Gjb2 (gap junction protein, beta 2) - Rat Genome Database

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Gene: Gjb2 (gap junction protein, beta 2) Rattus norvegicus
Analyze
Symbol: Gjb2
Name: gap junction protein, beta 2
RGD ID: 728891
Description: Enables gap junction channel activity. Involved in several processes, including cellular response to glucagon stimulus; reproductive structure development; and response to steroid hormone. Located in several cellular components, including astrocyte projection; gap junction; and lateral plasma membrane. Used to study hepatocellular carcinoma and lung adenocarcinoma. Biomarker of autoimmune thyroiditis; extrahepatic cholestasis; ischemia; sensorineural hearing loss; and urethral obstruction. Human ortholog(s) of this gene implicated in Bart-Pumphrey syndrome; Vohwinkel syndrome; autosomal dominant keratitis-ichthyosis-deafness syndrome; nonsyndromic deafness (multiple); and palmoplantar keratoderma-deafness syndrome. Orthologous to human GJB2 (gap junction protein beta 2); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: connexin 26; connexin e; connexin-26; Cx26; CXN-26; Cxne; gap junction beta-2 protein; gap junction channel protein connexin 26; gap junction membrane channel protein beta 2; MGC93804
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21531,260,390 - 31,278,222 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1531,260,357 - 31,278,177 (-)Ensembl
Rnor_6.01537,377,313 - 37,394,494 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1537,377,316 - 37,383,277 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01541,224,497 - 41,236,203 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41536,153,526 - 36,159,490 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11536,169,226 - 36,175,190 (-)NCBI
Celera1530,972,813 - 30,978,777 (-)NCBICelera
Cytogenetic Map15p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-dinitrotoluene  (EXP)
2-acetamidofluorene  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
8-Br-cAMP  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
arsenite(3-)  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[e]pyrene  (ISO)
Benzoyl peroxide  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromobenzene  (EXP)
butan-1-ol  (ISO)
butanal  (ISO)
cadmium sulfate  (ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chenodeoxycholic acid  (ISO)
chloral hydrate  (EXP)
chlordecone  (ISO)
chloropicrin  (ISO)
chloroquine  (EXP)
cisplatin  (EXP,ISO)
cocaine  (ISO)
coumarin  (EXP)
Cuprizon  (EXP)
cyclosporin A  (ISO)
deoxycholic acid  (ISO)
dibutyl phthalate  (EXP)
dieldrin  (EXP)
diethylstilbestrol  (ISO)
dimethyl sulfoxide  (EXP)
dorsomorphin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
flutamide  (EXP)
fonofos  (ISO)
fulvestrant  (ISO)
genistein  (EXP,ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
Heptachlor epoxide  (EXP)
hexachlorobenzene  (EXP)
Indeno[1,2,3-cd]pyrene  (ISO)
isobutanol  (ISO)
lead nitrate  (ISO)
limonene  (EXP)
mercury dibromide  (ISO)
mercury dichloride  (ISO)
methapyrilene  (EXP,ISO)
N-ethyl-N-nitrosourea  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (EXP)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
nefazodone  (EXP,ISO)
ochratoxin A  (EXP)
okadaic acid  (ISO)
oleamide  (ISO)
oxaliplatin  (EXP)
paclitaxel  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
parathion  (ISO)
pentanal  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (EXP,ISO)
pirinixic acid  (EXP,ISO)
progesterone  (ISO)
propanal  (ISO)
propiconazole  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
scopolamine  (EXP)
silicon dioxide  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
sodium dodecyl sulfate  (EXP)
Sunset Yellow FCF  (ISO)
tamoxifen  (ISO)
tartrazine  (ISO)
temozolomide  (ISO)
terbufos  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP,ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
urethane  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
zearalenone  (EXP)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
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11. Dufresne J, etal., Am J Physiol Cell Physiol 2003 Jan;284(1):C33-43.
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14. GOA data from the GO Consortium
15. Gravina LP, etal., Int J Pediatr Otorhinolaryngol. 2010 Mar;74(3):250-4. doi: 10.1016/j.ijporl.2009.11.014. Epub 2009 Dec 22.
16. Green LM, etal., Endocrinology. 1996 Jul;137(7):2823-32.
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20. Hochman JB, etal., Otol Neurotol. 2010 Aug;31(6):919-22. doi: 10.1097/MAO.0b013e3181e3d324.
21. Hsu WC, etal., Acta Otolaryngol. 2004 May;124(4):459-63.
22. Hu P, etal., B-ENT. 2012;8(2):77-84.
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24. Jiang SJ, etal., Int J Pediatr Otorhinolaryngol. 2014 Sep;78(9):1461-6. doi: 10.1016/j.ijporl.2014.06.008. Epub 2014 Jun 16.
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29. Lautermann J, etal., Dev Genet. 1999;25(4):306-11.
30. Lazic T, etal., Pediatr Dermatol. 2008 Sep-Oct;25(5):535-40. doi: 10.1111/j.1525-1470.2008.00767.x.
31. Liang C, etal., Neurosci Lett. 2012 Oct 18;528(1):36-41. doi: 10.1016/j.neulet.2012.08.085. Epub 2012 Sep 11.
32. Liu XZ, etal., Hum Mol Genet. 2001 Dec 1;10(25):2945-51.
33. Lu Y, etal., J Biomed Res. 2011 Sep;25(5):309-18. doi: 10.1016/S1674-8301(11)60042-0.
34. Ly A, etal., Invest Ophthalmol Vis Sci. 2011 Dec 2;52(13):9316-26. doi: 10.1167/iovs.11-7879.
35. Maestrini E, etal., Hum Mol Genet. 1999 Jul;8(7):1237-43.
36. Matos TD, etal., Int J Audiol. 2013 Jul;52(7):466-71. doi: 10.3109/14992027.2013.783719. Epub 2013 May 13.
37. Mercier F and Hatton GI, J Comp Neurol. 2001 Feb 26;431(1):88-104.
38. Mese G, etal., Mol Biol Cell. 2011 Dec;22(24):4776-86. doi: 10.1091/mbc.E11-09-0778. Epub 2011 Oct 26.
39. MGD data from the GO Consortium
40. NCBI rat LocusLink and RefSeq merged data October 15, 2003
41. OMIM Disease Annotation Pipeline
42. Orlando-Mathur CE, etal., Biol Reprod. 1996 Apr;54(4):905-13.
43. Orsino A, etal., Endocrinology. 1996 May;137(5):1545-53.
44. Ou CW, etal., Endocrinology. 1997 Dec;138(12):5398-407.
45. Popova DP, etal., Eur Arch Otorhinolaryngol. 2012 Jun;269(6):1589-92. doi: 10.1007/s00405-011-1817-2. Epub 2011 Oct 29.
46. Prera N, etal., Laryngorhinootologie. 2013 Sep 10.
47. Rash JE, etal., Cell Commun Adhes 2001;8(4-6):315-20.
48. RGD automated data pipeline
49. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
50. RGD automated import pipeline for gene-chemical interactions
51. Riahi Z, etal., Gene. 2013 Aug 1;525(1):1-4. doi: 10.1016/j.gene.2013.04.078. Epub 2013 May 13.
52. Richard G, etal., J Invest Dermatol. 2004 Nov;123(5):856-63.
53. Risek B, etal., J Cell Sci. 1998 May;111 ( Pt 10):1395-404.
54. Sakamoto H, etal., Jpn J Cancer Res. 1992 Nov;83(11):1210-5.
55. Schutz M, etal., Hum Mol Genet. 2011 Jan 1;20(1):28-39. doi: 10.1093/hmg/ddq429. Epub 2010 Oct 6.
56. Shimizu K, etal., Mol Carcinog. 2006 Sep;45(9):710-4.
57. Shin BC, etal., Cell Tissue Res. 1996 Jul;285(1):83-9.
58. Solomon IC, etal., Respir Physiol. 2001 Dec;129(1-2):101-21.
59. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
60. Sukarova Stefanovska E, etal., Balkan J Med Genet. 2012 Dec;15(Suppl):57-9. doi: 10.2478/v10034-012-0020-0.
61. Sunagawa M, etal., World J Urol. 2015 Feb;33(2):275-80. doi: 10.1007/s00345-014-1298-1. Epub 2014 Apr 12.
62. Takiguchi Y, etal., Neurosci Res. 2013 Jul 1. pii: S0168-0102(13)00159-4. doi: 10.1016/j.neures.2013.06.003.
63. Tawadros T, etal., Cell Commun Adhes 2001;8(4-6):303-6.
64. Terrinoni A, etal., Biochem Biophys Res Commun. 2010 Apr 23;395(1):25-30. doi: 10.1016/j.bbrc.2010.03.098. Epub 2010 Mar 20.
65. Tsujiuchi T, etal., Mol Carcinog. 2007 Apr;46(4):269-74.
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67. Wonkam A, etal., BMC Med Genet. 2013 Aug 7;14:81. doi: 10.1186/1471-2350-14-81.
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Additional References at PubMed
PMID:2557354   PMID:2823143   PMID:11745652   PMID:12767933   PMID:14595769   PMID:14676473   PMID:15028626   PMID:15128867   PMID:15489334   PMID:15692151   PMID:17551008   PMID:17693411  
PMID:17713529   PMID:19194037   PMID:19340074   PMID:19775242   PMID:20089884   PMID:20441744   PMID:20654614   PMID:21094651   PMID:24590285   PMID:25365227   PMID:26590355   PMID:26753910  
PMID:27053364   PMID:27143357   PMID:27816814   PMID:29207085   PMID:33171391  


Genomics

Comparative Map Data
Gjb2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21531,260,390 - 31,278,222 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1531,260,357 - 31,278,177 (-)Ensembl
Rnor_6.01537,377,313 - 37,394,494 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1537,377,316 - 37,383,277 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01541,224,497 - 41,236,203 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41536,153,526 - 36,159,490 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11536,169,226 - 36,175,190 (-)NCBI
Celera1530,972,813 - 30,978,777 (-)NCBICelera
Cytogenetic Map15p12NCBI
GJB2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1320,187,463 - 20,192,938 (-)EnsemblGRCh38hg38GRCh38
GRCh381320,187,470 - 20,192,938 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371320,761,609 - 20,767,077 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361319,659,605 - 19,665,114 (-)NCBINCBI36hg18NCBI36
Build 341319,659,608 - 19,665,037NCBI
Celera131,823,407 - 1,828,919 (-)NCBI
Cytogenetic Map13q12.11NCBI
HuRef131,567,054 - 1,572,566 (-)NCBIHuRef
CHM1_11320,730,111 - 20,735,623 (-)NCBICHM1_1
Gjb2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391457,336,059 - 57,342,159 (-)NCBIGRCm39mm39
GRCm39 Ensembl1457,336,057 - 57,342,159 (-)Ensembl
GRCm381457,098,602 - 57,104,702 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1457,098,600 - 57,104,702 (-)EnsemblGRCm38mm10GRCm38
MGSCv371457,717,439 - 57,723,539 (-)NCBIGRCm37mm9NCBIm37
MGSCv361456,052,728 - 56,058,775 (-)NCBImm8
Celera1454,889,190 - 54,895,282 (-)NCBICelera
Cytogenetic Map14C3NCBI
cM Map1430.1NCBI
Gjb2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955497988,422 - 989,099 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955497987,213 - 989,477 (-)NCBIChiLan1.0ChiLan1.0
GJB2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11319,829,838 - 19,831,999 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1319,831,274 - 19,831,954 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0131,514,714 - 1,520,239 (-)NCBIMhudiblu_PPA_v0panPan3
GJB2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12517,952,851 - 17,958,289 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2517,952,851 - 17,958,289 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2517,983,495 - 17,988,934 (+)NCBI
ROS_Cfam_1.02518,090,743 - 18,096,185 (+)NCBI
UMICH_Zoey_3.12517,957,195 - 17,962,619 (+)NCBI
UNSW_CanFamBas_1.02517,968,886 - 17,974,320 (+)NCBI
UU_Cfam_GSD_1.02518,025,532 - 18,030,958 (+)NCBI
Gjb2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945119,960,764 - 119,982,667 (+)NCBI
SpeTri2.0NW_0049367201,528,205 - 1,530,296 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GJB2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.111774,090 - 781,252 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
GJB2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.13801,786 - 808,165 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl3807,379 - 808,059 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605743,777,267 - 43,781,704 (-)NCBIVero_WHO_p1.0
Gjb2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477617,517,824 - 17,522,683 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH129172  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21531,262,544 - 31,262,734 (+)MAPPERmRatBN7.2
Rnor_6.01537,379,468 - 37,379,657NCBIRnor6.0
Rnor_5.01541,226,652 - 41,226,841UniSTSRnor5.0
RGSC_v3.41536,155,681 - 36,155,870UniSTSRGSC3.4
Celera1530,974,968 - 30,975,157UniSTS
RH 3.4 Map15260.89UniSTS
Cytogenetic Map15p12UniSTS
RH133850  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21531,261,074 - 31,261,270 (+)MAPPERmRatBN7.2
Rnor_6.01537,377,998 - 37,378,193NCBIRnor6.0
Rnor_5.01541,225,182 - 41,225,377UniSTSRnor5.0
RGSC_v3.41536,154,211 - 36,154,406UniSTSRGSC3.4
Celera1530,973,498 - 30,973,693UniSTS
Cytogenetic Map15p12UniSTS
RH137073  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21531,260,535 - 31,260,727 (+)MAPPERmRatBN7.2
Rnor_6.01537,377,459 - 37,377,650NCBIRnor6.0
Rnor_5.01541,224,643 - 41,224,834UniSTSRnor5.0
RGSC_v3.41536,153,672 - 36,153,863UniSTSRGSC3.4
Celera1530,972,959 - 30,973,150UniSTS
RH 3.4 Map15214.77UniSTS
Cytogenetic Map15p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)151985656634924750Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:167
Count of miRNA genes:115
Interacting mature miRNAs:137
Transcripts:ENSRNOT00000011711
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 2 27 21 6 21 34 23 3
Low 1 20 22 20 13 20 3 4 38 12 27 11 3
Below cutoff 21 8 5 7 2 11 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011711   ⟹   ENSRNOP00000011711
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1531,260,357 - 31,266,463 (-)Ensembl
Rnor_6.0 Ensembl1537,377,316 - 37,383,277 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104368   ⟹   ENSRNOP00000082358
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1531,260,403 - 31,278,177 (-)Ensembl
RefSeq Acc Id: NM_001004099   ⟹   NP_001004099
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21531,260,390 - 31,266,367 (-)NCBI
Rnor_6.01537,377,313 - 37,383,277 (-)NCBI
Rnor_5.01541,224,497 - 41,236,203 (-)NCBI
RGSC_v3.41536,153,526 - 36,159,490 (-)RGD
Celera1530,972,813 - 30,978,777 (-)RGD
Sequence:
RefSeq Acc Id: XM_017599765   ⟹   XP_017455254
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21531,260,390 - 31,278,222 (-)NCBI
Rnor_6.01537,377,313 - 37,394,494 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039093557   ⟹   XP_038949485
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21531,260,390 - 31,272,192 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001004099   ⟸   NM_001004099
- UniProtKB: P21994 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017455254   ⟸   XM_017599765
- Peptide Label: isoform X1
- UniProtKB: P21994 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011711   ⟸   ENSRNOT00000011711
RefSeq Acc Id: XP_038949485   ⟸   XM_039093557
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000082358   ⟸   ENSRNOT00000104368
Protein Domains
CNX   Connexin_CCC

Transcriptome

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

Promoters
RGD ID:13699717
Promoter ID:EPDNEW_R10240
Type:multiple initiation site
Name:Gjb2_1
Description:gap junction protein, beta 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01537,383,288 - 37,383,348EPDNEW

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