Lyn (LYN proto-oncogene, Src family tyrosine kinase) - Rat Genome Database

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Gene: Lyn (LYN proto-oncogene, Src family tyrosine kinase) Rattus norvegicus
Analyze
Symbol: Lyn
Name: LYN proto-oncogene, Src family tyrosine kinase
RGD ID: 621017
Description: Enables several functions, including gamma-tubulin binding activity; signaling receptor binding activity; and ubiquitin protein ligase binding activity. Involved in several processes, including histamine secretion by mast cell; neurogenesis; and positive regulation of Fc receptor mediated stimulatory signaling pathway. Located in several cellular components, including glutamatergic synapse; mitochondrial envelope; and postsynaptic specialization. Part of integrin alpha2-beta1 complex. Biomarker of Parkinsonism and endometriosis. Orthologous to human LYN (LYN proto-oncogene, Src family tyrosine kinase); PARTICIPATES IN eicosanoid signaling pathway; ephrin - ephrin receptor bidirectional signaling axis; erythropoietin signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2-ethoxyethanol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: lyn protein non-receptor kinase; p53Lyn; p56Lyn; tyrosine-protein kinase Lyn; v-yes-1 Yamaguchi sarcoma viral related oncogene homolog; Yamaguchi sarcoma viral (v-yes-1) oncogene homolog
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
mRatBN7.2516,639,512 - 16,755,501 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl516,639,466 - 16,756,868 (+)Ensembl
Rnor_6.0516,526,058 - 16,642,648 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl516,526,058 - 16,642,648 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0521,307,094 - 21,422,842 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4516,933,111 - 17,054,564 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1516,933,105 - 17,054,560 (+)NCBI
Celera516,004,013 - 16,119,589 (+)NCBICelera
RH 3.4 Map586.9RGD
Cytogenetic Map5q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(R,R,R)-alpha-tocopherol  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-ethoxyethanol  (EXP)
2-methoxyethanol  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
acetylsalicylic acid  (ISO)
afimoxifene  (ISO)
all-trans-retinoic acid  (ISO)
aluminium trifluoride  (ISO)
alvocidib  (ISO)
ammonium chloride  (EXP)
antigen  (ISO)
antirheumatic drug  (ISO)
aripiprazole  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzamide  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
bortezomib  (ISO)
bosutinib  (EXP)
butan-1-ol  (ISO)
calcitriol  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
Cuprizon  (EXP)
cytarabine  (ISO)
dexamethasone  (EXP,ISO)
diazinon  (ISO)
dichlorine  (EXP)
diethylstilbestrol  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (EXP,ISO)
flutamide  (EXP)
glutathione  (ISO)
Honokiol  (ISO)
indometacin  (ISO)
isotretinoin  (ISO)
ivermectin  (ISO)
L-ascorbic acid  (ISO)
leflunomide  (EXP)
manganese(II) chloride  (ISO)
masitinib  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
mycophenolic acid  (ISO)
N-formyl-L-methionyl-L-leucyl-L-phenylalanine  (ISO)
nickel atom  (ISO)
nickel dichloride  (EXP)
nickel sulfate  (ISO)
oxaliplatin  (EXP)
ozone  (EXP,ISO)
panobinostat  (ISO)
paracetamol  (ISO)
phenylmercury acetate  (ISO)
phosgene  (ISO)
pirinixic acid  (ISO)
ponatinib  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
quercetin  (ISO)
raloxifene  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium dodecyl sulfate  (ISO)
Soman  (EXP)
tamibarotene  (ISO)
tamoxifen  (ISO)
taurine  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
triptonide  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
zinc oxide  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adaptive immune response  (IEA)
B cell homeostasis  (ISO,ISS)
B cell receptor signaling pathway  (ISO)
cell differentiation  (IBA)
cellular response to DNA damage stimulus  (IBA,ISO)
cellular response to extracellular stimulus  (IEP)
cellular response to heat  (IEP)
cellular response to retinoic acid  (ISO)
cytokine production  (IMP)
dendritic cell differentiation  (IBA,ISO,ISS)
erythrocyte differentiation  (ISO,ISS)
Fc receptor mediated inhibitory signaling pathway  (ISO,ISS)
Fc receptor mediated stimulatory signaling pathway  (IBA,ISO,ISS)
hemopoiesis  (ISO)
histamine secretion by mast cell  (IMP)
immune response-regulating cell surface receptor signaling pathway  (ISO,ISS)
innate immune response  (IBA)
intracellular signal transduction  (ISO)
lipopolysaccharide-mediated signaling pathway  (ISO,ISS)
negative regulation of B cell proliferation  (IBA,ISO)
negative regulation of cell population proliferation  (ISO,ISS)
negative regulation of ERK1 and ERK2 cascade  (ISO,ISS)
negative regulation of intracellular signal transduction  (ISO,ISS)
negative regulation of MAP kinase activity  (ISO,ISS)
negative regulation of mast cell proliferation  (IBA,ISO,ISS)
negative regulation of myeloid leukocyte differentiation  (ISO)
negative regulation of protein phosphorylation  (ISO,ISS)
negative regulation of toll-like receptor 2 signaling pathway  (ISO,ISS)
negative regulation of toll-like receptor 4 signaling pathway  (ISO,ISS)
neuron projection development  (IBA,ISO)
oligodendrocyte development  (IEP)
peptidyl-tyrosine phosphorylation  (ISO)
platelet degranulation  (IBA,ISO,ISS)
positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process  (ISO)
positive regulation of cell migration  (ISO)
positive regulation of cell population proliferation  (ISO,ISS)
positive regulation of cellular component movement  (ISO)
positive regulation of dendritic cell apoptotic process  (IBA,ISO,ISS)
positive regulation of Fc receptor mediated stimulatory signaling pathway  (IMP)
positive regulation of glial cell proliferation  (IDA)
positive regulation of mast cell proliferation  (ISO)
positive regulation of neuron projection development  (ISO)
positive regulation of oligodendrocyte progenitor proliferation  (IMP)
positive regulation of phosphatidylinositol 3-kinase activity  (ISO)
positive regulation of phosphorylation  (IMP)
positive regulation of protein phosphorylation  (ISO)
positive regulation of stress-activated protein kinase signaling cascade  (ISO)
positive regulation of tyrosine phosphorylation of STAT protein  (ISO,ISS)
protein autophosphorylation  (ISO)
protein phosphorylation  (ISO)
regulation of B cell apoptotic process  (IBA,ISO)
regulation of B cell receptor signaling pathway  (IBA,ISO,ISS)
regulation of cell adhesion mediated by integrin  (ISO)
regulation of cytokine production  (ISO,ISS)
regulation of ERK1 and ERK2 cascade  (ISO,ISS)
regulation of erythrocyte differentiation  (ISO,ISS)
regulation of inflammatory response  (ISO)
regulation of mast cell activation  (ISO,ISS)
regulation of mast cell degranulation  (IBA,ISO,ISS)
regulation of monocyte chemotaxis  (ISO)
regulation of platelet aggregation  (IBA,ISO,ISS)
regulation of release of sequestered calcium ion into cytosol  (IMP,ISO)
response to amino acid  (IEP)
response to axon injury  (IEP)
response to carbohydrate  (IEP)
response to hormone  (ISO,ISS)
response to insulin  (IEP)
response to organic cyclic compound  (IEP)
response to peptide hormone  (IEP)
response to sterol depletion  (IEP)
response to toxic substance  (IEP)
response to xenobiotic stimulus  (IEP)
tolerance induction to self antigen  (IBA,ISO,ISS)
toll-like receptor 4 signaling pathway  (ISO)
transmembrane receptor protein tyrosine kinase signaling pathway  (IBA,ISO)

References

References - curated
1. Alessandri-Haber N, etal., J Neurosci. 2008 Jan 30;28(5):1046-57.
2. Amir-Moazami O, etal., J Biol Chem. 2008 Sep 12;283(37):25514-23. Epub 2008 Jun 25.
3. Anderwald C, etal., Mol Endocrinol 2002 Jul;16(7):1612-28.
4. Colognato H, etal., J Cell Biol. 2004 Oct 25;167(2):365-75.
5. Das R, etal., Biophys J. 2008 Jun;94(12):4996-5008. Epub 2008 Mar 7.
6. Draberova L, et al., Int Immunol. 1999 Nov;11(11):1829-39.
7. Fazal N, etal., Am J Physiol Cell Physiol. 2002 Nov;283(5):C1469-79.
8. Fujii Y, etal., FEBS Lett 2003 Apr 10;540(1-3):111-6.
9. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. GOA data from the GO Consortium
11. He H, etal., Cardiovasc Drugs Ther. 2006 Aug;20(4):259-71.
12. Honda Z, etal., J Biol Chem. 1997 Oct 10;272(41):25753-60.
13. Kalia LV and Salter MW, Neuropharmacology. 2003 Nov;45(6):720-8.
14. Kamei T, etal., Mol Endocrinol 2002 Jul;16(7):1469-81.
15. Kasahara K, etal., J Biol Chem. 2000 Nov 3;275(44):34701-9.
16. Kato N, etal., J Immunol. 2006 Jul 1;177(1):147-54.
17. Kimura T, etal., J Biol Chem. 1996 Nov 1;271(44):27962-8.
18. Konno R, etal., Am J Reprod Immunol. 2007 Oct;58(4):330-43.
19. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
20. Kyo S, etal., Genes Cells. 2003 Oct;8(10):825-36.
21. Lara M, etal., J Immunol. 2001 Oct 15;167(8):4329-37.
22. Leung WH and Bolland S, J Immunol. 2007 Jul 1;179(1):95-102.
23. Maeno K, etal., J Biol Chem. 2003 Jul 4;278(27):24912-20. Epub 2003 Apr 22.
24. Mallozzi C, etal., J Neurosci Res. 2007 Sep;85(12):2770-7.
25. MGD data from the GO Consortium
26. Minoguchi K, etal., J Biol Chem. 1994 Feb 18;269(7):5249-54.
27. Minoguchi K, etal., Mol Immunol. 1994 May;31(7):519-29.
28. Muller G, etal., Biochem Pharmacol. 2005 Mar 1;69(5):761-80. Epub 2005 Jan 25.
29. Napolitano M, etal., Neurosci Lett. 2006 May 8;398(3):211-4. Epub 2006 Mar 9.
30. Narisawa-Saito M, etal., Clin Exp Immunol. 1996 Oct;106(1):86-90.
31. NCBI rat LocusLink and RefSeq merged data July 26, 2002
32. Pace A, etal., Biochim Biophys Acta. 2006 Apr;1763(4):356-65. Epub 2006 Apr 7.
33. Pipeline to import KEGG annotations from KEGG into RGD
34. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
35. Pipeline to import SMPDB annotations from SMPDB into RGD
36. Pullar CE, etal., J Immunol. 1996 Aug 1;157(3):1226-32.
37. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
38. RGD automated import pipeline for gene-chemical interactions
39. Rider LG, etal., Gene 1994 Jan 28;138(1-2):219-22.
40. Salvi M, etal., Biochim Biophys Acta 2002 Apr 3;1589(2):181-95.
41. Sheets ED, etal., J Cell Biol. 1999 May 17;145(4):877-87.
42. Song JS, etal., Oncogene. 1998 Jul 2;16(26):3357-68.
43. Stenberg PE, etal., Blood. 1997 Apr 1;89(7):2384-93.
44. Tsuda M, etal., Glia. 2008 Jan 1;56(1):50-8.
45. Tsukita S, et al., J Cell Biol. 1991 May;113(4):867-79.
46. Vonakis BM, etal., J Biol Chem 1997 Sep 19;272(38):24072-80.
47. Vonakis BM, etal., J Immunol. 2005 Oct 1;175(7):4543-54.
48. Wu X, etal., J Neurochem. 2004 Aug;90(4):807-18.
49. Xie ZH, etal., J Immunol. 2002 May 1;168(9):4682-91.
50. Xu R, etal., J Immunol 2001 Dec 1;167(11):6394-402.
Additional References at PubMed
PMID:1381360   PMID:7499277   PMID:7526393   PMID:7682714   PMID:8128248   PMID:8627181   PMID:8761480   PMID:9000133   PMID:9064343   PMID:9252121   PMID:9799234   PMID:10594694  
PMID:10713104   PMID:10748115   PMID:10861086   PMID:10872802   PMID:10891478   PMID:11110698   PMID:11137137   PMID:11313396   PMID:11358993   PMID:11435302   PMID:11448999   PMID:11517336  
PMID:11672542   PMID:11744621   PMID:11782428   PMID:11826099   PMID:12504103   PMID:12538589   PMID:12670955   PMID:12923167   PMID:14525964   PMID:14604964   PMID:14726379   PMID:14769131  
PMID:15173188   PMID:16034130   PMID:16116174   PMID:16249387   PMID:16272347   PMID:16467205   PMID:16791881   PMID:16921024   PMID:17462920   PMID:17910947   PMID:17977829   PMID:18250449  
PMID:18682390   PMID:18697750   PMID:18802065   PMID:18817770   PMID:19064729   PMID:19118221   PMID:19356729   PMID:19832701   PMID:20189992   PMID:20385881   PMID:20605918   PMID:20645409  
PMID:22871113   PMID:23376485   PMID:23509253   PMID:23533145   PMID:24217950   PMID:25289695   PMID:28098138  


Genomics

Candidate Gene Status
Lyn is a candidate Gene for QTL Vetf1
Lyn is a candidate Gene for QTL Vetf3
Comparative Map Data
Lyn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2516,639,512 - 16,755,501 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl516,639,466 - 16,756,868 (+)Ensembl
Rnor_6.0516,526,058 - 16,642,648 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl516,526,058 - 16,642,648 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0521,307,094 - 21,422,842 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4516,933,111 - 17,054,564 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1516,933,105 - 17,054,560 (+)NCBI
Celera516,004,013 - 16,119,589 (+)NCBICelera
RH 3.4 Map586.9RGD
Cytogenetic Map5q12NCBI
LYN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl855,879,835 - 56,014,169 (+)EnsemblGRCh38hg38GRCh38
GRCh38855,876,041 - 56,014,169 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37856,792,394 - 56,926,728 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36856,954,926 - 57,085,685 (+)NCBINCBI36hg18NCBI36
Build 34856,954,925 - 57,085,685NCBI
Celera852,784,229 - 52,915,775 (+)NCBI
Cytogenetic Map8q12.1NCBI
HuRef852,260,576 - 52,393,067 (+)NCBIHuRef
CHM1_1856,844,030 - 56,976,630 (+)NCBICHM1_1
Lyn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3943,676,865 - 3,791,612 (+)NCBIGRCm39mm39
GRCm39 Ensembl43,678,115 - 3,813,122 (+)Ensembl
GRCm3843,678,068 - 3,791,612 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl43,678,115 - 3,813,122 (+)EnsemblGRCm38mm10GRCm38
MGSCv3743,605,268 - 3,718,759 (+)NCBIGRCm37mm9NCBIm37
MGSCv3643,205,785 - 3,233,451 (+)NCBImm8
MGSCv3643,605,272 - 3,718,759 (+)NCBImm8
Celera43,624,290 - 3,748,767 (+)NCBICelera
Cytogenetic Map4A1NCBI
cM Map42.05NCBI
Lyn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545415,035,979 - 15,111,142 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545415,025,967 - 15,111,142 (+)NCBIChiLan1.0ChiLan1.0
LYN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1849,755,745 - 49,825,287 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl849,755,708 - 49,825,287 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0852,318,497 - 52,455,741 (+)NCBIMhudiblu_PPA_v0panPan3
LYN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1297,367,617 - 7,448,862 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl297,332,684 - 7,448,507 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha297,646,390 - 7,761,519 (+)NCBI
ROS_Cfam_1.0297,407,120 - 7,522,482 (+)NCBI
UMICH_Zoey_3.1297,421,443 - 7,536,515 (+)NCBI
UNSW_CanFamBas_1.0297,554,220 - 7,669,329 (+)NCBI
UU_Cfam_GSD_1.0297,830,951 - 7,946,216 (+)NCBI
Lyn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530372,085,767 - 72,205,721 (-)NCBI
SpeTri2.0NW_0049364962,578,598 - 2,698,165 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LYN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl475,786,099 - 75,868,591 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1475,793,273 - 75,903,710 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2482,711,087 - 82,843,221 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LYN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1851,919,656 - 52,057,376 (+)NCBI
ChlSab1.1 Ensembl851,919,808 - 52,057,959 (+)Ensembl
Vero_WHO_p1.0NW_02366603989,742,858 - 89,881,060 (-)NCBI
Lyn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248864,029,318 - 4,168,797 (-)NCBI

Position Markers
D5Rat206  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0516,634,965 - 16,635,349NCBIRnor6.0
Rnor_5.0521,415,159 - 21,415,543UniSTSRnor5.0
RGSC_v3.4517,046,881 - 17,047,265UniSTSRGSC3.4
RGSC_v3.1517,046,880 - 17,047,265RGD
Celera516,111,906 - 16,112,290UniSTS
Cytogenetic Map5q12UniSTS
D5Got317  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2516,749,066 - 16,749,249 (+)MAPPERmRatBN7.2
Rnor_6.0516,636,216 - 16,636,396NCBIRnor6.0
Rnor_5.0521,416,410 - 21,416,590UniSTSRnor5.0
RGSC_v3.4517,048,132 - 17,048,312UniSTSRGSC3.4
Celera516,113,157 - 16,113,337UniSTS
Cytogenetic Map5q12UniSTS
RH140554  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2516,754,625 - 16,754,836 (+)MAPPERmRatBN7.2
Rnor_6.0516,641,773 - 16,641,983NCBIRnor6.0
Rnor_5.0521,421,967 - 21,422,177UniSTSRnor5.0
RGSC_v3.4517,053,689 - 17,053,899UniSTSRGSC3.4
Celera516,118,714 - 16,118,924UniSTS
RH 3.4 Map590.6UniSTS
Cytogenetic Map5q12UniSTS
RH94837  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2516,754,362 - 16,754,500 (+)MAPPERmRatBN7.2
Rnor_6.0516,641,510 - 16,641,647NCBIRnor6.0
Rnor_5.0521,421,704 - 21,421,841UniSTSRnor5.0
RGSC_v3.4517,053,426 - 17,053,563UniSTSRGSC3.4
Celera516,118,451 - 16,118,588UniSTS
RH 3.4 Map586.9UniSTS
Cytogenetic Map5q12UniSTS
RH94838  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2516,754,827 - 16,755,000 (+)MAPPERmRatBN7.2
Rnor_6.0516,641,975 - 16,642,147NCBIRnor6.0
Rnor_5.0521,422,169 - 21,422,341UniSTSRnor5.0
RGSC_v3.4517,053,891 - 17,054,063UniSTSRGSC3.4
Celera516,118,916 - 16,119,088UniSTS
Cytogenetic Map5q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5818750118616199Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:189
Count of miRNA genes:129
Interacting mature miRNAs:157
Transcripts:ENSRNOT00000011130
Prediction methods:Miranda, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 1 1 10 35 30 11 1
Low 7 10 64 11 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011130   ⟹   ENSRNOP00000011130
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl516,639,466 - 16,756,868 (+)Ensembl
Rnor_6.0 Ensembl516,526,058 - 16,642,648 (+)Ensembl
RefSeq Acc Id: NM_001111098   ⟹   NP_001104568
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2516,639,512 - 16,755,501 (+)NCBI
Rnor_6.0516,526,058 - 16,642,648 (+)NCBI
Rnor_5.0521,307,094 - 21,422,842 (+)NCBI
RGSC_v3.4516,933,111 - 17,054,564 (+)RGD
Celera516,004,013 - 16,119,589 (+)RGD
Sequence:
RefSeq Acc Id: NM_030857   ⟹   NP_110484
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2516,639,512 - 16,755,501 (+)NCBI
Rnor_6.0516,526,058 - 16,642,648 (+)NCBI
Rnor_5.0521,307,094 - 21,422,842 (+)NCBI
RGSC_v3.4516,933,111 - 17,054,564 (+)RGD
Celera516,004,013 - 16,119,589 (+)RGD
Sequence:
RefSeq Acc Id: XM_006237834   ⟹   XP_006237896
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2516,695,773 - 16,754,954 (+)NCBI
Rnor_6.0516,582,849 - 16,642,101 (+)NCBI
Rnor_5.0521,307,094 - 21,422,842 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_110484   ⟸   NM_030857
- Peptide Label: isoform A
- UniProtKB: Q07014 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001104568   ⟸   NM_001111098
- Peptide Label: isoform B
- UniProtKB: Q07014 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006237896   ⟸   XM_006237834
- Peptide Label: isoform X1
- UniProtKB: Q07014 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011130   ⟸   ENSRNOT00000011130
Protein Domains
Protein kinase   SH2   SH3

Transcriptome

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

Promoters
RGD ID:13693549
Promoter ID:EPDNEW_R4074
Type:initiation region
Name:Lyn_1
Description:LYN proto-oncogene, Src family tyrosine kinase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0516,526,015 - 16,526,075EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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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:621017 AgrOrtholog
Ensembl Genes ENSRNOG00000008180 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000011130 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000011130 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.505.10 UniProtKB/Swiss-Prot
InterPro Kinase-like_dom_sf UniProtKB/Swiss-Prot
  Lyn_SH2 UniProtKB/Swiss-Prot
  Lyn_SH3 UniProtKB/Swiss-Prot
  Prot_kinase_dom UniProtKB/Swiss-Prot
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot
  Ser-Thr/Tyr_kinase_cat_dom UniProtKB/Swiss-Prot
  SH2 UniProtKB/Swiss-Prot
  SH2_dom_sf UniProtKB/Swiss-Prot
  SH3-like_dom_sf UniProtKB/Swiss-Prot
  SH3_domain UniProtKB/Swiss-Prot
  Tyr_kinase_AS UniProtKB/Swiss-Prot
  Tyr_kinase_cat_dom UniProtKB/Swiss-Prot
KEGG Report rno:81515 UniProtKB/Swiss-Prot
NCBI Gene 81515 ENTREZGENE
Pfam Pkinase_Tyr UniProtKB/Swiss-Prot
  SH2 UniProtKB/Swiss-Prot
  SH3_1 UniProtKB/Swiss-Prot
PhenoGen Lyn PhenoGen
PRINTS SH2DOMAIN UniProtKB/Swiss-Prot
  SH3DOMAIN UniProtKB/Swiss-Prot
  TYRKINASE UniProtKB/Swiss-Prot
PROSITE PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot
  PROTEIN_KINASE_TYR UniProtKB/Swiss-Prot
  SH2 UniProtKB/Swiss-Prot
  SH3 UniProtKB/Swiss-Prot
SMART SH2 UniProtKB/Swiss-Prot
  SH3 UniProtKB/Swiss-Prot
  TyrKc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50044 UniProtKB/Swiss-Prot
  SSF55550 UniProtKB/Swiss-Prot
  SSF56112 UniProtKB/Swiss-Prot
UniProt LYN_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q63320 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-10 Lyn  LYN proto-oncogene, Src family tyrosine kinase  Lyn  v-yes-1 Yamaguchi sarcoma viral related oncogene homolog  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-18 Lyn  v-yes-1 Yamaguchi sarcoma viral related oncogene homolog  Lyn  Yamaguchi sarcoma viral (v-yes-1) oncogene homolog  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Lyn  Yamaguchi sarcoma viral (v-yes-1) oncogene homolog    lyn protein non-receptor kinase  Name updated 1299863 APPROVED
2002-08-07 Lyn  lyn protein non-receptor kinase      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction interacts with PI3-K 632179
gene_process mediates PI3-K/Akt signaling pathway 632179
gene_process mediates PI3-K/Akt signaling pathway 632179