RT1-Db1 (RT1 class II, locus Db1) - Rat Genome Database

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Gene: RT1-Db1 (RT1 class II, locus Db1) Rattus norvegicus
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Symbol: RT1-Db1
Name: RT1 class II, locus Db1
RGD ID: 1593282
Description: Predicted to enable several functions, including MHC class II receptor activity; peptide antigen binding activity; and signaling receptor binding activity. Involved in response to dexamethasone. Predicted to be located in external side of plasma membrane and immunological synapse. Predicted to be part of MHC class II protein complex. Predicted to be active in late endosome membrane and lysosomal membrane. Human ortholog(s) of this gene implicated in several diseases, including asthma (multiple); autoimmune disease (multiple); bacterial infectious disease (multiple); eye disease (multiple); and sarcoidosis (multiple). Orthologous to several human genes including HLA-DRB1 (major histocompatibility complex, class II, DR beta 1); PARTICIPATES IN interleukin-12 signaling pathway; allograft rejection pathway; antigen processing and presentation pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Db1; MGC105710; MHC class II RT1D beta1 chain antigen; rano class II histocompatibility antigen, D-1 beta chain; RT1 class II histocompatibility antigen, D-1 beta chain; RT1 class II, locus Db1 (mapped); RT1-D beta; RT1-Db; RT1-Db1_mapped; RT1-Db1n
RGD Orthologs
Human
Mouse
Dog
Alliance Genes
More Info more info ...
Is Marker For: Strains:   DA.KHW-(RT1-Db1-RT1-DMb)  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,548,664 - 4,558,237 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl204,548,666 - 4,558,258 (-)Ensembl
Rnor_6.0204,087,621 - 4,097,190 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,087,618 - 4,097,190 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,167,759 - 6,177,328 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,671,489 - 4,681,058 (-)NCBIRGSC3.4rn4RGSC3.4
Celera206,150,824 - 6,160,393 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
abdominal aortic aneurysm  (ISO)
Actinic Prurigo  (ISO)
acute disseminated encephalomyelitis  (ISO)
Addison's disease  (ISO)
allergic asthma  (ISO)
allergic bronchopulmonary aspergillosis  (ISO)
allergic disease  (ISO)
Alport syndrome  (ISO)
alveolar echinococcosis  (ISO)
Alzheimer's disease  (ISO)
Amebic Liver Abscess  (ISO)
angioedema  (ISO)
ankylosing spondylitis  (ISO)
anti-basement membrane glomerulonephritis  (ISO)
antiphospholipid syndrome  (ISO)
aspirin-induced respiratory disease  (ISO)
asthma  (ISO)
atrophic gastritis  (ISO)
autistic disorder  (ISO)
autoimmune disease  (ISO)
autoimmune hepatitis  (ISO)
autoimmune polyendocrine syndrome  (ISO)
autoimmune polyendocrine syndrome type 2  (ISO)
autoimmune thrombocytopenic purpura  (ISO)
autoimmune thyroiditis  (ISO)
bacterial infectious disease  (ISO)
Behcet's disease  (ISO)
berylliosis  (ISO)
breast cancer  (ISO)
breast carcinoma  (ISO)
celiac disease  (ISO)
cervix uteri carcinoma in situ  (ISO)
Chagas Cardiomyopathy  (ISO)
Chagas disease  (ISO)
Chemical and Drug Induced Liver Injury  (ISO)
choreatic disease  (ISO)
Chronic Hepatitis B  (ISO)
Chronic Hepatitis C  (ISO)
cicatricial pemphigoid  (ISO)
COVID-19  (ISO)
Crohn's disease  (ISO)
cystic echinococcosis  (ISO)
diabetic angiopathy  (ISO)
diabetic retinopathy  (ISO)
drug allergy  (ISO)
End Stage Liver Disease  (ISO)
endometriosis  (ISO)
eosinophilia-myalgia syndrome  (ISO)
Experimental Arthritis  (ISO)
Experimental Autoimmune Encephalomyelitis  (ISO)
Experimental Liver Cirrhosis  (EXP)
Germ Cell and Embryonal Neoplasms  (ISO)
glaucoma  (ISO)
Graves' disease  (ISO)
Hantavirus hemorrhagic fever with renal syndrome  (ISO)
Hashimoto Disease  (ISO)
Helicobacter Infections  (ISO)
hepatitis C  (ISO)
HIV Seropositivity  (ISO)
human immunodeficiency virus infectious disease  (ISO)
Human Influenza  (ISO)
hypothyroidism  (ISO)
Idiopathic Hypersomnolence  (ISO)
idiopathic pulmonary fibrosis  (ISO)
infectious mononucleosis  (ISO)
Juvenile Pauciarticular Chronic Arthritis  (ISO)
juvenile rheumatoid arthritis  (ISO)
latex allergy  (ISO)
leprosy  (ISO)
liver cirrhosis  (ISO)
lupus nephritis  (ISO)
membranous glomerulonephritis  (ISO)
Meniere's disease  (ISO)
mixed connective tissue disease  (ISO)
Multibacillary Leprosy  (ISO)
multidrug-resistant tuberculosis  (ISO)
multiple sclerosis  (ISO)
myasthenia gravis  (ISO)
Mycobacterium Infections  (ISO)
myositis  (ISO)
narcolepsy  (ISO)
Nasal Polyps  (ISO)
nephrotic syndrome  (ISO)
neuromyelitis optica  (ISO)
non-Hodgkin lymphoma  (ISO)
optic neuritis  (ISO)
Oropharyngeal Neoplasms  (ISO)
Ovarian Neoplasms  (ISO)
pancreatitis  (ISO)
papillomavirus infectious disease  (ISO)
paracoccidioidomycosis  (ISO)
Parkinson's disease  (ISO)
pemphigus  (ISO)
peptic ulcer disease  (ISO)
PERITONEAL GLIOMATOSIS  (ISO)
Pneumocystis Infections  (IEP)
polyneuropathy  (ISO)
primary progressive multiple sclerosis  (ISO)
prostate cancer  (ISO)
proteinuria  (ISO)
pulmonary sarcoidosis  (ISO)
pulmonary tuberculosis  (ISO)
pure red-cell aplasia  (ISO)
Recurrent Respiratory Papillomatosis  (ISO)
renal cell carcinoma  (ISO)
retinopathy of prematurity  (ISO)
rheumatic fever  (ISO)
rheumatic heart disease  (ISO)
rheumatoid arthritis  (ISO)
sarcoidosis  (ISO)
schistosomiasis  (ISO)
schizophrenia  (ISO)
sensorineural hearing loss  (ISO)
severe acute respiratory syndrome  (ISO)
Sjogren's syndrome  (ISO)
Stroke  (ISO)
Sudden Hearing Loss  (ISO)
sympathetic ophthalmia  (ISO)
systemic lupus erythematosus  (ISO)
temporal arteritis  (ISO)
toxic shock syndrome  (ISO)
Trichiasis  (ISO)
tuberculosis  (ISO)
Tubulointerstitial Nephritis and Uveitis  (ISO)
type 1 diabetes mellitus  (ISO)
typhoid fever  (ISO)
ulcerative colitis  (ISO)
urticaria  (ISO)
Uterine Cervical Neoplasms  (ISO)
uveitis  (ISO)
uveoparotid fever  (ISO)
visceral leishmaniasis  (ISO)
vitiligo  (ISO)
Vogt-Koyanagi-Harada disease  (ISO)
vulva cancer  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2-hydroxypropanoic acid  (ISO)
3,7-dihydropurine-6-thione  (EXP,ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
acetylsalicylic acid  (ISO)
acrylamide  (EXP)
amitriptyline  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
auranofin  (ISO)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
beryllium sulfate  (ISO)
bexarotene  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
C60 fullerene  (ISO)
cadmium dichloride  (EXP,ISO)
carbon nanotube  (ISO)
cefepime  (ISO)
celecoxib  (ISO)
choline  (ISO)
ciprofloxacin  (ISO)
clindamycin  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
Cuprizon  (EXP)
cyclosporin A  (ISO)
D-penicillamine  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
dichloromethane  (EXP)
diclofenac  (ISO)
diethylstilbestrol  (ISO)
diltiazem  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
EC 3.4.15.1 (peptidyl-dipeptidase A) inhibitor  (ISO)
ethylbenzene  (EXP)
fenofibrate  (ISO)
ferric oxide  (ISO)
flutamide  (EXP)
gefitinib  (ISO)
genistein  (ISO)
gentamycin  (EXP)
hexachlorobenzene  (EXP)
hydrochlorothiazide  (ISO)
irinotecan  (ISO)
iron atom  (EXP)
iron(0)  (EXP)
isoprenaline  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lumiracoxib  (ISO)
mercaptopurine  (EXP,ISO)
metronidazole  (ISO)
monosodium L-glutamate  (EXP)
N-(6-acetamidohexyl)acetamide  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
nickel atom  (ISO)
nitric oxide  (ISO)
oxaliplatin  (EXP)
ozone  (EXP,ISO)
palladium  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
PCB138  (EXP)
pirinixic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (ISO)
purine-6-thiol  (EXP,ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
S-adenosyl-L-methioninate  (ISO)
S-adenosyl-L-methionine  (ISO)
succimer  (ISO)
tamoxifen  (EXP,ISO)
temozolomide  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
tremolite asbestos  (ISO)
Tributyltin oxide  (EXP)
trichloroethene  (EXP)
triclosan  (ISO)
triphenyl phosphate  (EXP)
triptonide  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adaptive immune response  (IEA)
antigen processing and presentation of endogenous peptide antigen via MHC class II  (ISO)
antigen processing and presentation of exogenous peptide antigen via MHC class II  (IBA,ISO)
antigen processing and presentation of peptide or polysaccharide antigen via MHC class II  (IEA)
detection of bacterium  (ISO)
humoral immune response  (ISO)
immune response  (ISO)
inflammatory response to antigenic stimulus  (ISO)
macrophage differentiation  (ISO)
myeloid dendritic cell antigen processing and presentation  (ISO)
negative regulation of inflammatory response to antigenic stimulus  (ISO)
negative regulation of interferon-gamma production  (ISO)
negative regulation of T cell proliferation  (ISO)
peptide antigen assembly with MHC class II protein complex  (IBA,ISO)
positive regulation of CD4-positive, alpha-beta T cell activation  (ISO)
positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation  (ISO)
positive regulation of ERK1 and ERK2 cascade  (ISO)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (ISO)
positive regulation of insulin secretion involved in cellular response to glucose stimulus  (ISO)
positive regulation of kinase activity  (ISO)
positive regulation of MAPK cascade  (ISO)
positive regulation of memory T cell differentiation  (ISO)
positive regulation of monocyte differentiation  (ISO)
positive regulation of protein phosphorylation  (ISO)
positive regulation of T cell activation  (IBA)
positive regulation of T cell mediated cytotoxicity  (ISO)
positive regulation of T cell mediated immune response to tumor cell  (ISO)
positive regulation of transcription, DNA-templated  (ISO)
positive regulation of viral entry into host cell  (ISO)
protein tetramerization  (ISO)
regulation of interleukin-10 production  (ISO)
regulation of interleukin-4 production  (ISO)
regulation of T-helper cell differentiation  (ISO)
response to dexamethasone  (IEP)
response to interferon-gamma  (ISO)
response to organic substance  (IEP)
signal transduction  (ISO)
T cell receptor signaling pathway  (ISO)
T-helper 1 type immune response  (ISO)

Cellular Component

References

References - curated
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125. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
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Additional References at PubMed
PMID:1300424   PMID:1448172   PMID:2388838   PMID:7477400   PMID:7606781   PMID:9354468   PMID:9745012   PMID:10369938   PMID:11027433   PMID:11465104   PMID:11714799   PMID:12136338  
PMID:12477932   PMID:12519789   PMID:15517241   PMID:15795121   PMID:16502470   PMID:18039812   PMID:18305173   PMID:19946888   PMID:20458337   PMID:20543955   PMID:21484216   PMID:21502329  
PMID:22321387   PMID:22733780   PMID:23376485   PMID:24586191   PMID:24942581  


Genomics

Comparative Map Data
RT1-Db1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,548,664 - 4,558,237 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl204,548,666 - 4,558,258 (-)Ensembl
Rnor_6.0204,087,621 - 4,097,190 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,087,618 - 4,097,190 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,167,759 - 6,177,328 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,671,489 - 4,681,058 (-)NCBIRGSC3.4rn4RGSC3.4
Celera206,150,824 - 6,160,393 (-)NCBICelera
Cytogenetic Map20p12NCBI
HLA-DRB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl632,578,769 - 32,589,848 (-)EnsemblGRCh38hg38GRCh38
GRCh38632,578,775 - 32,589,848 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37632,546,552 - 32,557,625 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36632,654,527 - 32,665,559 (-)NCBINCBI36hg18NCBI36
Build 34632,654,526 - 32,665,559NCBI
Cytogenetic Map6p21.32NCBI
CHM1_1632,549,025 - 32,560,089 (-)NCBICHM1_1
H2-Eb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391734,524,841 - 34,535,648 (+)NCBIGRCm39mm39
GRCm39 Ensembl1734,524,841 - 34,535,648 (+)Ensembl
GRCm381734,305,867 - 34,316,674 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1734,305,867 - 34,316,674 (+)EnsemblGRCm38mm10GRCm38
MGSCv371734,442,812 - 34,453,619 (+)NCBIGRCm37mm9NCBIm37
MGSCv361733,913,637 - 33,923,895 (+)NCBImm8
Celera1737,067,715 - 37,078,914 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1717.98NCBI
HLA-DRB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1122,151,409 - 2,164,564 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha122,300,636 - 2,313,266 (-)NCBI
ROS_Cfam_1.0122,427,792 - 2,440,407 (-)NCBI
UMICH_Zoey_3.1122,150,930 - 2,163,511 (-)NCBI
UNSW_CanFamBas_1.0122,232,117 - 2,244,754 (-)NCBI
UU_Cfam_GSD_1.0122,306,389 - 2,319,034 (-)NCBI


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2026463954597031Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2026463954597031Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
737973Pia21Pristane induced arthritis QTL 214.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2036216564606812Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
7175099Tcs2T cell selection QTL 2T cell selectionexpression2045025574693102Rat


Related Rat Strains
The following Strains have been annotated to RT1-Db1

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:270
Count of miRNA genes:148
Interacting mature miRNAs:163
Transcripts:ENSRNOT00000000522, ENSRNOT00000060327
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 4 23 9 19 9 2 18 9 11
Low 19 18 16 16 8 9 25 11 21 8
Below cutoff 18 16 16 16 39 6 11

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001008884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF084933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF246657 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ003231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ003234 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626207 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC087691 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX883043 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO563535 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CV111238 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223232 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225193 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226724 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226759 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226850 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227087 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228124 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228129 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231387 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231709 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232100 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232453 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233335 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233396 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233800 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233801 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234464 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234881 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234907 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC222950 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X53054 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000000522   ⟹   ENSRNOP00000000522
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,548,666 - 4,558,237 (-)Ensembl
Rnor_6.0 Ensembl204,087,618 - 4,097,090 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000060327   ⟹   ENSRNOP00000057075
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,549,323 - 4,558,240 (-)Ensembl
Rnor_6.0 Ensembl204,087,644 - 4,097,089 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078507
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,094,738 - 4,097,078 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080091
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,556,337 - 4,558,165 (-)Ensembl
Rnor_6.0 Ensembl204,087,693 - 4,089,521 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080590   ⟹   ENSRNOP00000069704
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,549,323 - 4,558,240 (-)Ensembl
Rnor_6.0 Ensembl204,087,685 - 4,096,777 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000086298
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,096,432 - 4,097,190 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089182
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,087,687 - 4,092,207 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090791
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,087,703 - 4,092,325 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113681   ⟹   ENSRNOP00000080217
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,548,666 - 4,558,258 (-)Ensembl
RefSeq Acc Id: NM_001008884   ⟹   NP_001008884
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,548,664 - 4,558,237 (-)NCBI
Rnor_6.0204,087,621 - 4,097,190 (+)NCBI
Rnor_5.0206,167,759 - 6,177,328 (+)NCBI
RGSC_v3.4204,671,489 - 4,681,058 (-)RGD
Celera206,150,824 - 6,160,393 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001008884   ⟸   NM_001008884
- Peptide Label: precursor
- UniProtKB: Q9TQA6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069704   ⟸   ENSRNOT00000080590
RefSeq Acc Id: ENSRNOP00000000522   ⟸   ENSRNOT00000000522
RefSeq Acc Id: ENSRNOP00000057075   ⟸   ENSRNOT00000060327
RefSeq Acc Id: ENSRNOP00000080217   ⟸   ENSRNOT00000113681
Protein Domains
Ig-like   Ig-like C1-type

Transcriptome

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

Promoters
RGD ID:13701330
Promoter ID:EPDNEW_R11853
Type:initiation region
Name:RT1-Db1_1
Description:RT1 class II, locus Db1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0204,087,633 - 4,087,693EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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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)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1593282 AgrOrtholog
Ensembl Genes ENSRNOG00000033215 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000522 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000057075 UniProtKB/TrEMBL
  ENSRNOP00000069704 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000522 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000060327 UniProtKB/TrEMBL
  ENSRNOT00000080590 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.10.320.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7310949 IMAGE-MGC_LOAD
InterPro Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig/MHC_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_C1-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_I/II-like_Ag-recog UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_II_a/b_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_II_b_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:294270 UniProtKB/TrEMBL
MGC_CLONE MGC:105710 IMAGE-MGC_LOAD
NCBI Gene 294270 ENTREZGENE
Pfam C1-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_II_beta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB HLA-DRB1 RGD
PhenoGen RT1-Db1 PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_MHC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART IGc1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_II_beta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54452 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JW17_RAT UniProtKB/TrEMBL
  F1M7F9_RAT UniProtKB/TrEMBL
  HB2D_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q5M933_RAT UniProtKB/TrEMBL
  Q9TQA6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-04-12 RT1-Db1  RT1 class II, locus Db1  RT1-Db1_mapped  RT1 class II, locus Db1 (mapped)  Data Merged 737654 APPROVED
2006-11-20 RT1-Db1_mapped  RT1 class II, locus Db1(mapped)  RT1-Db1  RT1 class II, locus Db1  Symbol set to symbol_mapped, name set to name (mapped) 1582166 APPROVED
2006-11-20 RT1-Db1  RT1 class II, locus Db1      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-02-11 RT1-Db1  RT1 class II, locus Db1      Symbol and Name status set to approved 625702 APPROVED
2002-06-10 RT1-Db1  RT1 class II, locus Db1      Symbol and Name status set to approved 70586 APPROVED