Pax6 (paired box 6) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Pax6 (paired box 6) Rattus norvegicus
Analyze
Symbol: Pax6
Name: paired box 6
RGD ID: 3258
Description: Enables DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and minor groove of adenine-thymine-rich DNA binding activity. Involved in several processes, including cellular response to hormone stimulus; enteroendocrine cell differentiation; and nervous system development. Located in chromatin and nucleus. Used to study autistic disorder. Biomarker of Smith-Lemli-Opitz syndrome and transient cerebral ischemia. Human ortholog(s) of this gene implicated in bilateral optic nerve hypoplasia; eye disease (multiple); glucose intolerance; and paranoid schizophrenia. Orthologous to human PAX6 (paired box 6); PARTICIPATES IN maturity-onset diabetes of the young pathway; INTERACTS WITH (S)-nicotine; 1,2-dimethylhydrazine; 3H-1,2-dithiole-3-thione.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: oculorhombin; paired box gene 6; Paired box homeotic gene 6; paired box protein Pax-6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Pax6Sey   Pax6Sey2  
Genetic Models: SD-Pax6Sey2/Mce SD-Pax6Sey/Mce
Is Marker For: Strains:   SD-Pax6Sey/Mce  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2392,128,772 - 92,157,022 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl392,135,637 - 92,157,014 (+)Ensembl
Rnor_6.0395,700,241 - 95,728,682 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl395,707,386 - 95,728,624 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03102,320,059 - 102,348,223 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4391,127,605 - 91,149,178 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1391,023,827 - 91,045,776 (+)NCBI
Celera391,190,477 - 91,211,449 (+)NCBICelera
RH 3.4 Map3722.9RGD
Cytogenetic Map3q33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-colchicine  (ISO)
(S)-nicotine  (EXP)
1,2-dimethylhydrazine  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
abacavir  (ISO)
acetaldehyde  (ISO)
acetic acid  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
aldehydo-D-glucose  (EXP)
aldicarb  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromochloroacetic acid  (ISO)
bucladesine  (ISO)
butanal  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (EXP)
calcium atom  (EXP)
calcium(0)  (EXP)
carbamazepine  (ISO)
carbaryl  (ISO)
carbofuran  (EXP)
CHIR 99021  (ISO)
CHIR-98014  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
curcumin  (EXP)
cyclosporin A  (ISO)
cyproconazole  (ISO)
cytarabine  (ISO)
D-glucose  (EXP)
dabigatran  (ISO)
DDT  (ISO)
decabromodiphenyl ether  (EXP,ISO)
dextran sulfate  (ISO)
diazinon  (ISO)
diclofenac  (ISO)
dieldrin  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (ISO)
ethosuximide  (EXP)
flusilazole  (ISO)
folic acid  (ISO)
gamma-hexachlorocyclohexane  (ISO)
glucose  (EXP)
heptachlor  (ISO)
hexachlorophene  (ISO)
isotretinoin  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
maneb  (ISO)
mercury dibromide  (ISO)
methylmercury chloride  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-ethyl-N-nitrosourea  (ISO)
nicotine  (EXP)
nilotinib  (ISO)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paraquat  (ISO)
perfluorooctanoic acid  (ISO)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
potassium chromate  (ISO)
propanal  (ISO)
propiconazole  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
T-2 toxin  (ISO)
tert-butyl hydroperoxide  (ISO)
Tetrachlorobisphenol A  (ISO)
thalidomide  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vismodegib  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure development  (IBA)
anterior/posterior pattern specification  (ISO)
astrocyte differentiation  (IEA,IMP,ISO)
axon guidance  (IEA,ISO)
axonogenesis  (ISO)
blood vessel development  (IEA,ISO)
brain development  (IMP,ISO)
camera-type eye development  (ISO)
cell differentiation  (ISO)
cell fate commitment  (ISO)
cell fate determination  (IEA,ISO)
cellular response to fibroblast growth factor stimulus  (IEP)
cellular response to glucose stimulus  (IEP)
cellular response to insulin stimulus  (IEP)
cellular response to leukemia inhibitory factor  (IEA,ISO)
cellular response to prostaglandin E stimulus  (IEP)
cellular response to xenobiotic stimulus  (IEP)
central nervous system development  (IEP)
cerebellum development  (IEP)
cerebral cortex regionalization  (IEA,ISO)
commitment of neuronal cell to specific neuron type in forebrain  (IEA,ISO)
cornea development in camera-type eye  (IEA,ISO)
dorsal/ventral axis specification  (IEA,ISO)
dorsal/ventral pattern formation  (ISO)
embryonic camera-type eye morphogenesis  (IEA,ISO)
epithelial cell development  (IMP)
establishment of mitotic spindle orientation  (IEA,ISO)
eye photoreceptor cell development  (IEA,ISO)
forebrain development  (ISO)
forebrain dorsal/ventral pattern formation  (IEA,ISO)
forebrain-midbrain boundary formation  (IEA,ISO)
gene expression  (IEA,ISO)
glucose homeostasis  (IEA,ISO)
habenula development  (IEA,ISO)
hindbrain development  (IDA,IMP)
insulin metabolic process  (IMP)
interkinetic nuclear migration  (IMP)
iris morphogenesis  (IEA,ISO)
keratinocyte differentiation  (IEA,ISO)
lacrimal gland development  (IEA,ISO)
learned vocalization behavior or vocal learning  (IMP)
lens development in camera-type eye  (IEA,ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of epithelial cell proliferation  (IEA,ISO)
negative regulation of neural precursor cell proliferation  (IEA,ISO)
negative regulation of neuron differentiation  (IEA,ISO)
negative regulation of protein phosphorylation  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IEA,ISO,ISS)
neural crest cell migration  (IMP)
neural precursor cell proliferation  (IMP)
neuron migration  (IEA,IMP,ISO)
olfactory bulb development  (IMP)
olfactory bulb mitral cell layer development  (IMP)
oligodendrocyte cell fate specification  (IEA,ISO)
pallium development  (ISO)
pancreatic A cell development  (IEA,IMP,ISO)
pancreatic A cell differentiation  (IMP)
pituitary gland development  (IEA,ISO)
positive regulation of cell death  (IMP)
positive regulation of cell fate specification  (IMP)
positive regulation of core promoter binding  (IEA,ISO,ISS)
positive regulation of epithelial cell differentiation  (IEA,ISO)
positive regulation of gene expression  (IEA,IMP,ISO)
positive regulation of glucagon secretion  (IMP)
positive regulation of glutamatergic neuron differentiation  (IMP)
positive regulation of neuroblast proliferation  (IEA,ISO)
positive regulation of neuron migration  (IGI)
positive regulation of transcription by RNA polymerase II  (IEA,IMP,ISO)
positive regulation of transcription, DNA-templated  (ISO,ISS)
protein localization to organelle  (IEA,ISO)
regionalization  (ISO)
regulation of asymmetric cell division  (IEA,ISO)
regulation of cell migration  (IEA,ISO)
regulation of gene expression  (ISO)
regulation of neurogenesis  (IMP,ISO)
regulation of neuron differentiation  (IDA)
regulation of neuron projection development  (IGI)
regulation of timing of cell differentiation  (IEA,ISO)
regulation of transcription by RNA polymerase II  (IBA,ISO)
response to ethanol  (IEP)
response to wounding  (IEA,ISO)
retina development in camera-type eye  (IEA,IEP,ISO)
rhombomere morphogenesis  (IMP)
salivary gland morphogenesis  (IEA,ISO)
sensory neuron migration  (IMP)
signal transduction involved in regulation of gene expression  (IEA,ISO)
smoothened signaling pathway  (IEA,ISO)
spinal cord development  (IEP)
telencephalon regionalization  (ISO)
type B pancreatic cell differentiation  (IEA,IMP,ISO)
ventral spinal cord development  (IEA,ISO)

Cellular Component
chromatin  (IDA,IEA,ISO)
cytoplasm  (ISO)
cytosol  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IDA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Abouzeid H, etal., Mol Vis. 2009 Oct 17;15:2074-83.
2. Andrews GL and Mastick GS, J Neurosci 2003 Oct 29;23(30):9873-80.
3. Arai Y, etal., J Neurosci. 2005 Oct 19;25(42):9752-61.
4. Axton R, etal., J Med Genet. 1997 Apr;34(4):279-86.
5. Azuma N, etal., Am J Hum Genet. 1999 Sep;65(3):656-63.
6. Azuma N, etal., Am J Hum Genet. 2003 Jun;72(6):1565-70. Epub 2003 Apr 29.
7. Balakrishnan S, etal., Life Sci. 2014 Jul 25;109(1):1-7. doi: 10.1016/j.lfs.2014.06.009. Epub 2014 Jun 20.
8. Cai F, etal., Mol Vis. 2010 Jun 22;16:1141-5.
9. Cao X, etal., Genet Mol Res. 2014 Oct 27;13(4):8679-85. doi: 10.4238/2014.October.27.8.
10. Chen JH, etal., Mol Vis. 2012;18:989-95. Epub 2012 Apr 21.
11. Chen P, etal., Mol Vis. 2013 May 30;19:1169-77. Print 2013.
12. Duncan MK, etal., J Cell Sci. 2000 Sep;113 ( Pt 18):3173-85.
13. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
14. GOA data from the GO Consortium
15. Gofflot F, etal., Am J Med Genet. 1999 Nov 26;87(3):207-16.
16. Gosmain Y, etal., Endocrinology. 2012 Sep;153(9):4204-15. doi: 10.1210/en.2012-1425. Epub 2012 Jul 9.
17. Gosmain Y, etal., J Biol Chem. 2010 Oct 22;285(43):33381-93. doi: 10.1074/jbc.M110.147215. Epub 2010 Jun 30.
18. Gosmain Y, etal., Mol Endocrinol. 2012 Apr;26(4):696-709. doi: 10.1210/me.2011-1256. Epub 2012 Mar 8.
19. Graw J, etal., Invest Ophthalmol Vis Sci. 2005 Dec;46(12):4671-83.
20. Hamamoto K, etal., J Cell Biochem. 2011 Jan;112(1):318-29. doi: 10.1002/jcb.22930.
21. Hamasaki A, etal., Biochem Biophys Res Commun. 2007 Feb 2;353(1):40-6. Epub 2006 Dec 4.
22. Han W, etal., Invest Ophthalmol Vis Sci. 2009 Jan;50(1):47-56. doi: 10.1167/iovs.07-0813.
23. Henley BM and McDermott KW, J Mol Neurosci. 2010 Mar 2.
24. Horie M, etal., Eur J Neurosci 2003 Jan;17(1):49-57.
25. Insua MF, etal., J Neurosci Res. 2008 May 15;86(7):1459-71. doi: 10.1002/jnr.21606.
26. Jiang B, etal., PLoS One. 2011 May 12;6(5):e19587. doi: 10.1371/journal.pone.0019587.
27. Jin C, etal., Mol Vis. 2012;18:465-70. Epub 2012 Feb 16.
28. Kang Y, etal., Mol Vis. 2012;18:1750-4. Epub 2012 Jun 27.
29. Kim KC, etal., J Biomed Sci. 2010 Nov 12;17:85. doi: 10.1186/1423-0127-17-85.
30. Kim KC, etal., Mol Neurobiol. 2014 Feb;49(1):512-28. doi: 10.1007/s12035-013-8535-2. Epub 2013 Sep 13.
31. Kriangkrai R, etal., Dev Dyn. 2006 Aug;235(8):2134-43.
32. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
33. Lang D, etal., Mol Carcinog. 2008 Feb;47(2):148-56.
34. Lin Y, etal., Mol Vis. 2011;17:3116-20. Epub 2011 Nov 26.
35. Lovicu FJ, etal., Invest Ophthalmol Vis Sci. 2004 Jun;45(6):1946-53.
36. Maekawa M, etal., Genes Cells. 2005 Oct;10(10):1001-14.
37. Manuel M, etal., BMC Dev Biol. 2008 May 28;8:59. doi: 10.1186/1471-213X-8-59.
38. Matsuo T, etal., Nat Genet. 1993 Apr;3(4):299-304.
39. MGD data from the GO Consortium
40. Mirzayans F, etal., Am J Hum Genet. 1995 Sep;57(3):539-48.
41. Miyake M, etal., Mol Vis. 2012;18:2726-35. Epub 2012 Nov 17.
42. NCBI rat LocusLink and RefSeq merged data July 26, 2002
43. Nomura T and Osumi N, Development. 2004 Feb;131(4):787-96. Epub 2004 Jan 21.
44. Nomura T, etal., Development. 2006 Apr;133(7):1335-45. Epub 2006 Mar 1.
45. Numayama-Tsuruta K, etal., BMC Dev Biol. 2010 Jan 18;10:6. doi: 10.1186/1471-213X-10-6.
46. Nural HF and Mastick GS, J Comp Neurol 2004 Nov 22;479(4):399-409.
47. OMIM Disease Annotation Pipeline
48. Osumi N, etal., Development 1997 Aug;124(15):2961-72.
49. Osumi-Yamashita N, etal., Dev Growth Differ. 1997 Feb;39(1):53-67.
50. Pipeline to import KEGG annotations from KEGG into RGD
51. Ramaesh T, etal., Exp Eye Res. 2005 Aug;81(2):224-35.
52. Ramaesh T, etal., Exp Eye Res. 2009 Aug;89(2):263-73. doi: 10.1016/j.exer.2009.03.016. Epub 2009 Apr 2.
53. Rath MF, etal., J Neurochem. 2009 Jan;108(1):285-94. Epub 2008 Nov 19.
54. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
55. RGD automated import pipeline for gene-chemical interactions
56. Sakai M, etal., Nucleic Acids Res. 2001 Mar 1;29(5):1228-37.
57. Sakayori N, etal., Neurosci Res. 2012 Oct;74(2):116-21. doi: 10.1016/j.neures.2012.08.004. Epub 2012 Aug 27.
58. Skala-Rubinson H, etal., J Biol Chem 2002 Dec 6;277(49):47190-6.
59. Steliga A, etal., Folia Neuropathol. 2013;51(3):203-13.
60. Stober G, etal., Biol Psychiatry 1999 Jun 15;45(12):1585-91.
61. Takahashi M and Osumi N, Development 2002 Mar;129(6):1327-38.
62. Takahashi M and Osumi N, Mech Dev. 2011 May-Jun;128(5-6):289-302. doi: 10.1016/j.mod.2011.04.001. Epub 2011 Apr 9.
63. Tamai H, etal., Genes Cells. 2007 Sep;12(9):983-96.
64. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
65. Umeda T, etal., PLoS One. 2010 Dec 21;5(12):e15500. doi: 10.1371/journal.pone.0015500.
66. Vincent MC, etal., Am J Ophthalmol. 2004 Dec;138(6):1016-21.
67. Wang L, etal., Ophthalmic Res. 2013;49(2):100-7. doi: 10.1159/000345256. Epub 2012 Dec 18.
68. Weisschuh N, etal., Mol Vis. 2012;18:751-7. Epub 2012 Mar 29.
69. Wen JH, etal., Diabetologia. 2009 Mar;52(3):504-13. Epub 2008 Nov 26.
70. Wentzel P and Eriksson UJ, Birth Defects Res B Dev Reprod Toxicol. 2011 Oct;92(5):487-97. doi: 10.1002/bdrb.20321. Epub 2011 Aug 4.
71. Winner B, etal., Exp Neurol. 2009 Oct;219(2):543-52. doi: 10.1016/j.expneurol.2009.07.013. Epub 2009 Jul 18.
72. Xu Y, etal., J Mol Neurosci. 2013 Sep;51(1):37-46. doi: 10.1007/s12031-012-9941-z. Epub 2013 Jan 9.
73. Yamasaki T, etal., Development. 2001 Aug;128(16):3133-44.
74. Yang K, etal., Cell Biol Int. 2009 Aug;33(8):861-6. doi: 10.1016/j.cellbi.2009.04.009. Epub 2009 Apr 23.
Additional References at PubMed
PMID:6877261   PMID:7550230   PMID:9169845   PMID:9230312   PMID:9828088   PMID:10409504   PMID:10588713   PMID:10821755   PMID:11050125   PMID:11062307   PMID:11069887   PMID:11124115  
PMID:11209945   PMID:11731698   PMID:11756345   PMID:11967891   PMID:12050133   PMID:12072567   PMID:12183364   PMID:12196586   PMID:12477932   PMID:12648492   PMID:12756174   PMID:12764040  
PMID:14625556   PMID:15031110   PMID:15229646   PMID:15489334   PMID:15548580   PMID:15758185   PMID:15793245   PMID:15878992   PMID:15905411   PMID:15917450   PMID:16024294   PMID:16035109  
PMID:16115881   PMID:16407227   PMID:16464444   PMID:16497297   PMID:16582099   PMID:16919471   PMID:16950124   PMID:17251190   PMID:17291498   PMID:17982423   PMID:18287938   PMID:18462699  
PMID:18467663   PMID:18590716   PMID:18628401   PMID:18653562   PMID:18701439   PMID:18799682   PMID:19146846   PMID:19217949   PMID:19258013   PMID:19409883   PMID:19521500   PMID:19749747  
PMID:20439489   PMID:20725088   PMID:20852734   PMID:20943817   PMID:21084637   PMID:21397028   PMID:21698109   PMID:22031545   PMID:22162276   PMID:22764048   PMID:23431145   PMID:23434913  
PMID:23622063   PMID:23637604   PMID:23643363   PMID:23679989   PMID:24466353   PMID:24488179   PMID:24528677   PMID:24952136   PMID:25100583   PMID:25931508   PMID:26191217   PMID:27355350  
PMID:29102934   PMID:29451327   PMID:29482641   PMID:31301380  


Genomics

Comparative Map Data
Pax6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2392,128,772 - 92,157,022 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl392,135,637 - 92,157,014 (+)Ensembl
Rnor_6.0395,700,241 - 95,728,682 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl395,707,386 - 95,728,624 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03102,320,059 - 102,348,223 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4391,127,605 - 91,149,178 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1391,023,827 - 91,045,776 (+)NCBI
Celera391,190,477 - 91,211,449 (+)NCBICelera
RH 3.4 Map3722.9RGD
Cytogenetic Map3q33NCBI
PAX6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1131,784,779 - 31,817,961 (-)EnsemblGRCh38hg38GRCh38
GRCh381131,789,026 - 31,817,961 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371131,810,574 - 31,839,509 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361131,767,034 - 31,789,455 (-)NCBINCBI36hg18NCBI36
Build 341131,768,057 - 31,789,341NCBI
Celera1131,953,799 - 31,986,960 (-)NCBI
Cytogenetic Map11p13NCBI
HuRef1131,501,758 - 31,535,259 (-)NCBIHuRef
CHM1_11131,805,847 - 31,839,030 (-)NCBICHM1_1
Pax6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392105,499,241 - 105,528,755 (+)NCBIGRCm39mm39
GRCm39 Ensembl2105,499,245 - 105,527,709 (+)Ensembl
GRCm382105,668,896 - 105,698,410 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2105,668,900 - 105,697,364 (+)EnsemblGRCm38mm10GRCm38
MGSCv372105,516,602 - 105,537,226 (+)NCBIGRCm37mm9NCBIm37
MGSCv362105,477,284 - 105,497,908 (+)NCBImm8
Celera2106,897,827 - 106,918,452 (+)NCBICelera
Cytogenetic Map2E3NCBI
cM Map255.31NCBI
Pax6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547610,058,961 - 10,074,162 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495547610,058,979 - 10,074,668 (-)NCBIChiLan1.0ChiLan1.0
PAX6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11131,641,813 - 31,671,071 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1131,641,813 - 31,664,474 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01131,753,190 - 31,782,225 (-)NCBIMhudiblu_PPA_v0panPan3
PAX6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha1835,260,520 - 35,281,796 (+)NCBI
ROS_Cfam_1.01836,247,894 - 36,277,423 (+)NCBI
UMICH_Zoey_3.11835,828,719 - 35,849,973 (+)NCBI
UNSW_CanFamBas_1.01835,410,013 - 35,431,263 (+)NCBI
UU_Cfam_GSD_1.01836,045,041 - 36,066,313 (+)NCBI
Pax6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494732,827,732 - 32,856,209 (+)NCBI
SpeTri2.0NW_0049365335,952,529 - 5,980,889 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PAX6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl228,971,567 - 29,001,200 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1228,971,565 - 29,001,149 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2231,478,545 - 31,510,656 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PAX6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1133,386,165 - 33,414,605 (+)NCBI
ChlSab1.1 Ensembl133,392,970 - 33,414,587 (+)Ensembl
Vero_WHO_p1.0NW_023666038130,542,963 - 130,572,341 (+)NCBI
Pax6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476620,536,581 - 20,554,589 (-)NCBI

Position Markers
RH94662  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2392,156,482 - 92,156,661 (+)MAPPERmRatBN7.2
Rnor_6.0395,728,022 - 95,728,200NCBIRnor6.0
Rnor_5.03102,347,862 - 102,348,040UniSTSRnor5.0
RGSC_v3.4391,148,817 - 91,148,995UniSTSRGSC3.4
Celera391,211,088 - 91,211,266UniSTS
RH 3.4 Map3722.9UniSTS
Cytogenetic Map3q32UniSTS
RH94663  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2392,135,747 - 92,135,857 (+)MAPPERmRatBN7.2
Rnor_6.0395,707,292 - 95,707,401NCBIRnor6.0
Rnor_5.03102,327,132 - 102,327,241UniSTSRnor5.0
RGSC_v3.4391,127,511 - 91,127,620UniSTSRGSC3.4
Celera391,190,383 - 91,190,492UniSTS
Cytogenetic Map3q32UniSTS
GDB:197570  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2392,155,250 - 92,156,096 (+)MAPPERmRatBN7.2
Rnor_6.0395,726,790 - 95,727,635NCBIRnor6.0
Rnor_5.03102,346,630 - 102,347,475UniSTSRnor5.0
RGSC_v3.4391,147,585 - 91,148,430UniSTSRGSC3.4
Celera391,209,856 - 91,210,701UniSTS
Cytogenetic Map3q32UniSTS
GDB:344354  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2392,143,651 - 92,143,782 (+)MAPPERmRatBN7.2
Rnor_6.0395,715,194 - 95,715,324NCBIRnor6.0
Rnor_5.03102,335,034 - 102,335,164UniSTSRnor5.0
RGSC_v3.4391,135,415 - 91,135,545UniSTSRGSC3.4
Celera391,198,289 - 91,198,419UniSTS
Cytogenetic Map3q32UniSTS
PMC186446P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2392,152,539 - 92,152,720 (+)MAPPERmRatBN7.2
Rnor_6.0395,724,079 - 95,724,259NCBIRnor6.0
Rnor_5.03102,343,919 - 102,344,099UniSTSRnor5.0
RGSC_v3.4391,144,340 - 91,144,520UniSTSRGSC3.4
Celera391,207,145 - 91,207,325UniSTS
Cytogenetic Map3q32UniSTS
Pax6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2392,143,668 - 92,143,780 (+)MAPPERmRatBN7.2
Rnor_6.0395,715,211 - 95,715,322NCBIRnor6.0
Rnor_5.03102,335,051 - 102,335,162UniSTSRnor5.0
RGSC_v3.4391,135,432 - 91,135,543UniSTSRGSC3.4
Celera391,198,306 - 91,198,417UniSTS
Cytogenetic Map3q32UniSTS
D12Bir2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2392,143,663 - 92,144,747 (+)MAPPERmRatBN7.2
Rnor_6.0395,715,206 - 95,716,289NCBIRnor6.0
Rnor_5.03102,335,046 - 102,336,129UniSTSRnor5.0
RGSC_v3.4391,135,427 - 91,136,510UniSTSRGSC3.4
Celera391,198,301 - 91,199,384UniSTS
Cytogenetic Map3q32UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)33035677398535386Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333703347104104347Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)341874578104104347Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)353184593115665732Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)364655305115665732Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)364655305115665732Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)373376539118376539Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
2302273Gluco35Glucose level QTL 355.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)380800231114297550Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)389772419134772419Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat


Related Rat Strains
The following Strains have been annotated to Pax6


Genetic Models
This gene Pax6 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:162
Count of miRNA genes:63
Interacting mature miRNAs:78
Transcripts:ENSRNOT00000005882, ENSRNOT00000006302
Prediction methods:Miranda, 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 63
Low 1 4 4 4 11 15
Below cutoff 2 16 22 14 11 14 3 3 13 20 5 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_013001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234633 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234634 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234635 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234636 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591494 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591495 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104376 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AJ627631 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY540905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY540906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC128741 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HQ121510 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U69644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000005882   ⟹   ENSRNOP00000005882
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl392,135,637 - 92,157,014 (+)Ensembl
Rnor_6.0 Ensembl395,707,386 - 95,728,382 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000006302   ⟹   ENSRNOP00000006302
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl392,143,229 - 92,157,014 (+)Ensembl
Rnor_6.0 Ensembl395,711,555 - 95,728,624 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089525   ⟹   ENSRNOP00000071013
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl392,135,637 - 92,157,014 (+)Ensembl
Rnor_6.0 Ensembl395,715,193 - 95,727,664 (+)Ensembl
RefSeq Acc Id: NM_013001   ⟹   NP_037133
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2392,135,842 - 92,156,844 (+)NCBI
Rnor_6.0395,707,386 - 95,728,383 (+)NCBI
Rnor_5.03102,320,059 - 102,348,223 (+)NCBI
RGSC_v3.4391,127,605 - 91,149,178 (+)RGD
Celera391,190,477 - 91,211,449 (+)RGD
Sequence:
RefSeq Acc Id: XM_006234633   ⟹   XP_006234695
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2392,135,285 - 92,157,022 (+)NCBI
Rnor_6.0395,706,982 - 95,728,682 (+)NCBI
Rnor_5.03102,320,059 - 102,348,223 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006234634   ⟹   XP_006234696
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2392,133,177 - 92,157,022 (+)NCBI
Rnor_6.0395,706,015 - 95,728,682 (+)NCBI
Rnor_5.03102,320,059 - 102,348,223 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006234635   ⟹   XP_006234697
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2392,135,285 - 92,157,022 (+)NCBI
Rnor_6.0395,706,892 - 95,728,682 (+)NCBI
Rnor_5.03102,320,059 - 102,348,223 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006234636   ⟹   XP_006234698
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2392,128,772 - 92,157,022 (+)NCBI
Rnor_6.0395,700,241 - 95,728,682 (+)NCBI
Rnor_5.03102,320,059 - 102,348,223 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039104376   ⟹   XP_038960304
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2392,135,888 - 92,157,022 (+)NCBI
RefSeq Acc Id: XM_039104377   ⟹   XP_038960305
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2392,135,269 - 92,153,260 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_037133   ⟸   NM_013001
- UniProtKB: P63016 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006234698   ⟸   XM_006234636
- Peptide Label: isoform X1
- UniProtKB: P63016 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006234696   ⟸   XM_006234634
- Peptide Label: isoform X1
- UniProtKB: P63016 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006234697   ⟸   XM_006234635
- Peptide Label: isoform X1
- UniProtKB: P63016 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006234695   ⟸   XM_006234633
- Peptide Label: isoform X1
- UniProtKB: P63016 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006302   ⟸   ENSRNOT00000006302
RefSeq Acc Id: ENSRNOP00000071013   ⟸   ENSRNOT00000089525
RefSeq Acc Id: ENSRNOP00000005882   ⟸   ENSRNOT00000005882
RefSeq Acc Id: XP_038960305   ⟸   XM_039104377
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038960304   ⟸   XM_039104376
- Peptide Label: isoform X1
Protein Domains
Homeobox   Paired

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 (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
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 (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (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
F344/N (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (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
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
F344/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (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
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
FXLE16/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
FXLE18/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
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/FarMcwi (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
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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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
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
LEXF10A/StmMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/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
LEXF1A/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (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: 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)
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/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)
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: 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)
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
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)
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: 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)
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
PVG/Seac (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
SHR/OlalpcvMcwi (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
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)
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: 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)
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/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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
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 (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: 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:3258 AgrOrtholog
Ensembl Genes ENSRNOG00000004410 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005882 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000006302 UniProtKB/Swiss-Prot
  ENSRNOP00000071013 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005882 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000006302 UniProtKB/Swiss-Prot
  ENSRNOT00000089525 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:8363963 IMAGE-MGC_LOAD
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PAIRED_DNA_bd_dom UniProtKB/Swiss-Prot
  Paired_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PAX_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25509 UniProtKB/Swiss-Prot
MGC_CLONE MGC:156670 IMAGE-MGC_LOAD
NCBI Gene 25509 ENTREZGENE
PANTHER PTHR45636 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PAX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pax6 PhenoGen
PRINTS PAIREDBOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PAIRED_1 UniProtKB/Swiss-Prot
  PAIRED_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PAX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC214153
UniProt A0A0G2JZE2_RAT UniProtKB/TrEMBL
  P63016 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A1A5N7 UniProtKB/Swiss-Prot
  P32117 UniProtKB/Swiss-Prot
  P70601 UniProtKB/Swiss-Prot
  Q62222 UniProtKB/Swiss-Prot
  Q64037 UniProtKB/Swiss-Prot
  Q6QHS5 UniProtKB/Swiss-Prot
  Q701Q8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Pax6  Paired box homeotic gene 6      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease mutations in human homolog are associated with several eye disorders, including aniridia and Peter's anomoly 731242
gene_expression protein expressed in hindbrain and forebrain 731242
gene_mutations_overexpression point mutation in rat (rSey) exhibits abnormal development of hindbrain motor neurons 731242
gene_process controls ventral neurons specification by establishing the correct progenitor domains 729590
gene_process may regulate Isl2 and Wnt7b expression 731242
gene_process involved with the specification of hindbrain motor neuron subtype 731242
gene_process regulates specific neural pathways during forebrain development 731242
gene_process plays role in axon guidance of specific motor neurons in the hindbrain 731242
gene_process role in axon guidance crucial for development of the thalamocortical neuronal pathway 731243