Jak1 (Janus kinase 1) - Rat Genome Database

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Gene: Jak1 (Janus kinase 1) Rattus norvegicus
Analyze
Symbol: Jak1
Name: Janus kinase 1
RGD ID: 69056
Description: Enables CCR5 chemokine receptor binding activity and growth hormone receptor binding activity. Predicted to be involved in several processes, including cell surface receptor signaling pathway; positive regulation of homotypic cell-cell adhesion; and positive regulation of sprouting angiogenesis. Predicted to act upstream of or within several processes, including cell surface receptor signaling pathway; cellular response to cytokine stimulus; and positive regulation of receptor signaling pathway via STAT. Predicted to be located in cytoplasm and nucleus. Biomarker of sciatic neuropathy and transient cerebral ischemia. Human ortholog(s) of this gene implicated in T-cell acute lymphoblastic leukemia; carcinoma (multiple); gastrointestinal system cancer (multiple); and reproductive organ cancer (multiple). Orthologous to human JAK1 (Janus kinase 1); PARTICIPATES IN Interleukin-10 signaling pathway; interleukin-2 signaling pathway; interleukin-27 signaling pathway; INTERACTS WITH (R)-mevalonic acid; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Janus protein tyrosine kinase 1; tyrosine-protein kinase JAK1
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
mRatBN7.25115,780,248 - 115,888,841 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl5115,780,248 - 115,888,926 (-)Ensembl
Rnor_6.05119,982,503 - 120,091,452 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5119,982,943 - 120,083,904 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05123,865,078 - 123,973,772 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45121,804,586 - 121,905,581 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15121,813,666 - 121,843,676 (-)NCBI
Celera5114,318,185 - 114,418,922 (-)NCBICelera
Cytogenetic Map5q33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(R)-mevalonic acid  (EXP)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-phenylprop-2-enal  (EXP)
4-hydroxyphenyl retinamide  (ISO)
4-vinylcyclohexene dioxide  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
6alpha-methylprednisolone  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amantadine  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
baricitinib  (ISO)
benzbromarone  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
buspirone  (EXP)
cadmium dichloride  (ISO)
calcitriol  (ISO)
capsaicin  (ISO)
carbon nanotube  (ISO)
clobetasol  (ISO)
clofibrate  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cyanidin cation  (ISO)
cyclosporin A  (ISO)
DDT  (ISO)
deoxynivalenol  (ISO)
diarsenic trioxide  (ISO)
dioxygen  (ISO)
divanadium pentaoxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
emodin  (ISO)
ethanol  (EXP,ISO)
Fidarestat  (ISO)
filipin III  (ISO)
gentamycin  (EXP)
hesperetin  (ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
isotretinoin  (ISO)
L-ethionine  (EXP)
lead diacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
lycopene  (ISO)
menadione  (ISO)
mercury dichloride  (ISO)
methoxychlor  (ISO)
methyl beta-cyclodextrin  (ISO)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
microcystin-LR  (ISO)
myricetin  (ISO)
N-acetyl-L-cysteine  (ISO)
N-ethyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP)
nimesulide  (EXP)
nitric oxide  (ISO)
oleic acid  (ISO)
omeprazole  (EXP)
oridonin  (ISO)
paracetamol  (ISO)
perfluorooctanoic acid  (ISO)
phenethyl isothiocyanate  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pipoxolan  (ISO)
pirinixic acid  (EXP)
ponatinib  (ISO)
potassium dichromate  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
quercetin 3-O-beta-D-glucofuranoside  (ISO)
quercetin 3-O-beta-D-glucopyranoside  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
rutin  (EXP)
ruxolitinib  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
Salinomycin  (ISO)
SB 431542  (ISO)
simvastatin  (EXP)
sodium arsenite  (ISO)
sunitinib  (ISO)
T-2 toxin  (ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
testosterone  (EXP)
testosterone enanthate  (EXP)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
thapsigargin  (ISO)
theophylline  (ISO)
thioacetamide  (EXP)
tofacitinib  (ISO)
torcetrapib  (ISO)
trichostatin A  (ISO)
trimethyltin  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (ISO)
verteporfin  (ISO)
zoledronic acid  (ISO)

References

References - curated
1. Albacker LA, etal., PLoS One. 2017 Nov 9;12(11):e0176181. doi: 10.1371/journal.pone.0176181. eCollection 2017.
2. Booz GW, etal., Mol Cell Biochem 2002 Nov;240(1-2):39-46.
3. Chen K, etal., Genet Test Mol Biomarkers. 2012 Oct;16(10):1206-10. doi: 10.1089/gtmb.2012.0141. Epub 2012 Aug 17.
4. Chen L, etal., Oncol Rep. 2018 Mar;39(3):1081-1089. doi: 10.3892/or.2018.6198. Epub 2018 Jan 8.
5. Chen P, etal., Int J Mol Med. 2011 May;27(5):731-8. doi: 10.3892/ijmm.2011.632. Epub 2011 Mar 1.
6. Chough C, etal., Bioorg Med Chem. 2018 May 1;26(8):1495-1510. doi: 10.1016/j.bmc.2018.01.021. Epub 2018 Feb 3.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. GOA data from the GO Consortium
9. Hellgren G, etal., J Interferon Cytokine Res. 2001 Feb;21(2):75-83.
10. Jeong EG, etal., Clin Cancer Res. 2008 Jun 15;14(12):3716-21. doi: 10.1158/1078-0432.CCR-07-4839.
11. Jones SA, etal., J Clin Invest. 2011 Sep 1;121(9):3375-83. doi: 10.1172/JCI57158. Epub 2011 Sep 1.
12. Justicia C, etal., Glia. 2000 May;30(3):253-70. doi: 10.1002/(sici)1098-1136(200005)30:3<253::aid-glia5>3.0.co;2-o.
13. Kan Z, etal., Genome Res. 2013 Sep;23(9):1422-33. doi: 10.1101/gr.154492.113. Epub 2013 Jun 20.
14. Kurdi M and Booz GW, J Cell Physiol. 2007 Aug;212(2):424-31.
15. Lejeune D, etal., J Biol Chem 2002 Sep 13;277(37):33676-82. Epub 2002 Jun 26.
16. Li H, etal., J Periodontal Res. 2017 Feb;52(1):1-7. doi: 10.1111/jre.12360. Epub 2016 Jan 30.
17. Li HR, etal., Parasitology. 2016 Oct;143(12):1629-38. doi: 10.1017/S0031182016001128. Epub 2016 Jul 21.
18. Liu D, etal., Oncol Lett. 2017 Oct;14(4):3959-3966. doi: 10.3892/ol.2017.6690. Epub 2017 Aug 1.
19. MGD data from the GO Consortium
20. Murray PJ J Immunol. 2007 Mar 1;178(5):2623-9.
21. NCBI rat LocusLink and RefSeq merged data July 26, 2002
22. Park EJ, etal., J Biol Chem 2003 Apr 25;278(17):14747-52. Epub 2003 Feb 12.
23. Pipeline to import KEGG annotations from KEGG into RGD
24. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
25. RGD automated data pipeline
26. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
27. RGD automated import pipeline for gene-chemical interactions
28. RGD comprehensive gene curation
29. Sabat R, etal., Cytokine Growth Factor Rev. 2010 Oct;21(5):331-44. doi: 10.1016/j.cytogfr.2010.09.002. Epub 2010 Nov 5.
30. Shahrara S, etal., Arthritis Rheum. 2003 Dec;48(12):3568-83.
31. Sveen A, etal., Genome Med. 2017 May 24;9(1):46. doi: 10.1186/s13073-017-0434-0.
32. Szpirer C, etal., Mamm Genome 2000 Sep;11(9):729-35
33. Verma A, etal., Cancer Metastasis Rev 2003 Dec;22(4):423-34.
34. Wang GS, etal., Zhonghua Jie He He Hu Xi Za Zhi. 2003 Nov;26(11):664-7.
35. Wang L, etal., J Cell Physiol. 2020 Oct;235(10):6528-6535. doi: 10.1002/jcp.29465. Epub 2020 Feb 3.
36. Wang Q, etal., J Steroid Biochem Mol Biol. 2013 May;135:43-50. doi: 10.1016/j.jsbmb.2013.01.008. Epub 2013 Jan 18.
37. Wen W, etal., Mol Cancer Ther. 2014 Dec;13(12):3037-48. doi: 10.1158/1535-7163.MCT-14-0077. Epub 2014 Oct 15.
38. Yang S, etal., Oncotarget. 2016 Feb 2;7(5):5461-9. doi: 10.18632/oncotarget.6684.
39. Yu DL, etal., Oncol Rep. 2017 Aug;38(2):1075-1082. doi: 10.3892/or.2017.5781. Epub 2017 Jul 3.
40. Zhou F, etal., Oncotarget. 2016 May 10;7(19):28112-23. doi: 10.18632/oncotarget.8492.
Additional References at PubMed
PMID:1386289   PMID:8022486   PMID:8232552   PMID:8378315   PMID:10502458   PMID:10825200   PMID:10872802   PMID:11909529   PMID:12477932   PMID:15126250   PMID:16280321   PMID:16413512  
PMID:17993459   PMID:18636982   PMID:18665395   PMID:19176616   PMID:19457567   PMID:20299512   PMID:21423176   PMID:21679692   PMID:22875468   PMID:22939972   PMID:22971540   PMID:24152426  
PMID:24882218   PMID:25129435   PMID:25986861   PMID:27003918   PMID:27671227   PMID:29581031   PMID:30664158  


Genomics

Comparative Map Data
Jak1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25115,780,248 - 115,888,841 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl5115,780,248 - 115,888,926 (-)Ensembl
Rnor_6.05119,982,503 - 120,091,452 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5119,982,943 - 120,083,904 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05123,865,078 - 123,973,772 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45121,804,586 - 121,905,581 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15121,813,666 - 121,843,676 (-)NCBI
Celera5114,318,185 - 114,418,922 (-)NCBICelera
Cytogenetic Map5q33NCBI
JAK1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl164,833,229 - 65,067,754 (-)EnsemblGRCh38hg38GRCh38
GRCh38164,833,229 - 65,067,746 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37165,298,912 - 65,533,429 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36165,071,494 - 65,204,775 (-)NCBINCBI36hg18NCBI36
Build 34165,012,228 - 65,064,007NCBI
Celera163,589,792 - 63,723,086 (-)NCBI
Cytogenetic Map1p31.3NCBI
HuRef163,407,815 - 63,541,120 (-)NCBIHuRef
CHM1_1165,415,253 - 65,548,498 (-)NCBICHM1_1
Jak1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394101,009,171 - 101,122,493 (-)NCBIGRCm39mm39
GRCm39 Ensembl4101,009,564 - 101,122,479 (-)Ensembl
GRCm384101,151,974 - 101,265,282 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4101,152,367 - 101,265,282 (-)EnsemblGRCm38mm10GRCm38
MGSCv374100,824,579 - 100,937,887 (-)NCBIGRCm37mm9NCBIm37
MGSCv364100,650,964 - 100,763,165 (-)NCBImm8
Celera499,494,673 - 99,536,518 (-)NCBICelera
Cytogenetic Map4C6NCBI
cM Map446.19NCBI
Jak1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542325,524,075 - 25,580,604 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542325,501,989 - 25,581,826 (+)NCBIChiLan1.0ChiLan1.0
JAK1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1165,972,568 - 66,025,070 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl165,973,904 - 66,024,991 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0164,083,562 - 64,315,909 (-)NCBIMhudiblu_PPA_v0panPan3
JAK1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1545,251,653 - 45,408,571 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl545,251,653 - 45,408,571 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha545,310,150 - 45,467,121 (+)NCBI
ROS_Cfam_1.0545,434,808 - 45,591,981 (+)NCBI
ROS_Cfam_1.0 Ensembl545,434,808 - 45,596,544 (+)Ensembl
UMICH_Zoey_3.1545,401,193 - 45,555,602 (+)NCBI
UNSW_CanFamBas_1.0545,345,182 - 45,501,830 (+)NCBI
UU_Cfam_GSD_1.0545,594,991 - 45,751,867 (+)NCBI
Jak1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505877,982,726 - 78,038,725 (-)NCBI
SpeTri2.0NW_0049366922,298,149 - 2,354,084 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JAK1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6147,429,106 - 147,567,179 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16147,320,288 - 147,567,188 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26135,899,431 - 135,917,892 (-)NCBISscrofa10.2Sscrofa10.2susScr3
JAK1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12068,122,134 - 68,253,361 (+)NCBIChlSab1.1chlSab2
ChlSab1.12068,122,134 - 68,253,361 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2068,122,173 - 68,252,042 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603349,273,104 - 49,510,023 (-)NCBIVero_WHO_p1.0
Jak1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474229,631,391 - 29,723,981 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D5Got132  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25115,813,691 - 115,813,986 (+)MAPPERmRatBN7.2
Rnor_6.05120,015,945 - 120,016,239NCBIRnor6.0
Rnor_5.05123,898,520 - 123,898,814UniSTSRnor5.0
RGSC_v3.45121,837,588 - 121,837,882UniSTSRGSC3.4
Celera5114,351,188 - 114,351,482UniSTS
Cytogenetic Map5q31.3-q35UniSTS
RH128695  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25115,780,301 - 115,780,513 (+)MAPPERmRatBN7.2
Rnor_6.05119,982,557 - 119,982,768NCBIRnor6.0
Rnor_5.05123,865,132 - 123,865,343UniSTSRnor5.0
RGSC_v3.45121,804,200 - 121,804,411UniSTSRGSC3.4
Celera5114,317,799 - 114,318,010UniSTS
RH 3.4 Map5787.8UniSTS
Cytogenetic Map5q31.3-q35UniSTS
RH129388  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25115,778,575 - 115,778,760 (+)MAPPERmRatBN7.2
Rnor_6.05119,980,831 - 119,981,015NCBIRnor6.0
Rnor_5.05123,863,406 - 123,863,590UniSTSRnor5.0
RGSC_v3.45121,802,474 - 121,802,658UniSTSRGSC3.4
Celera5114,316,073 - 114,316,257UniSTS
RH 3.4 Map5788.3UniSTS
Cytogenetic Map5q31.3-q35UniSTS
Cytogenetic Map5q33UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)566174080124160948Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1298070Scl18Serum cholesterol level QTL 183.7blood LDL cholesterol amount (VT:0000181)calculated plasma low density lipoprotein cholesterol level (CMO:0001245)579584860124584860Rat
1598846Bp293Blood pressure QTL 2933.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)579584860124584860Rat
1598859Cm66Cardiac mass QTL 662heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)579584860124584860Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1298086Bp156Blood pressure QTL 156arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)584132602129132602Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)587468046132468046Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)587765973132765973Rat
1358889Bp261Blood pressure QTL 2612.86arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)590067849128034027Rat
1358909Kidm25Kidney mass QTL 251.87kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)590067849128034027Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)590450144135450144Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)597570330136479578Rat
1582212Livw2Liver weight QTL 23.50.0004liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)599016066119085810Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5103689353148689353Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5105999803150999803Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
7794743Bp373Blood pressure QTL 3730.0058arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5112175546116047089Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:398
Count of miRNA genes:221
Interacting mature miRNAs:263
Transcripts:ENSRNOT00000064542
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 40 11 8
Low 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000064542   ⟹   ENSRNOP00000061649
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5115,780,688 - 115,881,400 (-)Ensembl
Rnor_6.0 Ensembl5119,982,943 - 120,083,904 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102260   ⟹   ENSRNOP00000089963
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5115,780,688 - 115,821,945 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104244   ⟹   ENSRNOP00000093955
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5115,780,248 - 115,888,926 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105145   ⟹   ENSRNOP00000082397
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5115,780,248 - 115,888,926 (-)Ensembl
RefSeq Acc Id: NM_053466   ⟹   NP_445918
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25115,780,688 - 115,881,400 (-)NCBI
Rnor_6.05119,982,943 - 120,083,904 (-)NCBI
Rnor_5.05123,865,078 - 123,973,772 (-)NCBI
RGSC_v3.45121,804,586 - 121,905,581 (-)RGD
Celera5114,318,185 - 114,418,922 (-)RGD
Sequence:
RefSeq Acc Id: XM_006238452   ⟹   XP_006238514
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25115,780,248 - 115,888,841 (-)NCBI
Rnor_6.05119,982,503 - 120,091,452 (-)NCBI
Rnor_5.05123,865,078 - 123,973,772 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238453   ⟹   XP_006238515
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25115,780,248 - 115,845,523 (-)NCBI
Rnor_6.05119,982,503 - 120,051,586 (-)NCBI
Rnor_5.05123,865,078 - 123,973,772 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039110879   ⟹   XP_038966807
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25115,785,104 - 115,888,841 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_445918   ⟸   NM_053466
- UniProtKB: G3V9W2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238514   ⟸   XM_006238452
- Peptide Label: isoform X1
- UniProtKB: G3V9W2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238515   ⟸   XM_006238453
- Peptide Label: isoform X1
- UniProtKB: G3V9W2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000061649   ⟸   ENSRNOT00000064542
RefSeq Acc Id: XP_038966807   ⟸   XM_039110879
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000089963   ⟸   ENSRNOT00000102260
RefSeq Acc Id: ENSRNOP00000082397   ⟸   ENSRNOT00000105145
RefSeq Acc Id: ENSRNOP00000093955   ⟸   ENSRNOT00000104244
Protein Domains
FERM   Protein kinase   SH2

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)
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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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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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
MNS/Gib (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
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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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
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69056 AgrOrtholog
Ensembl Genes ENSRNOG00000011157 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061649 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000082397 ENTREZGENE
Ensembl Transcript ENSRNOT00000064542 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000105145 ENTREZGENE
Gene3D-CATH 3.30.505.10 UniProtKB/TrEMBL
InterPro Band_41_domain UniProtKB/TrEMBL
  FERM_2 UniProtKB/TrEMBL
  FERM_central UniProtKB/TrEMBL
  FERM_domain UniProtKB/TrEMBL
  FERM_F1 UniProtKB/TrEMBL
  FERM_F2 UniProtKB/TrEMBL
  Jak1_PHL_dom UniProtKB/TrEMBL
  Kinase-like_dom UniProtKB/TrEMBL
  Prot_kinase_cat_dom UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/TrEMBL
  Ser-Thr/Tyr_kinase_cat_dom UniProtKB/TrEMBL
  SH2 UniProtKB/TrEMBL
  SH2_dom_sf UniProtKB/TrEMBL
  Tyr_kinase_AS UniProtKB/TrEMBL
  Tyr_kinase_cat_dom UniProtKB/TrEMBL
  Tyr_kinase_non-rcpt_Jak/Tyk2 UniProtKB/TrEMBL
  Tyr_kinase_non-rcpt_Jak1 UniProtKB/TrEMBL
KEGG Report rno:84598 UniProtKB/TrEMBL
NCBI Gene 84598 ENTREZGENE
Pfam FERM_F1 UniProtKB/TrEMBL
  FERM_F2 UniProtKB/TrEMBL
  Jak1_Phl UniProtKB/TrEMBL
  Pkinase_Tyr UniProtKB/TrEMBL
PhenoGen Jak1 PhenoGen
PIRSF TyrPK_Jak UniProtKB/TrEMBL
PRINTS JANUSKINASE UniProtKB/TrEMBL
  JANUSKINASE1 UniProtKB/TrEMBL
  TYRKINASE UniProtKB/TrEMBL
PROSITE FERM_3 UniProtKB/TrEMBL
  PROTEIN_KINASE_ATP UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/TrEMBL
  PROTEIN_KINASE_TYR UniProtKB/TrEMBL
  SH2 UniProtKB/TrEMBL
SMART B41 UniProtKB/TrEMBL
  SH2 UniProtKB/TrEMBL
  TyrKc UniProtKB/TrEMBL
Superfamily-SCOP FERM_3-hlx UniProtKB/TrEMBL
  Kinase_like UniProtKB/TrEMBL
  SSF55550 UniProtKB/TrEMBL
UniProt G3V9W2 ENTREZGENE, UniProtKB/TrEMBL
  O35803_RAT UniProtKB/TrEMBL
  Q5FVF5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Jak1  Janus kinase 1      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_drugs phosphorylation reduced by 15-deoxy-Delta12,14-prostaglandin J(2) 1299058
gene_regulation activation induced by IL-22 1299182