Hmgb1 (high mobility group box 1) - Rat Genome Database

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Gene: Hmgb1 (high mobility group box 1) Rattus norvegicus
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Symbol: Hmgb1
Name: high mobility group box 1
RGD ID: 2802
Description: Enables several functions, including DNA binding activity; heparin binding activity; and signaling receptor binding activity. Involved in several processes, including positive regulation of cellular metabolic process; positive regulation of cytokine production; and response to bacterium. Located in several cellular components, including cytosol; extracellular space; and membrane raft. Used to study congestive heart failure; high grade glioma; myocardial infarction; pulmonary hypertension; and sciatic neuropathy. Biomarker of several diseases, including atherosclerosis; colon adenocarcinoma; hydrocephalus; middle cerebral artery infarction; and obstructive jaundice. Human ortholog(s) of this gene implicated in amyotrophic lateral sclerosis. Orthologous to human HMGB1 (high mobility group box 1); PARTICIPATES IN pro-inflammatory cytokine mediated pathway; cisplatin drug pathway; mismatch repair pathway; INTERACTS WITH (+)-pilocarpine; 1,2-dimethylhydrazine; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Ac2-008; Ac2-008-like; amphoterin; heparin-binding protein p30; high mobility group 1; high mobility group protein 1; high mobility group protein B1; HMG-1; Hmg1; LOC100361707; MGC93598; MGC93599
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Hmgb1-ps1   Hmgb1-ps2   Hmgb1-ps3   Hmgb1-ps4   LOC690117  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2125,973,062 - 5,978,565 (+)NCBI
Rnor_6.0 Ensembl1637,500,017 - 37,502,237 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0127,082,529 - 7,090,246 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0129,177,615 - 9,178,878 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.11637,462,230 - 37,464,451 (+)NCBI
Celera127,732,744 - 7,737,689 (+)NCBICelera
Cytogenetic Map12p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Acute Lung Injury  (IEP)
Acute-On-Chronic Liver Failure  (IMP)
Alzheimer's disease  (ISO)
amyotrophic lateral sclerosis  (ISO)
atherosclerosis  (IEP)
Brain Injuries  (IMP)
Burns  (IEP)
Cardiomegaly  (ISO)
cerebral infarction  (ISO)
Chemical and Drug Induced Liver Injury  (IEP,ISO)
Chronic Allograft Dysfunction  (IEP)
colon adenocarcinoma  (IEP)
congestive heart failure  (IMP,ISO)
Drug-Related Side Effects and Adverse Reactions  (ISO)
Endotoxemia  (IEP)
esophagus squamous cell carcinoma  (ISO)
Experimental Arthritis  (IEP)
Experimental Autoimmune Myocarditis  (IEP)
Experimental Diabetes Mellitus  (IEP)
Experimental Pancreatitis, Acute  (IMP)
extrahepatic cholestasis  (ISO)
Fever  (ISO)
Heat Stroke  (IEP)
high grade glioma  (IMP)
hydrocephalus  (IEP)
Hyperalgesia  (IEP,IMP,ISO)
hypertension  (ISO)
Inflammation  (ISO)
Intestinal Reperfusion Injury  (IEP)
Kawasaki disease  (ISO)
Knee Osteoarthritis  (ISO)
leukostasis  (ISO)
Liver Reperfusion Injury  (IEP,IMP)
Lung Reperfusion Injury  (IEP)
Lymphatic Metastasis  (IEP)
middle cerebral artery infarction  (IEP)
Multiple Organ Failure  (ISO)
myocardial infarction  (IDA,ISO)
Myocardial Ischemia  (ISO)
Myocardial Reperfusion Injury  (IDA,IEP,ISO)
Necrosis  (ISO)
Neuralgia  (ISO)
obstructive jaundice  (IEP)
osteoarthritis  (ISO)
Oxygen-Induced Retinopathy  (ISO)
Painful Neuropathy  (ISO)
periodontitis  (IEP)
Premature Aging  (ISO)
pulmonary fibrosis  (ISO)
pulmonary hypertension  (IMP)
Reperfusion Injury  (IMP)
Retina Reperfusion Injury  (IDA)
sciatic neuropathy  (IMP)
Sepsis  (IMP,ISO)
Spinal Cord Injuries  (IEP)
systemic scleroderma  (ISO)
Systemic Vasculitis  (ISO)
transient cerebral ischemia  (ISO)
Ventilator-Induced Lung Injury  (IMP)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2,6-dinitrotoluene  (EXP)
2-tert-butylhydroquinone  (ISO)
3,4-dihydroxybenzaldehyde  (EXP,ISO)
3-phenylprop-2-enal  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
acteoside  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
alendronic acid  (EXP)
ammonium chloride  (EXP)
ampicillin  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antirheumatic drug  (ISO)
apocynin  (ISO)
aristolochic acid  (ISO)
arsenous acid  (ISO)
astaxanthin  (ISO)
ATP  (ISO)
azathioprine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bis(2-chloroethyl) sulfide  (EXP)
bisphenol A  (EXP,ISO)
Bisphenol A diglycidyl ether  (EXP)
bleomycin A2  (EXP,ISO)
butyric acid  (ISO)
C60 fullerene  (ISO)
cadmium atom  (EXP)
caffeine  (ISO)
calciol  (EXP)
calcitriol  (EXP,ISO)
calycosin  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chlorpyrifos  (EXP)
chromium(6+)  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
corticosterone  (ISO)
Corynoxine B  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
curcumin  (EXP)
cyclosporin A  (ISO)
cytarabine  (ISO)
D-glucose  (ISO)
dapagliflozin  (EXP)
DAPT  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibenziodolium  (ISO)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (EXP)
diclofenac  (EXP,ISO)
dicloxacillin  (ISO)
dicrotophos  (ISO)
dienogest  (ISO)
dihydroartemisinin  (ISO)
Dihydrotanshinone I  (ISO)
dimethylarsinous acid  (ISO)
dioscin  (EXP)
dioxygen  (EXP,ISO)
doxorubicin  (EXP,ISO)
elemental selenium  (ISO)
enalapril  (EXP,ISO)
enalaprilat dihydrate  (EXP)
Enterolactone  (ISO)
enzyme inhibitor  (ISO)
Erionite  (ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
Ethyl pyruvate  (ISO)
etoposide  (ISO)
febuxostat  (EXP)
flucloxacillin  (ISO)
flutamide  (ISO)
folic acid  (ISO)
fulvestrant  (ISO)
furosemide  (EXP)
gadolinium trichloride  (EXP)
gallic acid  (ISO)
gamma-mangostin  (ISO)
Gastrodin  (EXP)
gefitinib  (ISO)
gentamycin  (EXP)
glucose  (ISO)
glycerol 2-phosphate  (ISO)
glycyrrhizinic acid  (EXP,ISO)
glyphosate  (ISO)
graphene oxide  (ISO)
halothane  (ISO)
hexadecanoic acid  (ISO)
Hexadimethrine bromide  (EXP)
hydrogen peroxide  (EXP,ISO)
ibuprofen  (ISO)
iodixanol  (EXP)
iohexol  (EXP)
ionomycin  (ISO)
isoflurane  (ISO)
isoquinoline-1,5-diol  (ISO)
kaempferol 3-O-beta-D-glucosyl-(1->2)-beta-D-glucoside  (ISO)
L-ascorbic acid  (ISO)
lead diacetate  (EXP)
lidocaine  (ISO)
lignan  (ISO)
lipopolysaccharide  (EXP,ISO)
lithium chloride  (EXP)
LY294002  (ISO)
lycopene  (ISO)
manganese(II) chloride  (ISO)
melatonin  (EXP)
mesalamine  (EXP)
metformin  (ISO)
methimazole  (EXP)
methyl methanesulfonate  (ISO)
methylparaben  (ISO)
monocrotaline  (EXP,ISO)
N-acetyl-L-cysteine  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
naphthalene  (ISO)
nitrososulfamethoxazole  (ISO)
o-anisidine  (ISO)
olaparib  (EXP)
oleanolic acid  (ISO)
oroxylin A  (EXP)
oxaliplatin  (EXP)
ozone  (EXP)
paclitaxel  (EXP,ISO)
paracetamol  (ISO)
paraquat  (EXP)
permethrin  (ISO)
phenytoin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
polymyxin B2  (ISO)
potassium chromate  (ISO)
potassium nitrate  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
Pyridostigmine bromide  (ISO)
pyrrolidine dithiocarbamate  (ISO)
quercetin  (ISO)
raloxifene  (EXP,ISO)
resveratrol  (ISO)
rosmarinic acid  (EXP)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP,ISO)
saxagliptin  (EXP)
SB 203580  (ISO)
selenium atom  (ISO)
serpentine asbestos  (ISO)
Sesamol  (ISO)
silicon dioxide  (ISO)
simvastatin  (EXP,ISO)
sodium arsenate  (ISO)
sorafenib  (ISO)
streptozocin  (ISO)
sulfasalazine  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
taurine  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP,ISO)
toluene 2,4-diisocyanate  (ISO)
topotecan  (EXP,ISO)
triptonide  (ISO)
troglitazone  (ISO)
uranium atom  (ISO)
valproic acid  (ISO)
vincaleukoblastine  (ISO)
vinclozolin  (EXP)
vincristine  (EXP,ISO)
vitamin E  (ISO)
wortmannin  (ISO)
zinc protoporphyrin  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
actin cytoskeleton reorganization  (IMP)
activation of innate immune response  (ISO)
activation of protein kinase activity  (IEA)
adaptive immune response  (IEA)
apoptotic cell clearance  (ISO,ISS)
autophagy  (IEA)
base-excision repair  (ISO)
cell morphogenesis  (IMP)
cellular response to interleukin-1  (IEP)
cellular response to interleukin-7  (ISO)
cellular response to lipopolysaccharide  (ISO)
chemotaxis  (IDA,IEA)
chromatin assembly  (ISO)
circadian rhythm  (IEP)
DNA geometric change  (IDA,ISS)
DNA recombination  (IEA)
DNA repair  (IEA)
double-strand break repair via nonhomologous end joining  (ISO)
endothelial cell chemotaxis  (ISO)
endothelial cell proliferation  (ISO)
eye development  (ISO)
gene silencing  (ISO)
induction of positive chemotaxis  (IDA)
inflammatory response  (IEA,ISO)
inflammatory response to antigenic stimulus  (ISO)
innate immune response  (IEA)
lung development  (ISO)
macrophage activation involved in immune response  (ISO)
male-specific defense response to bacterium  (IDA)
MyD88-dependent toll-like receptor signaling pathway  (ISO)
myeloid dendritic cell activation  (ISO)
myoblast proliferation  (IMP)
negative regulation of apoptotic cell clearance  (ISO)
negative regulation of blood vessel endothelial cell migration  (ISO)
negative regulation of CD4-positive, alpha-beta T cell differentiation  (ISO)
negative regulation of DNA replication  (IDA)
negative regulation of interferon-gamma production  (ISO)
negative regulation of RNA polymerase II transcription preinitiation complex assembly  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
nervous system development  (IMP)
neuron projection development  (IGI)
neutrophil clearance  (ISO,ISS)
nucleosome assembly  (ISO)
plasmacytoid dendritic cell activation  (ISO)
positive regulation of activated T cell proliferation  (ISO)
positive regulation of apoptotic process  (IMP,ISO)
positive regulation of autophagy  (IMP,ISO)
positive regulation of blood vessel endothelial cell migration  (ISO)
positive regulation of cell death  (IMP)
positive regulation of cell migration  (IDA)
positive regulation of cell population proliferation  (IDA)
positive regulation of chemokine (C-X-C motif) ligand 2 production  (ISO)
positive regulation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
positive regulation of cytosolic calcium ion concentration  (ISO)
positive regulation of dendritic cell differentiation  (ISO)
positive regulation of DNA binding  (ISO)
positive regulation of DNA ligase activity  (ISO)
positive regulation of DNA ligation  (IDA)
positive regulation of ERK1 and ERK2 cascade  (ISO)
positive regulation of glycogen catabolic process  (ISO)
positive regulation of innate immune response  (ISO)
positive regulation of interferon-alpha production  (ISO)
positive regulation of interferon-beta production  (ISO)
positive regulation of interleukin-1 beta production  (ISO)
positive regulation of interleukin-1 production  (IDA,ISO)
positive regulation of interleukin-10 production  (ISO)
positive regulation of interleukin-12 production  (ISO)
positive regulation of interleukin-6 production  (IDA,IMP,ISO)
positive regulation of interleukin-8 production  (IDA,ISO)
positive regulation of JNK cascade  (ISO)
positive regulation of macrophage inflammatory protein 1 alpha production  (IDA)
positive regulation of MAPK cascade  (ISO)
positive regulation of mesenchymal cell proliferation  (IDA)
positive regulation of mismatch repair  (ISO)
positive regulation of mitotic cell cycle  (IDA)
positive regulation of monocyte chemotactic protein-1 production  (ISO)
positive regulation of monocyte chemotaxis  (ISO)
positive regulation of myeloid cell apoptotic process  (IDA)
positive regulation of myeloid cell differentiation  (ISO)
positive regulation of myoblast differentiation  (IMP)
positive regulation of neuron projection development  (IMP)
positive regulation of NIK/NF-kappaB signaling  (ISO)
positive regulation of protein phosphorylation  (ISO)
positive regulation of smooth muscle cell migration  (IMP)
positive regulation of sprouting angiogenesis  (ISO)
positive regulation of toll-like receptor 2 signaling pathway  (ISO)
positive regulation of toll-like receptor 4 signaling pathway  (ISO)
positive regulation of toll-like receptor 9 signaling pathway  (ISS)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of tumor necrosis factor production  (IDA,IMP,ISO)
positive regulation of vascular endothelial cell proliferation  (ISO)
positive regulation of wound healing  (ISO)
protein-containing complex assembly  (IDA)
regulation of inflammatory response  (IDA)
regulation of nucleotide-excision repair  (ISO)
regulation of restriction endodeoxyribonuclease activity  (ISO)
regulation of T cell mediated immune response to tumor cell  (ISO,ISS)
regulation of tolerance induction  (ISO)
regulation of transcription by RNA polymerase II  (IBA,ISO)
response to glucocorticoid  (ISO)
response to glucose  (IEP)
response to heat  (IEP)
response to insulin  (IEP)
response to interferon-gamma  (IMP)
response to lipopolysaccharide  (IEP)
response to xenobiotic stimulus  (IEP)
signal transduction  (IEA)
T-helper 1 cell activation  (ISO)
T-helper 1 cell differentiation  (ISO)
toll-like receptor 2 signaling pathway  (ISO)
toll-like receptor 4 signaling pathway  (ISO)
V(D)J recombination  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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Additional References at PubMed
PMID:2461949   PMID:2465778   PMID:3571199   PMID:7635200   PMID:7741753   PMID:8006019   PMID:8339930   PMID:8467791   PMID:8527432   PMID:9166431   PMID:9600082   PMID:9767109  
PMID:10391216   PMID:10617144   PMID:11275566   PMID:11748232   PMID:11954836   PMID:11989650   PMID:12609598   PMID:12614161   PMID:12765338   PMID:12925773   PMID:14660645   PMID:15005629  
PMID:15014079   PMID:15140875   PMID:15489334   PMID:15499593   PMID:15743787   PMID:15899848   PMID:15944249   PMID:16267105   PMID:16365390   PMID:16419037   PMID:16854843   PMID:17043795  
PMID:17092418   PMID:17628015   PMID:17786958   PMID:17803946   PMID:17903370   PMID:17975839   PMID:17988686   PMID:18277947   PMID:18631454   PMID:18644848   PMID:18650382   PMID:18665051  
PMID:18768881   PMID:18790172   PMID:18984601   PMID:19158276   PMID:19166815   PMID:19223331   PMID:19264983   PMID:19302753   PMID:19401149   PMID:19435558   PMID:19494177   PMID:19546838  
PMID:19564572   PMID:19786932   PMID:19800306   PMID:19841752   PMID:19842550   PMID:19890330   PMID:19997973   PMID:20107953   PMID:20231821   PMID:20392563   PMID:20399746   PMID:20691192  
PMID:20693722   PMID:20703492   PMID:20819940   PMID:20826760   PMID:21069420   PMID:21113057   PMID:21217446   PMID:21248133   PMID:21343866   PMID:21606643   PMID:21632128   PMID:21640719  
PMID:21642503   PMID:21647302   PMID:21660935   PMID:21756762   PMID:21772666   PMID:21872885   PMID:22039322   PMID:22246807   PMID:22370717   PMID:22473704   PMID:22494911   PMID:22529378  
PMID:22658674   PMID:22681889   PMID:22857898   PMID:22871113   PMID:23036589   PMID:23069071   PMID:23078219   PMID:23085216   PMID:23108142   PMID:23146691   PMID:23148224   PMID:23208066  
PMID:23364923   PMID:23532259   PMID:23628899   PMID:23714159   PMID:23769041   PMID:23861108   PMID:23884820   PMID:23895427   PMID:23974442   PMID:24004409   PMID:24012767   PMID:24133029  
PMID:24178442   PMID:24335635   PMID:24338536   PMID:24480450   PMID:24551219   PMID:24603876   PMID:24733965   PMID:24748429   PMID:24924349   PMID:24937603   PMID:24970310   PMID:24971542  
PMID:25004875   PMID:25014009   PMID:25062563   PMID:25194125   PMID:25228632   PMID:25292258   PMID:25420924   PMID:25446104   PMID:25510912   PMID:25538203   PMID:25568124   PMID:25736854  
PMID:25772012   PMID:25931416   PMID:25956731   PMID:26033363   PMID:26143914   PMID:26241550   PMID:26254235   PMID:26261566   PMID:26261580   PMID:26312770   PMID:26337661   PMID:26398163  
PMID:26406975   PMID:26513053   PMID:26524701   PMID:26565401   PMID:26648172   PMID:26705737   PMID:26722388   PMID:26765765   PMID:26782432   PMID:26806574   PMID:26822891   PMID:26857094  
PMID:26884873   PMID:26899371   PMID:26945830   PMID:26946264   PMID:26950148   PMID:26956363   PMID:26961863   PMID:27044405   PMID:27121079   PMID:27363991   PMID:27412936   PMID:27466339  
PMID:27544687   PMID:27579780   PMID:27599553   PMID:27666823   PMID:27704212   PMID:27760316   PMID:27821807   PMID:27878276   PMID:27889435   PMID:27997923   PMID:28036116   PMID:28050559  
PMID:28089662   PMID:28096568   PMID:28222432   PMID:28275217   PMID:28276476   PMID:28484719   PMID:28571757   PMID:28606778   PMID:28627626   PMID:28645008   PMID:28647749   PMID:28695466  
PMID:28699371   PMID:28882317   PMID:28887039   PMID:29117064   PMID:29178911   PMID:29329282   PMID:29448108   PMID:29478057   PMID:29581031   PMID:29633273   PMID:29715512   PMID:29884910  
PMID:29891998   PMID:29930087   PMID:29959419   PMID:30111205   PMID:30130540   PMID:30133517   PMID:30145795   PMID:30217406   PMID:30269353   PMID:30337736   PMID:30338842   PMID:30391757  
PMID:30392294   PMID:30395883   PMID:30417405   PMID:30480814   PMID:30517029   PMID:30610955   PMID:30840287   PMID:30867070   PMID:31003767   PMID:31041919   PMID:31056833   PMID:31078691  
PMID:31136947   PMID:31138780   PMID:31162822   PMID:31197745   PMID:31255677   PMID:31344138   PMID:31421824   PMID:31466775   PMID:31489582   PMID:31524228   PMID:31646380   PMID:31801411  
PMID:31809304   PMID:31816325   PMID:31858563   PMID:31879851   PMID:31886244   PMID:32208365   PMID:32373982   PMID:32389703   PMID:32417325   PMID:32596881   PMID:32678819   PMID:32833553  
PMID:33051415   PMID:33281190   PMID:33287126   PMID:33300062   PMID:33398367   PMID:33503060   PMID:33668863   PMID:33948998  


Genomics

Comparative Map Data
Hmgb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2125,973,062 - 5,978,565 (+)NCBI
Rnor_6.0 Ensembl1637,500,017 - 37,502,237 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0127,082,529 - 7,090,246 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0129,177,615 - 9,178,878 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.11637,462,230 - 37,464,451 (+)NCBI
Celera127,732,744 - 7,737,689 (+)NCBICelera
Cytogenetic Map12p11NCBI
HMGB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1330,456,704 - 30,617,597 (-)EnsemblGRCh38hg38GRCh38
GRCh381330,456,704 - 30,617,597 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371331,030,841 - 31,191,734 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361329,930,877 - 29,938,081 (-)NCBINCBI36hg18NCBI36
Celera1312,102,423 - 12,109,630 (-)NCBI
Cytogenetic Map13q12.3NCBI
HuRef1311,850,667 - 11,857,904 (-)NCBIHuRef
CHM1_11331,000,434 - 31,007,630 (-)NCBICHM1_1
Hmgb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395148,983,512 - 148,989,867 (-)NCBIGRCm39mm39
GRCm39 Ensembl5148,983,512 - 149,121,299 (-)Ensembl
GRCm385149,046,702 - 149,053,057 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5149,046,702 - 149,184,489 (-)EnsemblGRCm38mm10GRCm38
MGSCv375149,858,803 - 149,864,613 (-)NCBIGRCm37mm9NCBIm37
MGSCv365149,357,579 - 149,363,386 (-)NCBImm8
Celera5147,061,615 - 147,067,633 (-)NCBICelera
Cytogenetic Map5G3NCBI
cM Map589.18NCBI
Hmgb1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543115,373,207 - 15,377,339 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543115,373,207 - 15,377,339 (+)NCBIChiLan1.0ChiLan1.0
HMGB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11330,173,875 - 30,179,527 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1330,174,899 - 30,179,527 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01311,737,942 - 11,894,923 (-)NCBIMhudiblu_PPA_v0panPan3
HMGB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1259,431,223 - 9,558,167 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl259,431,218 - 9,558,165 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha259,596,948 - 9,603,279 (+)NCBI
ROS_Cfam_1.0259,542,952 - 9,670,011 (+)NCBI
UMICH_Zoey_3.1259,558,389 - 9,564,743 (+)NCBI
UNSW_CanFamBas_1.0259,566,227 - 9,572,605 (+)NCBI
UU_Cfam_GSD_1.0259,608,257 - 9,614,621 (+)NCBI
Hmgb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945170,705,559 - 170,715,427 (+)NCBI
SpeTri2.0NW_00493647225,236,728 - 25,246,585 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HMGB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1117,195,556 - 7,321,071 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2117,006,105 - 7,131,947 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HMGB1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.139,353,333 - 9,357,765 (-)NCBI
Vero_WHO_p1.0NW_02366605735,008,842 - 35,015,311 (+)NCBI
Hmgb1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247767,858,400 - 7,862,716 (+)NCBI

Position Markers
RH130603  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map12p11UniSTS
BE097853  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2125,978,946 - 5,979,110 (+)MAPPER
Rnor_6.0127,092,572 - 7,092,735NCBIRnor6.0
Rnor_6.0127,090,628 - 7,090,791NCBIRnor6.0
Rnor_5.0129,179,260 - 9,179,423UniSTSRnor5.0
Rnor_5.0129,177,316 - 9,177,479UniSTSRnor5.0
RGSC_v3.4126,480,818 - 6,480,981UniSTSRGSC3.4
Celera127,738,071 - 7,738,234UniSTS
RH 3.4 Map1242.3UniSTS
Cytogenetic Map12p11UniSTS
Hmgb1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0129,173,110 - 9,173,476NCBIRnor5.0
RGSC_v3.4126,476,220 - 6,476,585UniSTSRGSC3.4
Celera127,735,031 - 7,735,396UniSTS
Cytogenetic Map12p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300174Bw15Body weight QTL 152.93body mass (VT:0001259)body weight loss (CMO:0001399)12111765163Rat
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12122650917Rat
10450854Stl34Serum triglyceride level QTL 343.50.05blood LDL triglyceride amount (VT:0010699)blood lipoprotein triglyceride level (CMO:0002685)12122853017Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12123035872Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123758197Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12130749723Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12136919844Rat
7387292Kidm42Kidney mass QTL 423.030.0004kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)12138334225Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)1215081045150810Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1215081045150810Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)1249257845492578Rat
7243862Mcs30Mammary carcinoma susceptibility QTL 308.62mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)12125813910257059Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12247568747475687Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12251344247513442Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12251344247513442Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12421005149210051Rat
724526Uae3Urinary albumin excretion QTL 34.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)12540609412355490Rat


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 39 11 8
Low 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000081634   ⟹   ENSRNOP00000069851
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1637,500,017 - 37,502,237 (+)Ensembl
RefSeq Acc Id: NM_012963   ⟹   NP_037095
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2125,973,062 - 5,978,565 (+)NCBI
Rnor_6.0127,082,529 - 7,090,246 (+)NCBI
Rnor_5.0129,177,615 - 9,178,878 (+)NCBI
Celera127,732,744 - 7,737,689 (+)RGD
Sequence:
RefSeq Acc Id: XM_039089111   ⟹   XP_038945039
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2125,973,474 - 5,978,565 (+)NCBI
RefSeq Acc Id: XM_039089112   ⟹   XP_038945040
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2125,974,235 - 5,978,565 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_037095   ⟸   NM_012963
- UniProtKB: P63159 (UniProtKB/Swiss-Prot),   B4F758 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069851   ⟸   ENSRNOT00000081634
RefSeq Acc Id: XP_038945039   ⟸   XM_039089111
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038945040   ⟸   XM_039089112
- Peptide Label: isoform X2
Protein Domains
HMG box

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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 (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/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 (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)
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
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
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/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
LE/Stm (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/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
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
LL/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
LN/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
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
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 (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
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (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 (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2802 AgrOrtholog
Ensembl Genes ENSRNOG00000058908 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000069851 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000081634 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro HMG_box_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_boxA_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMGB1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25459 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 25459 ENTREZGENE
PANTHER PTHR48112:SF4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam HMG_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_box_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB HMGB1 RGD
PhenoGen Hmgb1 PhenoGen
PROSITE HMG_BOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_BOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HMG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47095 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B4F758 ENTREZGENE, UniProtKB/TrEMBL
  D3ZXR5_RAT UniProtKB/TrEMBL
  HMGB1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary P07155 UniProtKB/Swiss-Prot
  P27109 UniProtKB/Swiss-Prot
  P27428 UniProtKB/Swiss-Prot
  Q548R9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-29 Hmgb1  high mobility group box 1  LOC100361707  Ac2-008-like  Data Merged 737654 PROVISIONAL
2010-05-05 LOC100361707  Ac2-008-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-02-27 Hmgb1  high mobility group box 1      Symbol and Name updated to reflect Human and Mouse nomenclature 70292 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to plasma membrane filopodia in actively spreading cells 728426