453637634Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101940281464402814Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)1020170031102897474Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102152390683549467Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)12152390690312401Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102152390690312401Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102170776664648311Rat
631531Iresp2Immunoglobin response QTL26.3blood immunoglobulin E amount (VT:0002492)serum total immunoglobulin E level (CMO:0001542)102240281738204229Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102290149793886300Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102386101566539843Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1023861015112626471Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)102488408447487910Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102723753064648311Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)1027237530101482600Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1027237530102427718Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102878928073789280Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)103002135454057745Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)103009990975099909Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)103009990975099909Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)103098380575983805Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103191939778343192Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103317903078179030Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103334319278343192Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103513942480139424Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103566946546851407Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)103618592982675365Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103618592995845311Rat
1354614Hpcl1Hepatic cholesterol level QTL 13.3liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)103658437353645194Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103658437366539843Rat
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103658456066015527Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:111
Count of miRNA genes:80
Interacting mature miRNAs:106
Transcripts:ENSRNOT00000007621
Prediction methods: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 musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium
Low 1 2 1 1 2 1 2 1 1 2
Below cutoff 3 8 8 6 5 6 3 35 19 17 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007621   ⟹   ENSRNOP00000007621
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1037,535,871 - 37,554,664 (-)Ensembl
RefSeq Acc Id: NM_017039   ⟹   NP_058735
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21036,358,110 - 36,377,864 (+)NCBI
Rnor_6.01037,535,108 - 37,554,861 (-)NCBI
Rnor_5.01037,324,233 - 37,343,985 (+)NCBI
RGSC_v3.41037,621,256 - 37,641,008 (+)RGD
Celera1035,713,154 - 35,732,937 (+)RGD
Sequence:
RefSeq Acc Id: XM_017597004   ⟹   XP_017452493
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01037,534,449 - 37,554,646 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_058735   ⟸   NM_017039
- UniProtKB: P63331 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017452493   ⟸   XM_017597004
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000007621   ⟸   ENSRNOT00000007621

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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)
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: 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:3380 AgrOrtholog
Ensembl Genes ENSRNOG00000005389 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00000056485 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000007621 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000071286 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000007621 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000079985 UniProtKB/Swiss-Prot
Gene3D-CATH 3.60.21.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7096821 IMAGE-MGC_LOAD
  IMAGE:7104697 IMAGE-MGC_LOAD
InterPro Calcineurin-like_PHP_ApaH UniProtKB/Swiss-Prot
  Metallo-depent_PP-like UniProtKB/Swiss-Prot
  Ser/Thr-sp_prot-phosphatase UniProtKB/Swiss-Prot
KEGG Report rno:103694903 UniProtKB/Swiss-Prot
  rno:24672 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91734 IMAGE-MGC_LOAD
  MGC:91735 IMAGE-MGC_LOAD
NCBI Gene 24672 ENTREZGENE
Pfam Metallophos UniProtKB/Swiss-Prot
PhenoGen Ppp2ca PhenoGen
PRINTS STPHPHTASE UniProtKB/Swiss-Prot
PROSITE SER_THR_PHOSPHATASE UniProtKB/Swiss-Prot
SMART PP2Ac UniProtKB/Swiss-Prot
UniProt P63331 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary O88591 UniProtKB/Swiss-Prot
  P13353 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-01-02 Ppp2ca  protein phosphatase 2 catalytic subunit alpha  LOC103694903  serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform  Data Merged 737654 PROVISIONAL
2016-02-17 Ppp2ca  protein phosphatase 2 catalytic subunit alpha  Ppp2ca  protein phosphatase 2, catalytic subunit, alpha isozyme  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 LOC103694903  serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-06-26 Ppp2ca  protein phosphatase 2, catalytic subunit, alpha isozyme  Ppp2ca  protein phosphatase 2, catalytic subunit, alpha isoform  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-23 Ppp2ca  protein phosphatase 2, catalytic subunit, alpha isoform  Ppp2ca  protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Ppp2ca  protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform    protein phosphatase 2a, catalytic subunit, alpha isoform  Name updated 1299863 APPROVED
2002-06-10 Ppp2ca  Protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform      Symbol and Name status set to approved 70586 APPROVED