Vcam1 (vascular cell adhesion molecule 1) - Rat Genome Database

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Gene: Vcam1 (vascular cell adhesion molecule 1) Rattus norvegicus
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Symbol: Vcam1
Name: vascular cell adhesion molecule 1
RGD ID: 3952
Description: Enables integrin binding activity. Involved in several processes, including cellular response to tumor necrosis factor; nervous system development; and response to lipopolysaccharide. Located in cell surface; extracellular space; and sarcolemma. Used to study carotid stenosis and hypertension. Biomarker of several diseases, including artery disease (multiple); chronic kidney disease; colitis; periodontitis; and thromboangiitis obliterans. Orthologous to human VCAM1 (vascular cell adhesion molecule 1); PARTICIPATES IN eicosanoid signaling pathway; malaria pathway; sleeping sickness pathway; INTERACTS WITH (S)-colchicine; 1,2-dimethylhydrazine; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC100912479; MGC108734; V-CAM 1; vascular cell adhesion protein 1; vascular cell adhesion protein 1-like; VCAM-1; VCAM1B
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   SHRSP.WKY-(D2Rat13-D2Rat157)/Gcrc   SHRSP.WKY-(D2Mit21-D2Rat157)/Gcrc  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22204,038,120 - 204,057,852 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl2204,038,114 - 204,057,958 (-)Ensembl
Rnor_6.02219,071,193 - 219,090,931 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2219,071,193 - 219,097,619 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02237,158,192 - 237,177,779 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42212,277,654 - 212,297,376 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12212,240,407 - 212,260,130 (-)NCBI
Celera2196,537,457 - 196,557,044 (-)NCBICelera
RH 3.4 Map21480.6RGD
Cytogenetic Map2q41NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Albuminuria  (ISO)
Anaphylaxis  (IMP)
anemia  (ISO)
anti-basement membrane glomerulonephritis  (ISO)
aortic disease  (IEP)
arteriosclerosis  (ISO)
atherosclerosis  (ISO)
cardiovascular system disease  (ISO)
carotid artery disease  (ISO)
carotid stenosis  (IMP)
cholestasis  (ISO)
chronic kidney disease  (IEP,ISO)
colitis  (IEP)
dermatitis  (ISO)
Diabetic Nephropathies  (IEP,ISO)
diabetic neuropathy  (ISO)
diabetic retinopathy  (ISO)
Diaphragmatic Hernia  (ISO)
Endotoxemia  (IEP)
essential thrombocythemia  (ISO)
Experimental Autoimmune Encephalomyelitis  (IDA)
Experimental Diabetes Mellitus  (IEP,ISO)
familial hyperlipidemia  (IEP)
Gastrointestinal Diseases  (ISO)
glomerulonephritis  (ISO)
hepatocellular carcinoma  (ISO)
Hypercholesterolemia  (ISO)
hypertension  (IAGP,IEP,ISO)
Insulin Resistance  (ISO)
interstitial cystitis  (ISO)
intrahepatic cholestasis of pregnancy  (ISO)
Kidney Reperfusion Injury  (IEP)
Left Ventricular Hypertrophy  (ISO)
lupus nephritis  (ISO)
Lymphocytic Myocarditis  (ISO)
Metabolic Syndrome  (IEP)
multiple sclerosis  (ISO)
Myocardial Ischemia  (ISO)
Myocardial Reperfusion Injury  (IEP)
Neoplasm Metastasis  (ISO)
obesity  (ISO)
pancreatic cancer  (ISO)
pancreatitis  (ISO)
periodontitis  (IEP)
Pregnancy in Diabetics  (ISO)
Primary Graft Dysfunction  (ISO)
pulmonary embolism  (IEP)
pulmonary hypertension  (IEP)
Reperfusion Injury  (IEP)
rheumatic myocarditis  (ISO)
sickle cell anemia  (ISO)
Stroke  (ISO)
systemic lupus erythematosus  (ISO)
thromboangiitis obliterans  (IEP,ISO)
type 1 diabetes mellitus  (ISO)
type 2 diabetes mellitus  (ISO)
ulcerative colitis  (ISO)
uremia  (ISO)
urticaria  (ISO)
Venous Thrombosis  (IEP)
Vitamin A Deficiency  (IEP)
Vitamin D Deficiency  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
(2,4,5-trichlorophenoxy)acetic acid  (ISO)
(20S)-ginsenoside Rh1  (ISO)
(25R)-cholest-5-ene-3beta,26-diol  (ISO)
(4Z,7Z,10Z,13Z,15E,19Z)-17-hydroxydocosahexaenoic acid  (ISO)
(R)-linalyl acetate  (ISO)
(R)-mevalonic acid  (ISO)
(R,R,R)-alpha-tocopherol  (ISO)
(S)-colchicine  (EXP,ISO)
(S)-nicotine  (ISO)
1,2,3,4,6-pentakis-O-galloyl-beta-D-glucose  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
11-deoxycorticosterone  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP,ISO)
2-acetamidofluorene  (EXP,ISO)
2-butoxyethanol  (ISO)
2-methylcholine  (ISO)
22-Hydroxycholesterol  (ISO)
25-hydroxycholesterol  (ISO)
26-hydroxycholesterol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,3',4,4'-tetrachlorobiphenyl  (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  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
7-ketocholesterol  (ISO)
8-bromo-3',5'-cyclic GMP  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (EXP,ISO)
acteoside  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP,ISO)
aldrin  (ISO)
all-trans-retinoic acid  (EXP,ISO)
allyl isothiocyanate  (ISO)
alpha-linolenic acid  (EXP)
aluminium oxide  (ISO)
amiodarone  (ISO)
amlodipine  (EXP)
ammonium chloride  (EXP)
anagliptin  (ISO)
andrographolide  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antirheumatic drug  (ISO)
apigenin  (ISO)
apocynin  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
aspalathin  (ISO)
astemizole  (ISO)
atorvastatin calcium  (EXP,ISO)
atropine  (ISO)
bacitracin  (EXP)
beclomethasone  (ISO)
benazepril  (EXP)
benzene  (ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bezafibrate  (EXP,ISO)
bicalutamide  (ISO)
biochanin A  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol A diglycidyl ether  (EXP)
budesonide  (EXP,ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
cadmium sulfate  (ISO)
calmidazolium  (ISO)
candesartan  (EXP)
capsaicin  (EXP,ISO)
carbon monoxide  (EXP,ISO)
carbon nanotube  (ISO)
carrageenan  (EXP)
cefaloridine  (EXP)
celastrol  (ISO)
chenodeoxycholic acid  (ISO)
chlordecone  (ISO)
chloroprene  (ISO)
cholesterol  (EXP,ISO)
choline  (ISO)
chrysene  (ISO)
chrysin  (ISO)
ciguatoxin CTX1B  (ISO)
cilostazol  (ISO)
cisplatin  (EXP,ISO)
clobetasol  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
cobalt atom  (ISO)
cobalt dichloride  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (EXP,ISO)
cortisol  (ISO)
crocidolite asbestos  (EXP,ISO)
Cuprizon  (EXP)
curcumin  (EXP,ISO)
Curcumol  (ISO)
cycloheximide  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
cytochalasin D  (ISO)
D-glucose  (EXP,ISO)
D-mannitol  (ISO)
dabrafenib  (ISO)
daidzein  (ISO)
dantrolene  (ISO)
daunorubicin  (EXP)
decabromodiphenyl ether  (EXP,ISO)
delta-tocotrienol  (ISO)
deoxycholic acid  (ISO)
Deoxycorticosterone acetate  (ISO)
desferrioxamine B  (EXP,ISO)
desflurane  (ISO)
desogestrel  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (EXP,ISO)
dibenziodolium  (ISO)
diclofenac  (ISO)
diethylstilbestrol  (ISO)
digitoxin  (ISO)
dioxygen  (EXP,ISO)
dipyridamole  (ISO)
disodium selenite  (ISO)
diuron  (EXP)
divanadium pentaoxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
dutasteride  (ISO)
edaravone  (EXP)
enalapril  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
erythromycin A  (ISO)
esculetin  (EXP)
estriol  (ISO)
estrone  (EXP)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
felodipine  (ISO)
fenofibrate  (ISO)
filipin III  (ISO)
fluoranthene  (ISO)
fluticasone  (ISO)
fluvoxamine  (EXP,ISO)
folic acid  (EXP,ISO)
formaldehyde  (ISO)
Fraxinellone  (ISO)
fructose  (EXP,ISO)
fulvestrant  (EXP,ISO)
fumaric acid  (ISO)
furan  (EXP)
furosemide  (EXP)
gallic acid  (EXP)
Garcinol  (ISO)
gemcitabine  (ISO)
gemfibrozil  (EXP)
genistein  (ISO)
gentamycin  (EXP)
geraniol  (ISO)
ginkgolide B  (ISO)
ginsenoside C-K  (ISO)
glafenine  (EXP)
glucose  (EXP,ISO)
glutathione  (ISO)
Goe 6976  (ISO)
griseofulvin  (ISO)
GW 3965  (ISO)
GW 4064  (ISO)
GW 501516  (ISO)
halothane  (ISO)
helenalin  (ISO)
hesperidin  (ISO)
hexachlorobenzene  (EXP)
hexadecanoic acid  (ISO)
homocysteine  (ISO)
hydrogen peroxide  (ISO)
hydroxamic acid  (EXP)
hydroxysafflor yellow A  (EXP,ISO)
hydroxytyrosol  (ISO)
ibuprofen  (ISO)
indometacin  (EXP,ISO)
indoxyl sulfate  (ISO)
irbesartan  (ISO)
iron atom  (ISO)
iron(0)  (ISO)
isocarbophos  (EXP)
isoprenaline  (ISO)
jaspamide  (ISO)
kaempferol  (ISO)
kaempferol 3-O-beta-D-glucosyl-(1->2)-beta-D-glucoside  (ISO)
ketamine  (ISO)
ketotifen  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
levofloxacin  (EXP)
levonorgestrel  (ISO)
linalool  (ISO)
linalyl acetate  (ISO)
lipopolysaccharide  (EXP,ISO)
lithium chloride  (ISO)
lithocholic acid  (ISO)
losartan  (EXP)
luteolin  (ISO)
LY294002  (ISO)
lycopene  (ISO)
lysophosphatidylcholine  (ISO)
manganese(II) chloride  (EXP)
mangiferin  (ISO)
manidipine  (EXP)
medroxyprogesterone acetate  (ISO)
melamine  (ISO)
melittin  (ISO)
mercury dibromide  (ISO)
mercury dichloride  (EXP)
metacetamol  (ISO)
methapyrilene  (EXP)
methcathinone  (ISO)
methotrexate  (ISO)
methyl beta-cyclodextrin  (ISO)
methyl methanesulfonate  (ISO)
methylglyoxal  (EXP)
methylmercury chloride  (ISO)
methyltestosterone  (ISO)
Methylthiouracil  (ISO)
mifepristone  (EXP,ISO)
miquelianin  (ISO)
mometasone furoate  (ISO)
monocrotaline  (EXP)
N(gamma)-nitro-L-arginine methyl ester  (EXP)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-tosyl-L-phenylalanyl chloromethyl ketone  (ISO)
naproxen  (EXP)
naringin  (ISO)
nebivolol  (ISO)
neocuproine  (ISO)
nevirapine  (EXP)
nickel atom  (ISO)
nickel dichloride  (ISO)
nicotine  (ISO)
nicotinic acid  (ISO)
nimesulide  (ISO)
nitrofen  (EXP)
nitrogen dioxide  (ISO)
notoginsenoside R1  (ISO)
NSC 23766  (ISO)
o-anisidine  (ISO)
oleanolic acid  (ISO)
oleuropein  (ISO)
oroxylin A  (EXP)
oxaliplatin  (EXP)
oxytocin  (ISO)
p-chloromercuribenzoic acid  (ISO)
p-cresol  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
parthenolide  (ISO)
pelargonidin  (ISO)
pentachlorophenol  (ISO)
Pentoxifylline  (EXP)
phenacetin  (EXP)
Phenelzine  (ISO)
phenethyl caffeate  (ISO)
phenobarbital  (ISO)
phenylephrine  (EXP)
phenylhydrazine  (EXP)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pioglitazone  (EXP,ISO)
pirinixic acid  (ISO)
polyphosphates  (ISO)
potassium dichromate  (ISO)
PR-39  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
probucol  (ISO)
procyanidin B2  (EXP)
progesterone  (EXP,ISO)
protoporphyrin  (ISO)
pyrrolidine dithiocarbamate  (EXP)
quercetin  (EXP,ISO)
quercetin 3-O-beta-D-galactopyranoside  (ISO)
quercetin 3-sulfate  (ISO)
Quinupristin-dalfopristin  (ISO)
resolvin D1  (ISO)
resolvin D2  (ISO)
resveratrol  (EXP,ISO)
ricinoleic acid  (ISO)
rimonabant  (ISO)
rutin  (ISO)
ryanodine  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
sarpogrelate  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
serotonin  (ISO)
serpentine asbestos  (EXP,ISO)
sertraline  (ISO)
silicon dioxide  (ISO)
simvastatin  (EXP,ISO)
sinigrin  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium chloride  (ISO)
sodium cholate  (EXP)
sodium dichromate  (ISO)
sodium fluoride  (ISO)
Soman  (ISO)
sphingosine 1-phosphate  (ISO)
SR 144528  (ISO)
streptozocin  (EXP,ISO)
sulfasalazine  (EXP,ISO)
sulfates  (ISO)
sulforaphane  (ISO)
sulfur dioxide  (EXP)
sulindac  (EXP)
sumatriptan  (EXP)
sunitinib  (ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
taurocholic acid  (ISO)
telmisartan  (EXP)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP,ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (ISO)
tetrathiomolybdate(2-)  (ISO)
thalidomide  (EXP)
thioacetamide  (EXP,ISO)
thiram  (ISO)
tibolone  (ISO)
Tiron  (ISO)
titanium dioxide  (ISO)
toluene 2,4-diisocyanate  (EXP,ISO)
topotecan  (EXP)
triamcinolone acetonide  (ISO)
trichloroethene  (EXP,ISO)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
tropan-3alpha-yl 3-hydroxy-2-phenylpropanoate  (ISO)
U-73122  (ISO)
valproic acid  (ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
vancomycin  (ISO)
vincaleukoblastine  (EXP)
vinclozolin  (EXP)
vincristine  (EXP,ISO)
vitamin E  (ISO)
wedelolactone  (ISO)
zileuton  (ISO)
zinc atom  (EXP,ISO)
zinc protoporphyrin  (EXP,ISO)
zinc(0)  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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3. Amoli MM, etal., J Rheumatol. 2001 May;28(5):1014-8.
4. Arrizabalaga P, etal., J Clin Immunol. 2008 Sep;28(5):411-9. doi: 10.1007/s10875-008-9215-2. Epub 2008 Jun 24.
5. Bartels ED, etal., Eur J Clin Invest. 2009 Mar;39(3):190-9.
6. Bessa SS, etal., Eur J Intern Med. 2010 Dec;21(6):530-5. doi: 10.1016/j.ejim.2010.09.011. Epub 2010 Oct 20.
7. Biaggio VS, etal., Exp Lung Res. 2010 Feb;36(1):31-44.
8. Bilgir F, etal., Panminerva Med. 2013 Dec;55(4):385-90.
9. Boulbou MS, etal., Acta Diabetol. 2004 Sep;41(3):118-22.
10. Bruno CM, etal., Minerva Med. 2008 Feb;99(1):1-5.
11. Burke DL, etal., Am J Physiol Lung Cell Mol Physiol. 2009 Aug;297(2):L238-50. Epub 2009 May 22.
12. Codoner-Franch P, etal., J Pediatr. 2012 Nov;161(5):848-54. doi: 10.1016/j.jpeds.2012.04.046. Epub 2012 Jun 5.
13. Corcoran AT, etal., World J Urol. 2013 Feb;31(1):241-6. doi: 10.1007/s00345-012-0852-y. Epub 2012 Mar 24.
14. Day RT, etal., Am J Physiol Renal Physiol. 2013 Jan 9.
15. Ekuni D, etal., Lab Invest. 2010 Mar;90(3):348-59. doi: 10.1038/labinvest.2009.141. Epub 2010 Jan 11.
16. Gao Z, etal., Exp Ther Med. 2012 Dec;4(6):993-998. Epub 2012 Sep 14.
17. Gatica LV, etal., Eur J Nutr. 2012 Feb;51(1):97-106. doi: 10.1007/s00394-011-0198-z. Epub 2011 Apr 22.
18. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
19. Graham D, etal., Hypertension. 2007 Oct 15;.
20. Grieve SM, etal., Eur Biophys J. 2013 Jan;42(1):61-70. doi: 10.1007/s00249-012-0857-x. Epub 2012 Sep 28.
21. Griffiths MM, etal., Curr Opin Immunol. 1999 Dec;11(6):689-700.
22. Gulko PS, etal., Arthritis Rheum 1998 Dec;41(12):2122-31
23. Hafez M, etal., Pediatr Cardiol. 2013 Mar;34(3):583-90. doi: 10.1007/s00246-012-0501-7. Epub 2012 Sep 18.
24. Halacheva K, etal., Acta Histochem. 2002;104(2):177-84.
25. Hao G, etal., PLoS One. 2013;8(2):e57418. doi: 10.1371/journal.pone.0057418. Epub 2013 Feb 27.
26. Hession C, etal., Biochem Biophys Res Commun 1992 Feb 28;183(1):163-9.
27. Hofmann N, etal., BMC Immunol. 2002 Aug 26;3:11.
28. Ibrahim A, etal., Nutrition. 2012 Jul;28(7-8):799-802. doi: 10.1016/j.nut.2011.10.008. Epub 2012 Jan 20.
29. Ino T, etal., Cardiovasc Res. 1997 May;34(2):323-8.
30. Ito T, etal., Muscle Nerve. 2002 Mar;25(3):409-18.
31. Johnston B, etal., J Immunol. 2000 Mar 15;164(6):3337-44.
32. Jung KJ, etal., Inflamm Res. 2009 Mar;58(3):143-50.
33. Kim HJ, etal., Clin Exp Nephrol. 2010 Sep 7.
34. Kong X, etal., J Vasc Surg. 2013 Jan;57(1):194-204. doi: 10.1016/j.jvs.2012.06.083. Epub 2012 Oct 13.
35. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
36. Li XJ, etal., Fa Yi Xue Za Zhi. 2011 Apr;27(2):87-90.
37. Lutz J, etal., J Mol Med. 2008 Dec;86(12):1329-39. Epub 2008 Sep 24.
38. Malmqvist K, etal., J Hypertens. 2002 Aug;20(8):1563-9.
39. Manning AM, etal., J Inflamm. 1995;45(4):283-96.
40. Markocka-Maczka K Wiad Lek. 2003;56(3-4):147-51.
41. Matsumoto K, etal., Atherosclerosis. 2002 Mar;161(1):243-4.
42. MGD data from the GO Consortium
43. Miller SJ, etal., Am J Physiol Heart Circ Physiol. 2007 Nov;293(5):H2634-43. Epub 2007 Sep 14.
44. Moriconi F, etal., Strahlenther Onkol. 2009 Jul;185(7):460-8. Epub 2009 Aug 28.
45. NCBI rat LocusLink and RefSeq merged data July 26, 2002
46. Norlinah MI, etal., Indian J Med Sci. 2009 Apr;63(4):131-8.
47. Nummer D, etal., J Natl Cancer Inst. 2007 Aug 1;99(15):1188-99. Epub 2007 Jul 24.
48. O'Sullivan JB, etal., J Neuroimmunol. 2010 Mar 30;220(1-2):34-42. doi: 10.1016/j.jneuroim.2009.12.007. Epub 2010 Jan 12.
49. Patel TV, etal., Nephron Clin Pract. 2008;110(4):c244-50. doi: 10.1159/000167872. Epub 2008 Oct 31.
50. Pipeline to import KEGG annotations from KEGG into RGD
51. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
52. Pizarro S, etal., Rev Alerg Mex. 2007 Nov-Dec;54(6):189-95.
53. Qu Y, etal., J Vasc Surg. 2009 Dec;50(6):1452-8. doi: 10.1016/j.jvs.2009.08.050.
54. Ran J, etal., Diabetes Res Clin Pract. 2010 May;88(2):177-83. doi: 10.1016/j.diabres.2010.01.021. Epub 2010 Feb 6.
55. RGD automated data pipeline
56. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
57. RGD automated import pipeline for gene-chemical interactions
58. Rubio-Guerra AF, etal., Cell Adh Migr. 2009 Oct 7;3(4).
59. Rubio-Guerra AF, etal., Gac Med Mex. 2008 Jan-Feb;144(1):11-4.
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61. Sahakyan K, etal., Am Heart J. 2010 Jun;159(6):1074-80. doi: 10.1016/j.ahj.2010.03.023.
62. Sawada H, etal., Chest. 2007 Oct;132(4):1265-74.
63. Shirpoor A, etal., Vascul Pharmacol. 2012 Sep;57(2-4):72-7. Epub 2012 Apr 12.
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69. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
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Additional References at PubMed
PMID:1377228   PMID:1381355   PMID:1715889   PMID:2688898   PMID:7530222   PMID:7539357   PMID:8145052   PMID:8562500   PMID:9290466   PMID:11078691   PMID:12021259   PMID:12082081  
PMID:12160302   PMID:12477932   PMID:15001568   PMID:15220135   PMID:15366013   PMID:15879141   PMID:15919506   PMID:16809613   PMID:17064783   PMID:17599409   PMID:17670746   PMID:18032781  
PMID:18095572   PMID:18221587   PMID:18308860   PMID:19738201   PMID:19922364   PMID:19997643   PMID:20197615   PMID:20687137   PMID:20936719   PMID:21121367   PMID:21184129   PMID:21464233  
PMID:21961520   PMID:22195873   PMID:22351665   PMID:22562815   PMID:22627111   PMID:23058024   PMID:23376485   PMID:23474851   PMID:23533145   PMID:23620790   PMID:24100802   PMID:24289084  
PMID:25182537   PMID:25708190   PMID:25868755   PMID:26351298   PMID:26531813   PMID:27072237   PMID:27620662   PMID:29789783   PMID:30431687  


Genomics

Candidate Gene Status
Vcam1 is a candidate Gene for QTL Cia10
Comparative Map Data
Vcam1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22204,038,120 - 204,057,852 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl2204,038,114 - 204,057,958 (-)Ensembl
Rnor_6.02219,071,193 - 219,090,931 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2219,071,193 - 219,097,619 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02237,158,192 - 237,177,779 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42212,277,654 - 212,297,376 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12212,240,407 - 212,260,130 (-)NCBI
Celera2196,537,457 - 196,557,044 (-)NCBICelera
RH 3.4 Map21480.6RGD
Cytogenetic Map2q41NCBI
VCAM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1100,719,742 - 100,739,045 (+)EnsemblGRCh38hg38GRCh38
GRCh381100,719,742 - 100,739,045 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371101,185,298 - 101,204,601 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361100,957,885 - 100,977,189 (+)NCBINCBI36hg18NCBI36
Build 341100,897,317 - 100,916,620NCBI
Celera199,446,448 - 99,465,752 (+)NCBI
Cytogenetic Map1p21.2NCBI
HuRef199,309,886 - 99,329,291 (+)NCBIHuRef
CHM1_11101,301,307 - 101,320,707 (+)NCBICHM1_1
Vcam1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393115,903,669 - 115,923,337 (-)NCBIGRCm39mm39
GRCm39 Ensembl3115,903,598 - 115,923,337 (-)Ensembl
GRCm383116,110,020 - 116,129,688 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3116,109,949 - 116,129,688 (-)EnsemblGRCm38mm10GRCm38
MGSCv373115,812,938 - 115,832,606 (-)NCBIGRCm37mm9NCBIm37
MGSCv363116,102,024 - 116,121,692 (-)NCBImm8
Celera3122,538,966 - 122,558,635 (-)NCBICelera
Cytogenetic Map3G1NCBI
cM Map350.17NCBI
Vcam1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554355,390,751 - 5,411,691 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554355,390,745 - 5,410,025 (+)NCBIChiLan1.0ChiLan1.0
VCAM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11102,091,121 - 102,108,494 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1102,091,336 - 102,107,732 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01103,377,815 - 103,395,118 (+)NCBIMhudiblu_PPA_v0panPan3
VCAM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1649,341,669 - 49,359,841 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl649,342,151 - 49,359,933 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha652,013,558 - 52,031,171 (-)NCBI
ROS_Cfam_1.0649,686,812 - 49,704,968 (-)NCBI
UMICH_Zoey_3.1649,380,130 - 49,397,749 (-)NCBI
UNSW_CanFamBas_1.0649,359,940 - 49,377,559 (-)NCBI
UU_Cfam_GSD_1.0649,789,615 - 49,807,229 (-)NCBI
Vcam1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405058110,980,297 - 110,997,141 (+)NCBI
SpeTri2.0NW_004936748785,491 - 802,791 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VCAM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4117,496,908 - 117,511,226 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14117,496,914 - 117,511,211 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24129,040,268 - 129,054,581 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VCAM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12032,616,425 - 32,635,903 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2032,615,333 - 32,635,862 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603825,428,596 - 25,448,051 (+)NCBIVero_WHO_p1.0
Vcam1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248573,606,573 - 3,625,991 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
AW524920  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22204,038,603 - 204,038,765 (+)MAPPERmRatBN7.2
Rnor_6.02219,071,677 - 219,071,838NCBIRnor6.0
Rnor_5.02237,158,685 - 237,158,846UniSTSRnor5.0
RGSC_v3.42212,278,138 - 212,278,299UniSTSRGSC3.4
Celera2196,537,941 - 196,538,102UniSTS
RH 3.4 Map21478.8UniSTS
Cytogenetic Map2q41UniSTS
RH94527  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22204,038,424 - 204,038,568 (+)MAPPERmRatBN7.2
Rnor_6.02219,071,498 - 219,071,641NCBIRnor6.0
Rnor_5.02237,158,506 - 237,158,649UniSTSRnor5.0
RGSC_v3.42212,277,959 - 212,278,102UniSTSRGSC3.4
Celera2196,537,762 - 196,537,905UniSTS
RH 3.4 Map21480.6UniSTS
Cytogenetic Map2q41UniSTS
RH141550  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22204,038,215 - 204,038,431 (+)MAPPERmRatBN7.2
Rnor_6.02219,071,289 - 219,071,504NCBIRnor6.0
Rnor_5.02237,158,297 - 237,158,512UniSTSRnor5.0
RGSC_v3.42212,277,750 - 212,277,965UniSTSRGSC3.4
Celera2196,537,553 - 196,537,768UniSTS
RH 3.4 Map21482.9UniSTS
Cytogenetic Map2q41UniSTS
PMC209298P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22204,051,846 - 204,052,133 (+)MAPPERmRatBN7.2
Rnor_6.02219,091,699 - 219,091,985NCBIRnor6.0
Rnor_6.02219,084,924 - 219,085,210NCBIRnor6.0
Rnor_5.02237,171,682 - 237,171,968UniSTSRnor5.0
Rnor_5.02237,178,457 - 237,178,743UniSTSRnor5.0
RGSC_v3.42212,291,369 - 212,291,655UniSTSRGSC3.4
Celera2196,551,051 - 196,551,337UniSTS
Cytogenetic Map2q41UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61458Bp10Blood pressure QTL 103.42arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189020722215287351Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2143157029210020885Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168358098223265385Rat
1331745Bp203Blood pressure QTL 2034.377arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2189599258218414891Rat
1298083Bp158Blood pressure QTL 1582.62arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189020722215287351Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141194931223265385Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2141194931223265385Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2168594495213594495Rat
1581499Esta2Estrogen-induced thymic atrophy QTL 2thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2189599258226936289Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2184165752229165752Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561221167075Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
1598813Memor9Memory QTL 92.7exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2199341726234244620Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2200990457245990457Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166539266211539266Rat
2301408Kidm36Kidney mass QTL 360.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2190613715226808892Rat
2298479Eau5Experimental allergic uveoretinitis QTL 50.0021uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)2202446871237938339Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2179335906224335906Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2161699179222436696Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2136916935213594495Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2164073756227146641Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2157142078211086598Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2185876309219753474Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2185876309219753474Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2193452645245889826Rat
2293084Iddm26Insulin dependent diabetes mellitus QTL 262.9blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2174930955213594495Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2189599258234599258Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189599258234599258Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2179946951224946951Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2182171407227171407Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2182171407227171407Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2182171407227171407Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2160564068205564068Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2162765032207765032Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2157142078226277316Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2182171407227171407Rat


Related Rat Strains
The following Strains have been annotated to Vcam1

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:69
Count of miRNA genes:60
Interacting mature miRNAs:62
Transcripts:ENSRNOT00000019377
Prediction methods:Miranda
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 22 37 27 19 27 66 27 13 11
Low 1 21 20 14 14 8 11 8 8 28 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019377   ⟹   ENSRNOP00000019377
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2204,052,303 - 204,057,870 (-)Ensembl
Rnor_6.0 Ensembl2219,071,921 - 219,090,874 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077972   ⟹   ENSRNOP00000071676
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2204,038,114 - 204,057,958 (-)Ensembl
Rnor_6.0 Ensembl2219,071,208 - 219,094,730 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078806   ⟹   ENSRNOP00000071423
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2204,038,114 - 204,057,870 (-)Ensembl
Rnor_6.0 Ensembl2219,071,193 - 219,097,619 (-)Ensembl
RefSeq Acc Id: NM_012889   ⟹   NP_037021
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22204,038,120 - 204,057,852 (-)NCBI
Rnor_6.02219,071,193 - 219,090,931 (-)NCBI
Rnor_5.02237,158,192 - 237,177,779 (-)NCBI
RGSC_v3.42212,277,654 - 212,297,376 (-)RGD
Celera2196,537,457 - 196,557,044 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_037021 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA42332 (Get FASTA)   NCBI Sequence Viewer  
  AAH89812 (Get FASTA)   NCBI Sequence Viewer  
  CAA45254 (Get FASTA)   NCBI Sequence Viewer  
  EDL82023 (Get FASTA)   NCBI Sequence Viewer  
  P29534 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_037021   ⟸   NM_012889
- Peptide Label: precursor
- UniProtKB: P29534 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071676   ⟸   ENSRNOT00000077972
RefSeq Acc Id: ENSRNOP00000019377   ⟸   ENSRNOT00000019377
RefSeq Acc Id: ENSRNOP00000071423   ⟸   ENSRNOT00000078806
Protein Domains
Ig-like   Ig-like C2-type

Transcriptome

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

Promoters
RGD ID:13691702
Promoter ID:EPDNEW_R2227
Type:single initiation site
Name:Vcam1_2
Description:vascular cell adhesion molecule 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R2228  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02219,090,963 - 219,091,023EPDNEW
RGD ID:13691714
Promoter ID:EPDNEW_R2228
Type:single initiation site
Name:Vcam1_1
Description:vascular cell adhesion molecule 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R2227  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02219,097,651 - 219,097,711EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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
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)
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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
ACI/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
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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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
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)
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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
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)
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)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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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)
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)
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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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