Raf1 (Raf-1 proto-oncogene, serine/threonine kinase) - Rat Genome Database

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Gene: Raf1 (Raf-1 proto-oncogene, serine/threonine kinase) Rattus norvegicus
Analyze
Symbol: Raf1
Name: Raf-1 proto-oncogene, serine/threonine kinase
RGD ID: 3531
Description: Enables several functions, including ATP binding activity; adenylate cyclase activator activity; and enzyme binding activity. Involved in several processes, including MAPK cascade; protein phosphorylation; and response to hypoxia. Located in cytoplasm and plasma membrane. Biomarker of pancreatic carcinoma. Human ortholog(s) of this gene implicated in Noonan syndrome (multiple); Noonan syndrome with multiple lentigines 2; adenocarcinoma (multiple); and dilated cardiomyopathy 1NN. Orthologous to human RAF1 (Raf-1 proto-oncogene, serine/threonine kinase); PARTICIPATES IN the extracellular signal-regulated Raf/Mek/Erk signaling pathway; altered extracellular signal-regulated Raf/Mek/Erk signaling pathway; ceramide signaling pathway; INTERACTS WITH 1,2-dimethylhydrazine; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: C-RAF; cRaf; Murine leukemia viral (v-raf-1) oncogene homolog 1 (3611-MSV); proto-oncogene c-RAF; RAF proto-oncogene serine/threonine-protein kinase; raf-1; v-raf-1 murine leukemia viral oncogene homolog 1; v-raf-leukemia viral oncogene 1
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
mRatBN7.24148,679,534 - 148,740,265 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4148,679,530 - 148,740,317 (-)Ensembl
Rnor_6.04147,532,040 - 147,592,769 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4147,532,042 - 147,592,699 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04210,819,148 - 210,878,226 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44151,752,583 - 151,775,609 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14151,997,425 - 152,020,450 (-)NCBI
Celera4137,570,499 - 137,631,125 (-)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(20R)-protopanaxadiol  (ISO)
(S)-(-)-perillyl alcohol  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
15-deoxy-Delta(12,14)-prostaglandin J2  (ISO)
17beta-estradiol  (ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-deoxy-D-glucose  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxynon-2-enal  (ISO)
5-fluorouracil  (ISO)
7,12-dimethyltetraphene  (ISO)
acetylsalicylic acid  (ISO)
aconitine  (ISO)
acrylamide  (ISO)
actinomycin D  (EXP)
afimoxifene  (ISO)
AICA ribonucleotide  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
andrographolide  (ISO)
Aroclor 1254  (EXP,ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP)
bortezomib  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calciol  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
chaetoglobosin A  (EXP)
choline  (ISO)
ciglitazone  (ISO)
cis-caffeic acid  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
Cruentaren A  (ISO)
curcumin  (ISO)
cypermethrin  (ISO)
deoxycholic acid  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dibutylstannane  (ISO)
dieldrin  (ISO)
dimethyl sulfoxide  (ISO)
dimethylarsinic acid  (EXP,ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
eckol  (ISO)
emodin  (EXP,ISO)
endosulfan  (ISO)
erlotinib hydrochloride  (ISO)
ethanol  (ISO)
ethylene glycol bis(2-aminoethyl)tetraacetic acid  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
gamma-hexachlorocyclohexane  (ISO)
geldanamycin  (ISO)
genistein  (EXP,ISO)
gentamycin  (EXP)
geraniol  (ISO)
Goe 6976  (EXP)
GW 1929  (ISO)
heptachlor  (ISO)
hydrogen peroxide  (ISO)
hydroxyflutamide  (ISO)
indole-3-methanol  (EXP)
lapatinib  (ISO)
lead diacetate  (ISO)
letrozole  (ISO)
lipopolysaccharide  (EXP)
lipoteichoic acid  (ISO)
lovastatin  (ISO)
LY294002  (ISO)
maneb  (ISO)
mangiferin  (ISO)
manumycin A  (EXP)
melatonin  (ISO)
metformin  (ISO)
Methanandamide  (ISO)
methapyrilene  (ISO)
methylarsonic acid  (ISO)
methylmercury chloride  (EXP)
morphine  (EXP,ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-acetylsphingosine  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (ISO)
naphthalene  (ISO)
naringin  (EXP,ISO)
niclosamide  (ISO)
nicotine  (ISO)
nimodipine  (ISO)
nitric oxide  (EXP)
okadaic acid  (ISO)
ouabain  (ISO)
ozone  (ISO)
p-menthan-3-ol  (ISO)
paclitaxel  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
Parthenin  (ISO)
PD173074  (ISO)
perillyl alcohol  (ISO)
phenethyl isothiocyanate  (ISO)
phenobarbital  (EXP)
phenylephrine  (EXP)
PhIP  (ISO)
phlorizin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
Piplartine  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (ISO)
propofol  (ISO)
prostaglandin F2alpha  (ISO)
pyrogallol  (ISO)
quercetin  (ISO)
quinomethionate  (ISO)
resveratrol  (EXP,ISO)
rimonabant  (ISO)
romidepsin  (ISO)
rottlerin  (ISO)
S-nitroso-N-acetyl-D-penicillamine  (ISO)
Salvianolic acid A  (ISO)
sevoflurane  (EXP)
simvastatin  (EXP,ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
sorafenib  (ISO)
SR 144528  (ISO)
streptozocin  (EXP)
styrene  (ISO)
SU6656  (ISO)
tanespimycin  (ISO)
Tautomycin  (ISO)
testosterone  (EXP,ISO)
tetrahydropalmatine  (ISO)
thapsigargin  (ISO)
tipifarnib  (EXP)
titanium dioxide  (ISO)
trans-caffeic acid  (ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
trimethyltin  (ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
ursodeoxycholic acid  (ISO)
valproic acid  (ISO)
vemurafenib  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
wortmannin  (ISO)
zearalenone  (ISO)
zinc atom  (ISO)
zinc dichloride  (EXP)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IDA,ISO)
cytosol  (IBA,ISO,TAS)
Golgi apparatus  (ISO)
mitochondrion  (IBA)
nuclear speck  (IEA,ISO)
nucleus  (IEA)
plasma membrane  (IBA,IDA,ISO)
pseudopodium  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
acute myeloid leukemia pathway  (IEA)
altered extracellular signal-regulated Raf/Mek/Erk signaling pathway  (ISO)
B cell receptor signaling pathway  (IEA)
ceramide signaling pathway  (IEA,ISO)
chemokine mediated signaling pathway  (IEA)
chronic myeloid leukemia pathway  (IEA)
colorectal cancer pathway  (IEA)
endometrial cancer pathway  (IEA)
endothelin signaling pathway  (ISO)
epidermal growth factor/neuregulin signaling pathway  (IEA)
Fc epsilon receptor mediated signaling pathway  (IEA,ISO)
Fc gamma receptor mediated signaling pathway  (IEA)
glioma pathway  (IEA)
gonadotropin-releasing hormone signaling pathway  (IEA)
granulocyte-macrophage colony-stimulating factor signaling pathway  (ISO)
hepatitis C pathway  (IEA)
influenza A pathway  (IEA)
insulin signaling pathway  (IEA,ISO)
insulin-like growth factor signaling pathway  (ISO)
interleukin-2 signaling pathway  (ISO)
long term depression  (IEA)
long term potentiation  (IEA)
melanoma pathway  (IEA)
mitogen activated protein kinase signaling pathway  (IEA)
mTOR signaling pathway  (ISO)
neurotrophic factor signaling pathway  (IEA)
non-small cell lung carcinoma pathway  (IEA)
pancreatic cancer pathway  (IEA)
phosphatidylinositol 3-kinase-Akt signaling pathway  (ISO)
platelet-derived growth factor signaling pathway  (ISO)
prostate cancer pathway  (IEA)
renal cell carcinoma pathway  (IEA)
T cell receptor signaling pathway  (IEA)
the extracellular signal-regulated Raf/Mek/Erk signaling pathway  (IMP,ISO,TAS)
tuberculosis pathway  (IEA)
urinary bladder cancer pathway  (IEA)
vascular endothelial growth factor signaling pathway  (IEA,ISO)

References

References - curated
1. Alavi A, etal., Science 2003 Jul 4;301(5629):94-6.
2. Chan EY, etal., Mol Carcinog 2002 Apr;33(4):189-97.
3. DeFea KA, etal., J Cell Biol. 2000 Mar 20;148(6):1267-81.
4. Deng Y, etal., J Clin Invest. 2013 Mar;123(3):1202-15. doi: 10.1172/JCI63034. Epub 2013 Feb 8.
5. Ding Q, etal., Mol Pharmacol. 2004 Oct;66(4):921-8.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. GOA data from the GO Consortium
8. Gruppuso PA and Boylan JM, FEBS Lett. 2000 Jan 21;466(1):200-4.
9. Integration of LocusLink data, October 12, 2001
10. Ishikawa F, etal., Mol Cell Biol 1987 Mar;7(3):1226-32.
11. Kanwar M and Kowluru RA, Microvasc Res. 2008 Nov;76(3):189-93. Epub 2008 Apr 25.
12. Kim SO, etal., J Cell Biochem 1998 Nov 1;71(2):286-301.
13. Kobayashi T, etal., Hum Mutat. 2010 Mar;31(3):284-94. doi: 10.1002/humu.21187.
14. McCubrey JA, etal., Biochim Biophys Acta. 2007 Aug;1773(8):1263-84. Epub 2006 Oct 7.
15. McFarlin DR, etal., Carcinogenesis 2003 Jan;24(1):99-105.
16. MGD data from the GO Consortium
17. Mukherjee R, etal., Prostate. 2005 Jun 15;64(1):101-7. doi: 10.1002/pros.20211.
18. NCBI rat LocusLink and RefSeq merged data July 26, 2002
19. OMIM Disease Annotation Pipeline
20. Pal A, etal., Int J Oncol. 2005 Apr;26(4):1087-91.
21. Pandit B, etal., Nat Genet. 2007 Aug;39(8):1007-12. Epub 2007 Jul 1.
22. Pei J, etal., Anticancer Drugs. 2004 Mar;15(3):243-53.
23. Pipeline to import KEGG annotations from KEGG into RGD
24. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
25. Pipeline to import SMPDB annotations from SMPDB into RGD
26. Razzaque MA, etal., Nat Genet. 2007 Aug;39(8):1013-7. Epub 2007 Jul 1.
27. RGD automated data pipeline
28. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
29. RGD automated import pipeline for gene-chemical interactions
30. Roskoski R Jr Biochem Biophys Res Commun. 2012 Jan 6;417(1):5-10. Epub 2011 Dec 8.
31. Rushworth LK, etal., Mol Cell Biol. 2006 Mar;26(6):2262-72.
32. Santos SD, etal., Nat Cell Biol. 2007 Mar;9(3):324-30. Epub 2007 Feb 18.
33. Seko Y, etal., Circ Res. 1996 Jan;78(1):82-90.
34. Shu FJ, etal., Cell Signal. 2010 Mar;22(3):366-76. doi: 10.1016/j.cellsig.2009.10.005. Epub .
35. Silverman JA, etal., Mol Carcinog. 1990;3(6):379-86.
36. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
37. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
38. Trakul N, etal., J Biol Chem. 2005 Jul 1;280(26):24931-40. Epub 2005 May 10.
39. Willard FS, etal., PLoS One. 2009;4(3):e4884. doi: 10.1371/journal.pone.0004884. Epub 2009 Mar 25.
40. Williams AF, etal., Cold Spring Harb Symp Quant Biol 1977;41 Pt 1:51-61.
41. Wu WX, etal., Zhonghua Zhong Liu Za Zhi. 2010 Sep;32(9):671-5.
42. Wu X, etal., J Clin Invest. 2011 Mar;121(3):1009-25. doi: 10.1172/JCI44929. Epub 2011 Feb 21.
43. Wu X, etal., Mol Cell Biol. 2012 Oct;32(19):3872-90. doi: 10.1128/MCB.00751-12. Epub 2012 Jul 23.
44. Xu J, etal., J Biol Chem. 2006 Jan 13;281(2):982-92. Epub 2005 Nov 4.
45. Xuan YT, etal., Circulation. 2005 Sep 27;112(13):1971-8. Epub 2005 Sep 19.
Additional References at PubMed
PMID:8026469   PMID:8307946   PMID:9551081   PMID:9560161   PMID:9679960   PMID:9765203   PMID:9852579   PMID:9931261   PMID:10329666   PMID:10407019   PMID:10644344   PMID:10704835  
PMID:11698596   PMID:12194967   PMID:12551925   PMID:12821670   PMID:12954639   PMID:14654844   PMID:14978028   PMID:15211515   PMID:15489334   PMID:15975997   PMID:16009725   PMID:16365167  
PMID:16396499   PMID:16737746   PMID:16954213   PMID:17554210   PMID:17724343   PMID:17979178   PMID:18243549   PMID:18328477   PMID:18708364   PMID:18952847   PMID:19381846   PMID:19667065  
PMID:20110729   PMID:20130576   PMID:20442316   PMID:20718739   PMID:20953701   PMID:21440552   PMID:21817126   PMID:21917714   PMID:22169110   PMID:22510884   PMID:22610096   PMID:22983684  
PMID:23022482   PMID:23509299   PMID:23611784   PMID:23928917   PMID:24885948   PMID:25367879   PMID:28057484   PMID:30140388   PMID:31521821   PMID:33424842   PMID:34229010  


Genomics

Comparative Map Data
Raf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24148,679,534 - 148,740,265 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4148,679,530 - 148,740,317 (-)Ensembl
Rnor_6.04147,532,040 - 147,592,769 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4147,532,042 - 147,592,699 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04210,819,148 - 210,878,226 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44151,752,583 - 151,775,609 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14151,997,425 - 152,020,450 (-)NCBI
Celera4137,570,499 - 137,631,125 (-)NCBICelera
Cytogenetic Map4q42NCBI
RAF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl312,582,101 - 12,664,201 (-)EnsemblGRCh38hg38GRCh38
GRCh38312,583,601 - 12,664,117 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37312,625,100 - 12,705,616 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36312,600,108 - 12,680,678 (-)NCBINCBI36hg18NCBI36
Build 34312,600,107 - 12,680,678NCBI
Celera312,563,426 - 12,643,994 (-)NCBI
Cytogenetic Map3p25.2NCBI
HuRef312,559,317 - 12,640,382 (-)NCBIHuRef
CHM1_1312,575,179 - 12,655,743 (-)NCBICHM1_1
Raf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396115,595,530 - 115,653,596 (-)NCBIGRCm39mm39
GRCm39 Ensembl6115,595,028 - 115,653,596 (-)Ensembl
GRCm386115,618,569 - 115,676,635 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6115,618,067 - 115,676,635 (-)EnsemblGRCm38mm10GRCm38
MGSCv376115,568,591 - 115,626,653 (-)NCBIGRCm37mm9NCBIm37
MGSCv366115,584,216 - 115,642,122 (-)NCBImm8
Celera6117,458,696 - 117,516,733 (-)NCBICelera
Cytogenetic Map6E3NCBI
cM Map653.62NCBI
Raf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542918,025,932 - 18,049,723 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542917,980,956 - 18,049,723 (+)NCBIChiLan1.0ChiLan1.0
RAF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1312,853,415 - 12,932,871 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl312,853,415 - 12,932,871 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0312,510,084 - 12,590,598 (-)NCBIMhudiblu_PPA_v0panPan3
RAF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1205,892,839 - 5,972,672 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl205,892,834 - 5,972,090 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha205,929,501 - 6,009,310 (+)NCBI
ROS_Cfam_1.0205,921,808 - 6,000,868 (+)NCBI
ROS_Cfam_1.0 Ensembl205,921,827 - 6,000,864 (+)Ensembl
UMICH_Zoey_3.1205,637,969 - 5,717,035 (+)NCBI
UNSW_CanFamBas_1.0205,991,105 - 6,070,948 (+)NCBI
UU_Cfam_GSD_1.0205,966,879 - 6,046,000 (+)NCBI
Raf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494217,795,336 - 17,819,736 (-)NCBI
SpeTri2.0NW_0049366021,089,979 - 1,114,376 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RAF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1368,580,812 - 68,657,829 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11368,581,128 - 68,657,911 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21375,848,344 - 75,927,158 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RAF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12248,560,270 - 48,643,537 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2248,561,161 - 48,618,020 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041117,857,289 - 117,941,171 (+)NCBIVero_WHO_p1.0
Raf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624872204,357 - 284,487 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH127364  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24148,679,257 - 148,679,472 (+)MAPPERmRatBN7.2
Rnor_6.04147,531,764 - 147,531,978NCBIRnor6.0
Rnor_5.04210,818,872 - 210,819,086UniSTSRnor5.0
RGSC_v3.44151,752,307 - 151,752,521UniSTSRGSC3.4
Celera4137,570,223 - 137,570,437UniSTS
RH 3.4 Map15457.3UniSTS
Cytogenetic Map4q42UniSTS
RH142970  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24148,683,589 - 148,683,722 (+)MAPPERmRatBN7.2
Rnor_6.04147,536,095 - 147,536,227NCBIRnor6.0
Rnor_5.04210,823,203 - 210,823,335UniSTSRnor5.0
RGSC_v3.44151,756,638 - 151,756,770UniSTSRGSC3.4
Celera4137,574,554 - 137,574,686UniSTS
RH 3.4 Map4952.1UniSTS
Cytogenetic Map4q42UniSTS
BI284862  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24148,679,723 - 148,679,931 (+)MAPPERmRatBN7.2
Rnor_6.04147,532,230 - 147,532,437NCBIRnor6.0
Rnor_5.04210,819,338 - 210,819,545UniSTSRnor5.0
RGSC_v3.44151,752,773 - 151,752,980UniSTSRGSC3.4
Celera4137,570,689 - 137,570,896UniSTS
RH 3.4 Map4950.71UniSTS
Cytogenetic Map4q42UniSTS
RH139128  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24148,683,086 - 148,683,210 (+)MAPPERmRatBN7.2
Rnor_6.04147,535,592 - 147,535,715NCBIRnor6.0
Rnor_5.04210,822,700 - 210,822,823UniSTSRnor5.0
RGSC_v3.44151,756,135 - 151,756,258UniSTSRGSC3.4
Celera4137,574,051 - 137,574,174UniSTS
RH 3.4 Map4951.41UniSTS
Cytogenetic Map4q42UniSTS
UniSTS:469819  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24148,679,655 - 148,680,192 (+)MAPPERmRatBN7.2
Rnor_6.04147,532,162 - 147,532,698NCBIRnor6.0
Rnor_5.04210,819,270 - 210,819,806UniSTSRnor5.0
RGSC_v3.44151,752,705 - 151,753,241UniSTSRGSC3.4
Celera4137,570,621 - 137,571,157UniSTS
Cytogenetic Map4q42UniSTS
Raf1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24148,694,134 - 148,694,684 (+)MAPPERmRatBN7.2
Rnor_6.04147,546,640 - 147,547,189NCBIRnor6.0
Rnor_5.04210,833,748 - 210,834,297UniSTSRnor5.0
RGSC_v3.44151,767,183 - 151,767,732UniSTSRGSC3.4
Celera4137,585,099 - 137,585,648UniSTS
Cytogenetic Map4q42UniSTS
Raf1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24148,680,275 - 148,680,866 (+)MAPPERmRatBN7.2
Rnor_6.04147,532,782 - 147,533,371NCBIRnor6.0
Rnor_5.04210,819,890 - 210,820,479UniSTSRnor5.0
Celera4137,571,241 - 137,571,830UniSTS
Cytogenetic Map4q42UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)482798864152731274Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
12798523Anxrr56Anxiety related response QTL 562.830.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)485253748150276390Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
2302049Pia32Pristane induced arthritis QTL 325.10.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)4105789505150789505Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106649412151649412Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4106805662151805662Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109827074154827074Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109827074154827074Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4114627026159627026Rat
1300116Hrtrt5Heart rate QTL 53.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)4116179486151161268Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4147278504167139601Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
61446Coreg2Compensatory renal growth QTL 23.5kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)4148423102157580971Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:103
Count of miRNA genes:83
Interacting mature miRNAs:86
Transcripts:ENSRNOT00000013831
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

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

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013831   ⟹   ENSRNOP00000013831
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4148,679,530 - 148,740,210 (-)Ensembl
Rnor_6.0 Ensembl4147,532,042 - 147,592,699 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105918   ⟹   ENSRNOP00000082418
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4148,679,534 - 148,740,317 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109662   ⟹   ENSRNOP00000092271
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4148,679,534 - 148,740,317 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000119226   ⟹   ENSRNOP00000094673
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4148,679,534 - 148,740,317 (-)Ensembl
RefSeq Acc Id: NM_012639   ⟹   NP_036771
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24148,679,534 - 148,740,195 (-)NCBI
Rnor_6.04147,532,040 - 147,592,699 (-)NCBI
Rnor_5.04210,819,148 - 210,878,226 (-)NCBI
RGSC_v3.44151,752,583 - 151,775,609 (-)RGD
Celera4137,570,499 - 137,631,125 (-)RGD
Sequence:
RefSeq Acc Id: XM_008763217   ⟹   XP_008761439
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24148,679,541 - 148,740,265 (-)NCBI
Rnor_6.04147,532,047 - 147,592,769 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763218   ⟹   XP_008761440
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24148,679,635 - 148,739,511 (-)NCBI
Rnor_6.04147,532,047 - 147,592,039 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039107056   ⟹   XP_038962984
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24148,679,635 - 148,739,684 (-)NCBI
RefSeq Acc Id: XM_039107057   ⟹   XP_038962985
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24148,679,635 - 148,739,574 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_036771   ⟸   NM_012639
- UniProtKB: P11345 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008761439   ⟸   XM_008763217
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008761440   ⟸   XM_008763218
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000013831   ⟸   ENSRNOT00000013831
RefSeq Acc Id: XP_038962984   ⟸   XM_039107056
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038962985   ⟸   XM_039107057
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000094673   ⟸   ENSRNOT00000119226
RefSeq Acc Id: ENSRNOP00000082418   ⟸   ENSRNOT00000105918
RefSeq Acc Id: ENSRNOP00000092271   ⟸   ENSRNOT00000109662
Protein Domains
Protein kinase   RBD

Transcriptome

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

Promoters
RGD ID:13693324
Promoter ID:EPDNEW_R3849
Type:initiation region
Name:Raf1_1
Description:Raf-1 proto-oncogene, serine/threonine 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_6.04147,592,708 - 147,592,768EPDNEW

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)
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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)
FHH/EurMcwi (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
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)
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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
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)
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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
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)
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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
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)
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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
LE/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
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)
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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
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)
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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
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)
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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
LEXF3/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
LEXF4/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
LH/MavRrrc (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
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)
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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
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)
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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
M520/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
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3531 AgrOrtholog
Ensembl Genes ENSRNOG00000010153 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000013831 UniProtKB/Swiss-Prot
  ENSRNOP00000082418 ENTREZGENE
  ENSRNOP00000092271 ENTREZGENE
Ensembl Transcript ENSRNOT00000013831 UniProtKB/Swiss-Prot
  ENSRNOT00000105918 ENTREZGENE
  ENSRNOT00000109662 ENTREZGENE
IMAGE_CLONE IMAGE:5599540 IMAGE-MGC_LOAD
InterPro DAG/PE-bd UniProtKB/Swiss-Prot
  Kinase-like_dom_sf UniProtKB/Swiss-Prot
  PE/DAG-bd UniProtKB/Swiss-Prot
  Prot_kinase_dom UniProtKB/Swiss-Prot
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot
  RBD_dom UniProtKB/Swiss-Prot
  Ser-Thr/Tyr_kinase_cat_dom UniProtKB/Swiss-Prot
  Ser/Thr_kinase_AS UniProtKB/Swiss-Prot
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot
KEGG Report rno:24703 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72519 IMAGE-MGC_LOAD
NCBI Gene 24703 ENTREZGENE
Pfam C1_1 UniProtKB/Swiss-Prot
  Pkinase_Tyr UniProtKB/Swiss-Prot
  RBD UniProtKB/Swiss-Prot
PharmGKB RAF1 RGD
PhenoGen Raf1 PhenoGen
PRINTS DAGPEDOMAIN UniProtKB/Swiss-Prot
PROSITE PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot
  PROTEIN_KINASE_ST UniProtKB/Swiss-Prot
  RBD UniProtKB/Swiss-Prot
  ZF_DAG_PE_1 UniProtKB/Swiss-Prot
  ZF_DAG_PE_2 UniProtKB/Swiss-Prot
SMART RBD UniProtKB/Swiss-Prot
  S_TKc UniProtKB/Swiss-Prot
  SM00109 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54236 UniProtKB/Swiss-Prot
  SSF56112 UniProtKB/Swiss-Prot
TIGR TC216965
UniProt P11345 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-16 Raf1  Raf-1 proto-oncogene, serine/threonine kinase  Raf1  v-raf-leukemia viral oncogene 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-15 Raf1  v-raf-leukemia viral oncogene 1  Raf1  v-raf-1 murine leukemia viral oncogene homolog 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 Raf1  v-raf-1 murine leukemia viral oncogene homolog 1    murine leukemia viral (v-raf-1) oncogene homolog 1 (3611-MSV)  Name updated 1299863 APPROVED
2002-06-10 Raf1  v-raf-1 murine leukemia viral oncogene homolog 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function phosphorylates Map2k1 and Mek2 70317
gene_function phosphorylates Map2k1 and Mek2 70441
gene_process may activate Mapk1 and Mapk3 in fetal heart development 70317
gene_process may activate Mapk1 and Mapk3 in fetal heart development 70441