Jak3 (Janus kinase 3) - Rat Genome Database

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Gene: Jak3 (Janus kinase 3) Rattus norvegicus
Analyze
Symbol: Jak3
Name: Janus kinase 3
RGD ID: 2940
Description: Predicted to enable protein phosphatase binding activity and protein tyrosine kinase activity. Involved in several processes, including positive regulation of activated T cell proliferation; positive regulation of cytosolic calcium ion concentration; and positive regulation of nitric-oxide synthase biosynthetic process. Located in cytoplasm. Biomarker of tongue squamous cell carcinoma. Human ortholog(s) of this gene implicated in T-cell acute lymphoblastic leukemia; acute megakaryocytic leukemia; adult T-cell leukemia; and juvenile myelomonocytic leukemia. Orthologous to human JAK3 (Janus kinase 3); PARTICIPATES IN altered Jak-Stat signaling pathway; interleukin-2 signaling pathway; interleukin-4 signaling pathway; INTERACTS WITH amphetamine; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: JAK-3; Janus kinase 3 protein-tyrosine kinase; Janus kinase 3, protein-tyrosine kinase; RATJAK3; tyrosine-protein kinase JAK3
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
mRatBN7.21618,386,330 - 18,398,542 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1618,386,405 - 18,398,536 (+)Ensembl
Rnor_6.01620,107,471 - 20,120,678 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1620,109,200 - 20,120,668 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01619,968,486 - 19,981,132 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41618,878,139 - 18,889,441 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11618,878,136 - 18,889,439 (+)NCBI
Celera1618,589,820 - 18,601,138 (+)NCBICelera
RH 3.4 Map16181.8RGD
Cytogenetic Map16p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adaptive immune response  (IEA)
B cell differentiation  (IBA,ISO,ISS)
cellular response to cytokine stimulus  (ISO)
cytokine-mediated signaling pathway  (IBA,IDA,IEA,ISO)
enzyme linked receptor protein signaling pathway  (ISO,ISS)
erythrocyte differentiation  (IBA)
innate immune response  (IEA)
interleukin-4-mediated signaling pathway  (ISO)
intracellular signal transduction  (IEA,ISO,ISS)
negative regulation of complement-dependent cytotoxicity  (ISO)
negative regulation of dendritic cell cytokine production  (ISO,ISS)
negative regulation of FasL production  (ISO,ISS)
negative regulation of interleukin-10 production  (ISO,ISS)
negative regulation of interleukin-12 production  (ISO,ISS)
negative regulation of T cell activation  (ISO,ISS)
negative regulation of T-helper 1 cell differentiation  (ISO,ISS)
negative regulation of thymocyte apoptotic process  (ISO,ISS)
peptidyl-tyrosine phosphorylation  (IEA,ISO,ISS)
positive regulation of activated T cell proliferation  (IMP)
positive regulation of calcium ion transport  (IMP)
positive regulation of cytosolic calcium ion concentration  (IMP)
positive regulation of dendritic cell apoptotic process  (ISO)
positive regulation of extrinsic apoptotic signaling pathway in absence of ligand  (ISO)
positive regulation of nitric-oxide synthase biosynthetic process  (IMP)
positive regulation of T cell proliferation  (IBA,IDA)
positive regulation of transcription by RNA polymerase II  (ISO)
regulation of apoptotic process  (IBA)
regulation of T cell apoptotic process  (ISO,ISS)
response to interleukin-4  (ISO)
T cell homeostasis  (IBA,ISO,ISS)
tyrosine phosphorylation of STAT protein  (IBA)

Cellular Component

References

References - curated
1. Ban SA, etal., J Clin Immunol. 2014 Nov;34(8):941-53. doi: 10.1007/s10875-014-0088-2. Epub 2014 Sep 10.
2. Behbod F, etal., J Immunol. 2001 Mar 15;166(6):3724-32.
3. Bergmann AK, etal., Genes Chromosomes Cancer. 2014 Apr;53(4):309-16. doi: 10.1002/gcc.22141. Epub 2014 Jan 21.
4. Bingisser RM, etal., J Immunol. 1998 Jun 15;160(12):5729-34.
5. Bixler GV, etal., BMC Med Genomics. 2011 May 15;4:40. doi: 10.1186/1755-8794-4-40.
6. Bongfen SE, etal., PLoS One. 2012;7(2):e31012. doi: 10.1371/journal.pone.0031012. Epub 2012 Feb 21.
7. Bunting KD, etal., Nat Med. 1998 Jan;4(1):58-64.
8. Degryse S, etal., Blood. 2014 Nov 13;124(20):3092-100. doi: 10.1182/blood-2014-04-566687. Epub 2014 Sep 5.
9. Elliott NE, etal., Blood. 2011 Oct 6;118(14):3911-21. doi: 10.1182/blood-2010-12-319467. Epub 2011 Aug 5.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Ge S, etal., Mol Med Rep. 2016 Mar;13(3):2561-9. doi: 10.3892/mmr.2016.4883. Epub 2016 Feb 8.
12. GOA data from the GO Consortium
13. Kim BH, etal., Br J Pharmacol. 2011 Sep;164(1):106-18. doi: 10.1111/j.1476-5381.2011.01353.x.
14. Kirken RA, etal., J Biol Chem. 1994 Jul 22;269(29):19136-41.
15. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
16. Macchi P, etal., Nature. 1995 Sep 7;377(6544):65-8.
17. Mahajan S, etal., J Pharmacol Exp Ther. 2015 May;353(2):405-14. doi: 10.1124/jpet.114.221176. Epub 2015 Mar 11.
18. MGD data from the GO Consortium
19. Milici AJ, etal., Arthritis Res Ther. 2008;10(1):R14. doi: 10.1186/ar2365. Epub 2008 Jan 30.
20. Mizuno M, etal., Brain Res Mol Brain Res. 1997 Feb;44(1):163-6.
21. Murray PJ J Immunol. 2007 Mar 1;178(5):2623-9.
22. NCBI rat LocusLink and RefSeq merged data July 26, 2002
23. OMIM Disease Annotation Pipeline
24. Orellana DI, etal., Neurotox Res. 2005 Nov;8(3-4):295-304.
25. Pipeline to import KEGG annotations from KEGG into RGD
26. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
27. Rane SG and Reddy EP, Oncogene 2002 May 13;21(21):3334-58.
28. RGD automated data pipeline
29. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
30. RGD automated import pipeline for gene-chemical interactions
31. Ross JA, etal., Leukemia. 2014 Apr;28(4):941-4. doi: 10.1038/leu.2013.309. Epub 2013 Oct 23.
32. Saini MK, etal., Eur J Cancer Prev. 2013 May;22(3):215-28. doi: 10.1097/CEJ.0b013e3283584932.
33. Sakaguchi H, etal., Nat Genet. 2013 Aug;45(8):937-41. doi: 10.1038/ng.2698. Epub 2013 Jul 7.
34. Stepkowski SM, etal., Blood. 2002 Jan 15;99(2):680-9.
35. Takahashi T and Shirasawa T, FEBS Lett 1994 Apr 4;342(2):124-8.
36. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
37. Uckun FM, etal., Blood. 2002 Jun 1;99(11):4192-9.
38. Walters DK, etal., Cancer Cell. 2006 Jul;10(1):65-75.
39. Wang G, etal., J Neuroinflammation. 2012 Jul 12;9:170. doi: 10.1186/1742-2094-9-170.
40. Xu W, etal., PLoS One. 2012;7(2):e31721. doi: 10.1371/journal.pone.0031721. Epub 2012 Feb 16.
41. Yin L, etal., J Neuroimmunol. 2014 Sep 15;274(1-2):28-37. doi: 10.1016/j.jneuroim.2014.06.022. Epub 2014 Jun 28.
Additional References at PubMed
PMID:7538655   PMID:7594533   PMID:8022486   PMID:9498750   PMID:9973401   PMID:10485657   PMID:10872802   PMID:11909529   PMID:16020505   PMID:19220965   PMID:19233270   PMID:19414010  
PMID:19531027   PMID:21414324   PMID:22971540   PMID:24280217   PMID:26446793   PMID:28473442   PMID:30664158   PMID:33416962   PMID:33910370  


Genomics

Comparative Map Data
Jak3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21618,386,330 - 18,398,542 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1618,386,405 - 18,398,536 (+)Ensembl
Rnor_6.01620,107,471 - 20,120,678 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1620,109,200 - 20,120,668 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01619,968,486 - 19,981,132 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41618,878,139 - 18,889,441 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11618,878,136 - 18,889,439 (+)NCBI
Celera1618,589,820 - 18,601,138 (+)NCBICelera
RH 3.4 Map16181.8RGD
Cytogenetic Map16p14NCBI
JAK3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1917,824,780 - 17,848,071 (-)EnsemblGRCh38hg38GRCh38
GRCh381917,824,782 - 17,848,071 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371917,935,591 - 17,958,791 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361917,797,961 - 17,819,800 (-)NCBINCBI36hg18NCBI36
Build 341917,797,960 - 17,819,800NCBI
Celera1917,837,310 - 17,860,555 (-)NCBI
Cytogenetic Map19p13.11NCBI
HuRef1917,500,992 - 17,524,212 (-)NCBIHuRef
CHM1_11917,935,132 - 17,958,532 (-)NCBICHM1_1
Jak3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39872,129,027 - 72,143,221 (+)NCBIGRCm39mm39
GRCm39 Ensembl872,128,940 - 72,143,219 (+)Ensembl
GRCm38871,676,383 - 71,690,577 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl871,676,296 - 71,690,575 (+)EnsemblGRCm38mm10GRCm38
MGSCv37874,200,473 - 74,214,473 (+)NCBIGRCm37mm9NCBIm37
MGSCv36874,605,563 - 74,619,563 (+)NCBImm8
Celera874,191,138 - 74,205,120 (+)NCBICelera
Cytogenetic Map8B3.3NCBI
cM Map834.43NCBI
Jak3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555243,401,642 - 3,411,643 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555243,399,895 - 3,412,018 (+)NCBIChiLan1.0ChiLan1.0
JAK3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11918,283,157 - 18,304,641 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1918,283,560 - 18,300,964 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01917,299,129 - 17,330,700 (-)NCBIMhudiblu_PPA_v0panPan3
JAK3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12045,051,135 - 45,068,445 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2045,050,526 - 45,072,805 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2044,963,131 - 44,980,402 (+)NCBI
ROS_Cfam_1.02045,535,925 - 45,553,392 (+)NCBI
UMICH_Zoey_3.12044,772,769 - 44,789,998 (+)NCBI
UNSW_CanFamBas_1.02045,183,055 - 45,200,281 (+)NCBI
UU_Cfam_GSD_1.02045,459,016 - 45,476,242 (+)NCBI
Jak3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118203,661,414 - 203,676,227 (+)NCBI
SpeTri2.0NW_0049365963,212,593 - 3,224,426 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JAK3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl259,905,919 - 59,926,495 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1259,905,901 - 59,926,504 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2259,475,346 - 59,495,932 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JAK3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1616,301,760 - 16,323,343 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl616,300,525 - 16,322,859 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660743,064,511 - 3,086,605 (+)NCBIVero_WHO_p1.0
Jak3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249081,371,595 - 1,383,879 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D16Rat82  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21618,392,338 - 18,392,522 (+)MAPPERmRatBN7.2
Rnor_6.01620,114,475 - 20,114,658NCBIRnor6.0
Rnor_5.01619,974,929 - 19,975,112UniSTSRnor5.0
RGSC_v3.41618,883,254 - 18,883,437UniSTSRGSC3.4
RGSC_v3.41618,883,254 - 18,883,437RGDRGSC3.4
RGSC_v3.11618,883,252 - 18,883,435RGD
Celera1618,594,935 - 18,595,118UniSTS
RH 3.4 Map16186.4UniSTS
RH 3.4 Map16186.4RGD
RH 2.0 Map16165.9RGD
SHRSP x BN Map165.71RGD
Cytogenetic Map16p14UniSTS
RH142198  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map16181.8UniSTS
Cytogenetic Map16p14UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
631517Scl9Serum cholesterol level QTL 93.3blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)161572643321034895Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:54
Count of miRNA genes:43
Interacting mature miRNAs:49
Transcripts:ENSRNOT00000025312
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 4 8 19 8 14 4
Low 1 39 49 41 41 3 5 74 27 25 7 3
Below cutoff 5 6 2 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000025312   ⟹   ENSRNOP00000025312
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1618,386,405 - 18,398,536 (+)Ensembl
Rnor_6.0 Ensembl1620,110,148 - 20,120,668 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079784   ⟹   ENSRNOP00000071081
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1620,109,200 - 20,120,446 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080146   ⟹   ENSRNOP00000073659
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1620,110,148 - 20,120,662 (+)Ensembl
RefSeq Acc Id: NM_012855   ⟹   NP_036987
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21618,387,224 - 18,398,542 (+)NCBI
Rnor_6.01620,109,360 - 20,120,678 (+)NCBI
Rnor_5.01619,968,486 - 19,981,132 (+)NCBI
RGSC_v3.41618,878,139 - 18,889,441 (+)RGD
Celera1618,589,820 - 18,601,138 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008771064   ⟹   XP_008769286
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21618,386,330 - 18,398,542 (+)NCBI
Rnor_6.01620,107,472 - 20,120,678 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599993   ⟹   XP_017455482
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21618,386,330 - 18,398,542 (+)NCBI
Rnor_6.01620,107,471 - 20,120,678 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039094203   ⟹   XP_038950131
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21618,387,315 - 18,398,542 (+)NCBI
RefSeq Acc Id: XR_005494533
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21618,386,330 - 18,398,542 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036987   ⟸   NM_012855
- UniProtKB: F1LR79 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769286   ⟸   XM_008771064
- Peptide Label: isoform X1
- UniProtKB: F1LR79 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455482   ⟸   XM_017599993
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000073659   ⟸   ENSRNOT00000080146
RefSeq Acc Id: ENSRNOP00000071081   ⟸   ENSRNOT00000079784
RefSeq Acc Id: ENSRNOP00000025312   ⟸   ENSRNOT00000025312
RefSeq Acc Id: XP_038950131   ⟸   XM_039094203
- Peptide Label: isoform X1
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)
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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
BBDP/Wor (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
BN-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (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
BXH2/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (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
F344/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
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)
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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
F344/Stm (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
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)
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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)
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)
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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
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)
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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)
GK/FarMcwi (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
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)
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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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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
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)
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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
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)
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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
LEXF11/Stm (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: 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)
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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: 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)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 19972921 19972922 C G snv COP/CrCrl (MCW & UW), BDIX.Cg-Tal/NemOda (KyushuU), SBH/Ygl (MCW), MR/N (KNAW), WAG/Rij (KNAW), DA/BklArbNsi (KNAW), FHL/EurMcwi (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), MNS/Gib (KNAW), SBH/Ygl (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), LE/Stm (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), FHL/EurMcwi (MCW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 18390331 18390332 C G snv DA/OlaHsd (2019), LEW/Crl (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), WAG/RijCrl (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), MR/N (2020), LEXF4/Stm (2020)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 20112467 20112468 C G snv CDR, WAG/RijCrl (2020), COP/CrCrl (MCW & UW), FHL/EurMcwi (MCW), SBH/Ygl (MCW), MR/N (MCW), FHL/EurMcwi (RGD), LE/Stm (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), MNS/Gib (RGD), SBH/Ygl (RGD), WAG/Rij (RGD), DA/OlaHsd (2019), LEW/Crl (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), MR/N (2020), CDS


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 18881246 18881247 C G snv FHL/EurMcwi (MCW), DA/BklArbNsi (ICAHN), COP/CrCrl (MCW & UW), FHL/EurMcwi (ICL), LE/Stm (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), MNS/Gib (ICL), SBH/Ygl (ICL), WAG/Rij (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), MR/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2940 AgrOrtholog
Ensembl Genes ENSRNOG00000018669 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000025312 UniProtKB/Swiss-Prot
  ENSRNOP00000071081 UniProtKB/Swiss-Prot
  ENSRNOP00000073659 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025312 UniProtKB/Swiss-Prot
  ENSRNOT00000079784 UniProtKB/Swiss-Prot
  ENSRNOT00000080146 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.505.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Band_41_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FERM_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FERM_F1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FERM_F2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Jak1_PHL_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kinase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot_kinase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ser-Thr/Tyr_kinase_cat_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH2_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_cat_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_non-rcpt_Jak/Tyk2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_non-rcpt_Jak3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25326 UniProtKB/Swiss-Prot
NCBI Gene 25326 ENTREZGENE
Pfam FERM_F1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FERM_F2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Jak1_Phl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pkinase_Tyr UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Jak3 PhenoGen
PIRSF TyrPK_Jak UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS JANUSKINASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JANUSKINASE3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYRKINASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE FERM_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_TYR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART B41 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TyrKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF55550 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC231103
UniProt A0A0G2K636_RAT UniProtKB/TrEMBL
  F1LR79 ENTREZGENE
  JAK3_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary F1LR79 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Jak3  Janus kinase 3, protein-tyrosine kinase      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in spleen, lung, kidney and intestine 729028
gene_protein 1,100 amino acids 729028