Grin2b (glutamate ionotropic receptor NMDA type subunit 2B) - Rat Genome Database

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Gene: Grin2b (glutamate ionotropic receptor NMDA type subunit 2B) Rattus norvegicus
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Symbol: Grin2b
Name: glutamate ionotropic receptor NMDA type subunit 2B
RGD ID: 2738
Description: Enables several functions, including beta-catenin binding activity; extracellular ligand-gated ion channel activity; and signaling receptor binding activity. Involved in several processes, including cellular response to organic cyclic compound; learning or memory; and pallium development. Located in several cellular components, including dendrite; hippocampal mossy fiber to CA3 synapse; and synaptic cleft. Is integral component of postsynaptic density membrane and integral component of presynaptic membrane. Part of NMDA selective glutamate receptor complex. Is active in parallel fiber to Purkinje cell synapse. Used to study attention deficit hyperactivity disorder; fetal alcohol spectrum disorder; and hyperhomocysteinemia. Biomarker of several diseases, including attention deficit hyperactivity disorder; cognitive disorder (multiple); hypoglycemia; placental insufficiency; and sciatic neuropathy. Human ortholog(s) of this gene implicated in several diseases, including alcohol use disorder; autosomal dominant non-syndromic intellectual disability 6; bipolar disorder; developmental and epileptic encephalopathy 27; and neurodegenerative disease (multiple). Orthologous to human GRIN2B (glutamate ionotropic receptor NMDA type subunit 2B); PARTICIPATES IN excitatory synaptic transmission pathway; long term potentiation; calcium/calmodulin dependent kinase 2 signaling pathway; INTERACTS WITH (+)-pilocarpine; 1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: GluN2B; glutamate [NMDA] receptor subunit epsilon-2; Glutamate receptor ionotropic N-methyl D-aspartate 2B; glutamate receptor ionotropic, NMDA 2B; glutamate receptor, ionotropic, N-methyl D-aspartate 2B; glutamate receptor, ionotropic, NMDA2B; N-methyl D-aspartate receptor subtype 2B; NMDAR2B; NR2B
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Grin2bem1Mcwi  
Genetic Models: LE-Grin2bem1Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24168,580,824 - 169,044,110 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4168,599,546 - 169,042,279 (-)Ensembl
Rnor_6.04169,541,620 - 170,000,216 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4169,560,387 - 169,999,873 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04233,806,406 - 234,260,360 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44172,721,895 - 173,183,187 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14172,966,830 - 173,428,311 (-)NCBI
Celera4157,188,514 - 157,629,365 (-)NCBICelera
RH 3.4 Map41026.8RGD
Cytogenetic Map4q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3',5'-cyclic AMP  (ISO)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
3,5,6-trichloro-2-pyridinol  (ISO)
3,5,6-trichloropyridine-2-one  (ISO)
3-phenoxybenzoic acid  (ISO)
4-[1-hydroxy-2-[4-(phenylmethyl)-1-piperidinyl]propyl]phenol  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
ammonium acetate  (EXP)
ammonium chloride  (ISO)
amphetamine  (EXP)
arsenite(3-)  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
Butylbenzyl phthalate  (ISO)
Butylparaben  (EXP)
capsaicin  (EXP)
capsazepine  (EXP)
carbaryl  (EXP)
carbon dioxide  (EXP)
carbon nanotube  (EXP)
celecoxib  (ISO)
chaetocin  (EXP)
chloroquine  (EXP)
chlorpyrifos  (EXP)
choline  (EXP)
citalopram  (EXP)
clozapine  (EXP)
cocaine  (EXP)
colforsin daropate hydrochloride  (EXP)
crocidolite asbestos  (ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP)
DDE  (EXP,ISO)
decabromodiphenyl ether  (EXP,ISO)
dexamethasone  (EXP)
dextran sulfate  (ISO)
dextromethorphan  (EXP)
diazinon  (EXP,ISO)
dibutyl phthalate  (EXP,ISO)
dieldrin  (EXP)
diethyl phthalate  (ISO)
Diisodecyl phthalate  (ISO)
diminazene diaceturate  (ISO)
dioxygen  (EXP)
dizocilpine maleate  (EXP,ISO)
endosulfan  (EXP)
enzacamene  (EXP)
epoxiconazole  (EXP)
ethanol  (EXP,ISO)
excitatory amino acid agonist  (ISO)
felbamate  (EXP)
Fluorocitric acid  (EXP)
folic acid  (ISO)
formaldehyde  (EXP)
fulvestrant  (EXP)
haloperidol  (ISO)
ionomycin  (EXP)
isoflurane  (EXP)
kainic acid  (ISO)
ketamine  (EXP)
L-ascorbic acid  (ISO)
lead diacetate  (EXP,ISO)
leflunomide  (ISO)
linuron  (EXP)
lipopolysaccharide  (ISO)
lipoteichoic acid  (ISO)
lithium atom  (EXP)
lithium hydride  (EXP)
lovastatin  (EXP)
magnesium atom  (EXP)
manganese atom  (EXP)
manganese(0)  (EXP)
manganese(II) chloride  (EXP)
melamine  (EXP)
methamphetamine  (EXP,ISO)
methapyrilene  (ISO)
methylmercury chloride  (EXP)
morphine  (EXP,ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
N-acetyl-L-cysteine  (EXP)
nickel atom  (EXP)
nobiletin  (EXP)
notoginsenoside R1  (ISO)
NS-398  (EXP)
Ondansetron  (EXP)
oxidopamine  (EXP)
paclitaxel  (EXP)
paraquat  (EXP,ISO)
PCB138  (EXP,ISO)
pentobarbital  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
pyridine  (EXP)
remifentanil  (EXP)
resveratrol  (EXP)
Rhynchophylline  (EXP)
rimonabant  (ISO)
sarin  (ISO)
sevoflurane  (EXP)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (EXP)
spermine  (EXP)
sulfur dioxide  (EXP)
sulindac  (EXP)
sunitinib  (ISO)
testosterone  (EXP)
tetrodotoxin  (ISO)
thimerosal  (ISO)
titanium dioxide  (ISO)
toluene  (EXP,ISO)
tributylstannane  (EXP)
trimethyltin  (ISO)
triptonide  (ISO)
valproic acid  (EXP,ISO)
venlafaxine hydrochloride  (EXP)
vinclozolin  (EXP)
vorinostat  (EXP)
zinc atom  (EXP)
zinc dichloride  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
action potential  (IMP)
associative learning  (IMP)
behavioral fear response  (IMP,ISO)
behavioral response to pain  (ISO)
calcium ion transmembrane import into cytosol  (IEA,ISO,ISS)
calcium ion transport  (ISO)
calcium-mediated signaling  (IEA)
cation transport  (ISO)
cellular response to amino acid stimulus  (IEP)
cellular response to corticosterone stimulus  (IEP)
cellular response to curcumin  (IEP)
cellular response to dsRNA  (IEP)
cellular response to forskolin  (IEP)
cellular response to growth factor stimulus  (IEP)
cellular response to lipid  (IEP)
cellular response to magnesium starvation  (IEP)
cellular response to manganese ion  (IEP)
cellular response to organic cyclic compound  (IEP)
cerebral cortex development  (IEP)
chemical synaptic transmission  (ISO)
detection of mechanical stimulus involved in sensory perception of pain  (ISO)
excitatory postsynaptic potential  (IBA,ISO)
fear response  (ISO)
hippocampus development  (IEP)
in utero embryonic development  (ISO)
ionotropic glutamate receptor signaling pathway  (IDA,IEA)
learning  (ISO)
learning or memory  (IMP,TAS)
long-term memory  (IEP)
long-term synaptic potentiation  (IBA,ISO)
memory  (IDA,ISO)
multicellular organismal response to stress  (IEP)
negative regulation of dendritic spine maintenance  (ISO)
NMDA selective glutamate receptor signaling pathway  (IMP)
positive regulation of cell death  (IDA,IMP)
positive regulation of cysteine-type endopeptidase activity  (IGI)
positive regulation of glutamate secretion  (IDA)
positive regulation of neuron death  (ISO)
positive regulation of synaptic transmission  (IMP)
protein heterotetramerization  (IDA)
receptor clustering  (IDA)
regulation of long-term neuronal synaptic plasticity  (IMP)
regulation of MAPK cascade  (IMP)
regulation of postsynaptic cytosolic calcium ion concentration  (IMP)
regulation of postsynaptic membrane potential  (ISO)
regulation of protein kinase A signaling  (ISO)
regulation of synaptic plasticity  (ISO)
response to amine  (IEP)
response to amphetamine  (IEP)
response to calcium ion  (IEP)
response to carbohydrate  (IEP)
response to cocaine  (IEP)
response to cytokine  (IEP)
response to electrical stimulus  (IEP)
response to ethanol  (IEA,IEP,ISO)
response to fungicide  (IEP)
response to growth hormone  (IEP)
response to hypoxia  (IDA)
response to magnesium ion  (IEP)
response to manganese ion  (IEP)
response to mechanical stimulus  (IEP)
response to methylmercury  (IEP)
response to organic cyclic compound  (IEP)
response to organonitrogen compound  (IMP)
response to other organism  (IEP)
response to toxic substance  (IEP)
rhythmic process  (IDA)
sensitization  (IMP)
sensory organ development  (ISO)
startle response  (ISO)
suckling behavior  (ISO)

References

References - curated
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Additional References at PubMed
PMID:1377365   PMID:7524561   PMID:7531804   PMID:8789948   PMID:8840015   PMID:8940188   PMID:9003035   PMID:9147327   PMID:9458051   PMID:9581762   PMID:9670010   PMID:10479680  
PMID:10480938   PMID:10485705   PMID:10634899   PMID:10846156   PMID:10939335   PMID:11160393   PMID:11488959   PMID:11530236   PMID:11588171   PMID:11711849   PMID:11719203   PMID:11897109  
PMID:11911857   PMID:11929923   PMID:12147342   PMID:12391275   PMID:12486601   PMID:12579524   PMID:12586431   PMID:12676993   PMID:12684439   PMID:12716944   PMID:12764094   PMID:12816890  
PMID:12832518   PMID:12890763   PMID:14503841   PMID:14645471   PMID:14672996   PMID:15016095   PMID:15143284   PMID:15146049   PMID:15201510   PMID:15356193   PMID:15356198   PMID:15483135  
PMID:15537897   PMID:15574735   PMID:15580338   PMID:15610162   PMID:15629447   PMID:15634765   PMID:15649985   PMID:15673434   PMID:15748150   PMID:15790561   PMID:15804717   PMID:15885982  
PMID:15908129   PMID:15924861   PMID:15967799   PMID:16045501   PMID:16141268   PMID:16155008   PMID:16190898   PMID:16221859   PMID:16300633   PMID:16436603   PMID:16540573   PMID:16710293  
PMID:16741178   PMID:16794574   PMID:16901514   PMID:16980547   PMID:17047094   PMID:17114649   PMID:17124177   PMID:17156360   PMID:17196527   PMID:17229826   PMID:17255096   PMID:17331654  
PMID:17451646   PMID:17509768   PMID:17545075   PMID:17670980   PMID:17706601   PMID:17717018   PMID:17986236   PMID:18006154   PMID:18025808   PMID:18033811   PMID:18033813   PMID:18048007  
PMID:18230675   PMID:18272676   PMID:18339694   PMID:18342306   PMID:18356833   PMID:18378405   PMID:18445116   PMID:18468585   PMID:18538939   PMID:18673451   PMID:18688011   PMID:18694808  
PMID:18706452   PMID:18751892   PMID:18765272   PMID:18826591   PMID:18922773   PMID:18927268   PMID:18936081   PMID:18952054   PMID:19088076   PMID:19106110   PMID:19164281   PMID:19187438  
PMID:19193935   PMID:19275891   PMID:19302193   PMID:19335206   PMID:19376094   PMID:19428647   PMID:19520065   PMID:19531642   PMID:19543280   PMID:19587283   PMID:19625512   PMID:19656178  
PMID:19694907   PMID:19726645   PMID:19857555   PMID:19864302   PMID:20107120   PMID:20418887   PMID:20427654   PMID:20508838   PMID:20569495   PMID:20625810   PMID:20661302   PMID:20698836  
PMID:20831617   PMID:20850419   PMID:20887777   PMID:20974938   PMID:21029094   PMID:21144999   PMID:21171386   PMID:21177185   PMID:21182900   PMID:21364640   PMID:21384157   PMID:21397592  
PMID:21427228   PMID:21439793   PMID:21470075   PMID:21575722   PMID:21608225   PMID:21664258   PMID:21669274   PMID:21762679   PMID:21795692   PMID:21862938   PMID:21880917   PMID:21895803  
PMID:22027786   PMID:22055014   PMID:22084102   PMID:22089426   PMID:22100849   PMID:22177709   PMID:22179603   PMID:22335236   PMID:22359056   PMID:22364833   PMID:22366650   PMID:22375001  
PMID:22377595   PMID:22543102   PMID:22558458   PMID:22610100   PMID:22681877   PMID:22740692   PMID:22743575   PMID:22759925   PMID:22776695   PMID:22820466   PMID:22824136   PMID:22833681  
PMID:22871113   PMID:22902837   PMID:22906554   PMID:22931702   PMID:22965452   PMID:22982438   PMID:23022504   PMID:23069667   PMID:23091164   PMID:23113297   PMID:23146303   PMID:23219940  
PMID:23221411   PMID:23313317   PMID:23429044   PMID:23431156   PMID:23497405   PMID:23516288   PMID:23584669   PMID:23585298   PMID:23611155   PMID:23660833   PMID:23672716   PMID:23676200  
PMID:23811393   PMID:23839940   PMID:23981041   PMID:24032403   PMID:24041503   PMID:24069373   PMID:24120858   PMID:24189275   PMID:24336715   PMID:24388786   PMID:24431445   PMID:24440698  
PMID:24487031   PMID:24491052   PMID:24562683   PMID:24607230   PMID:24631206   PMID:24705401   PMID:24761931   PMID:24824341   PMID:25122884   PMID:25393018   PMID:25404733   PMID:25496357  
PMID:25521238   PMID:25772108   PMID:25838242   PMID:25917873   PMID:26027736   PMID:26190171   PMID:26197883   PMID:26204818   PMID:26229100   PMID:26343542   PMID:26391783   PMID:26401567  
PMID:26440419   PMID:26548659   PMID:26554229   PMID:26609151   PMID:26627310   PMID:26875626   PMID:26881126   PMID:26884337   PMID:26919761   PMID:26930443   PMID:27217103   PMID:27430327  
PMID:27457929   PMID:27487820   PMID:27497478   PMID:27523302   PMID:27531837   PMID:27839871   PMID:27865917   PMID:27926876   PMID:28160495   PMID:28326942   PMID:28358367   PMID:28393079  
PMID:28497343   PMID:28682239   PMID:28916627   PMID:29335819   PMID:29353374   PMID:29476059   PMID:29490264   PMID:30054528   PMID:30142538   PMID:30176218   PMID:30269991   PMID:30350722  
PMID:30400767   PMID:30639357   PMID:31080121   PMID:31213568   PMID:31245854   PMID:31277281   PMID:31424425   PMID:31672664   PMID:31840160   PMID:32032782   PMID:32386416   PMID:32816128  
PMID:32929031   PMID:33420399   PMID:33550485   PMID:34360755  


Genomics

Comparative Map Data
Grin2b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24168,580,824 - 169,044,110 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4168,599,546 - 169,042,279 (-)Ensembl
Rnor_6.04169,541,620 - 170,000,216 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4169,560,387 - 169,999,873 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04233,806,406 - 234,260,360 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44172,721,895 - 173,183,187 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14172,966,830 - 173,428,311 (-)NCBI
Celera4157,188,514 - 157,629,365 (-)NCBICelera
RH 3.4 Map41026.8RGD
Cytogenetic Map4q43NCBI
GRIN2B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1213,437,942 - 13,982,002 (-)EnsemblGRCh38hg38GRCh38
GRCh381213,537,337 - 13,982,012 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371213,690,271 - 14,134,536 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361213,605,411 - 14,024,319 (-)NCBINCBI36hg18NCBI36
Build 341213,605,410 - 14,024,319NCBI
Celera1218,858,978 - 19,277,660 (-)NCBI
Cytogenetic Map12p13.1NCBI
HuRef1213,479,858 - 13,898,402 (-)NCBIHuRef
CHM1_11213,679,406 - 14,098,101 (-)NCBICHM1_1
Grin2b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396135,690,219 - 136,150,658 (-)NCBIGRCm39mm39
GRCm39 Ensembl6135,690,231 - 136,150,509 (-)Ensembl
GRCm386135,713,221 - 136,173,615 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6135,713,233 - 136,173,511 (-)EnsemblGRCm38mm10GRCm38
MGSCv376135,679,813 - 136,123,529 (-)NCBIGRCm37mm9NCBIm37
MGSCv366135,697,791 - 136,009,994 (-)NCBImm8
Celera6138,678,301 - 139,123,902 (-)NCBICelera
Cytogenetic Map6G1NCBI
cM Map666.38NCBI
Grin2b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541310,376,597 - 10,779,145 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541310,358,931 - 10,780,004 (-)NCBIChiLan1.0ChiLan1.0
GRIN2B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11213,943,936 - 14,272,195 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1213,969,387 - 14,388,799 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01213,543,104 - 13,987,437 (-)NCBIMhudiblu_PPA_v0panPan3
GRIN2B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12732,470,889 - 32,883,606 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2732,471,153 - 32,877,680 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2713,572,169 - 13,850,223 (-)NCBI
ROS_Cfam_1.02732,702,956 - 33,191,598 (+)NCBI
UMICH_Zoey_3.12732,798,882 - 33,078,120 (+)NCBI
UNSW_CanFamBas_1.02732,748,401 - 33,027,217 (+)NCBI
UU_Cfam_GSD_1.02713,302,777 - 13,581,228 (-)NCBI
Grin2b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494593,677,907 - 94,094,419 (+)NCBI
SpeTri2.0NW_0049365873,406,055 - 3,806,956 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GRIN2B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl558,480,526 - 58,927,583 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1558,477,862 - 58,948,735 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2561,874,217 - 62,275,930 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GRIN2B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11113,444,155 - 13,873,034 (-)NCBI
ChlSab1.1 Ensembl1113,456,968 - 13,873,202 (-)Ensembl
Vero_WHO_p1.0NW_02366606921,440,620 - 21,872,881 (+)NCBI
Grin2b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475224,008,520 - 24,480,834 (+)NCBI

Position Markers
RH94749  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24168,599,595 - 168,599,850 (+)MAPPERmRatBN7.2
Rnor_6.04169,559,999 - 169,560,253NCBIRnor6.0
Rnor_5.04233,824,084 - 233,824,338UniSTSRnor5.0
RGSC_v3.44172,721,945 - 172,722,199UniSTSRGSC3.4
Celera4157,188,564 - 157,188,818UniSTS
RH 3.4 Map41026.8UniSTS
Cytogenetic Map4q43UniSTS
RH94750  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24169,041,996 - 169,042,191 (+)MAPPERmRatBN7.2
Rnor_6.04169,998,166 - 169,998,360NCBIRnor6.0
Rnor_5.04234,258,645 - 234,258,839UniSTSRnor5.0
RGSC_v3.44173,182,905 - 173,183,099UniSTSRGSC3.4
Celera4157,629,083 - 157,629,277UniSTS
Cytogenetic Map4q43UniSTS
RH143997  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24168,800,230 - 168,800,345 (+)MAPPERmRatBN7.2
Rnor_6.04169,761,521 - 169,761,635NCBIRnor6.0
Rnor_5.04234,025,258 - 234,025,372UniSTSRnor5.0
RGSC_v3.44172,924,073 - 172,924,187UniSTSRGSC3.4
Celera4157,389,977 - 157,390,091UniSTS
RH 3.4 Map41026.2UniSTS
Cytogenetic Map4q43UniSTS
Grin2b  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24168,600,099 - 168,600,280 (+)MAPPERmRatBN7.2
Rnor_6.04169,560,503 - 169,560,683NCBIRnor6.0
Rnor_5.04233,824,588 - 233,824,768UniSTSRnor5.0
RGSC_v3.44172,722,449 - 172,722,629UniSTSRGSC3.4
Celera4157,189,068 - 157,189,248UniSTS
Cytogenetic Map4q43UniSTS
UniSTS:465389  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24168,601,222 - 168,601,681 (+)MAPPERmRatBN7.2
Rnor_6.04169,561,626 - 169,562,084NCBIRnor6.0
Rnor_5.04233,825,711 - 233,826,169UniSTSRnor5.0
RGSC_v3.44172,723,572 - 172,724,030UniSTSRGSC3.4
Celera4157,190,191 - 157,190,649UniSTS
Cytogenetic Map4q43UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat


Genetic Models
This gene Grin2b is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:104
Count of miRNA genes:72
Interacting mature miRNAs:87
Transcripts:ENSRNOT00000011697
Prediction methods: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 34
Low 1 30 5 2
Below cutoff 2 6 17 4 14 4 6 6 8 20 30 9 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011697   ⟹   ENSRNOP00000011697
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4168,599,546 - 169,042,279 (-)Ensembl
Rnor_6.0 Ensembl4169,560,387 - 169,999,873 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108335   ⟹   ENSRNOP00000083097
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4168,739,363 - 169,042,279 (-)Ensembl
RefSeq Acc Id: NM_012574   ⟹   NP_036706
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24168,599,546 - 169,042,279 (-)NCBI
Rnor_6.04169,559,949 - 169,998,448 (-)NCBI
Rnor_5.04233,806,406 - 234,260,360 (-)NCBI
RGSC_v3.44172,721,895 - 173,183,187 (-)RGD
Celera4157,188,514 - 157,629,365 (-)RGD
Sequence:
RefSeq Acc Id: XM_017592436   ⟹   XP_017447925
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24168,580,824 - 169,043,806 (-)NCBI
Rnor_6.04169,558,166 - 169,999,881 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592437   ⟹   XP_017447926
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24168,599,546 - 169,044,110 (-)NCBI
Rnor_6.04169,558,166 - 170,000,216 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592438   ⟹   XP_017447927
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24168,599,546 - 169,044,002 (-)NCBI
Rnor_6.04169,558,166 - 170,000,138 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592439   ⟹   XP_017447928
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24168,580,824 - 169,043,803 (-)NCBI
Rnor_6.04169,541,620 - 169,999,881 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036706   ⟸   NM_012574
- Peptide Label: precursor
- UniProtKB: Q00960 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017447928   ⟸   XM_017592439
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017447926   ⟸   XM_017592437
- Peptide Label: isoform X1
- UniProtKB: G3V746 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447927   ⟸   XM_017592438
- Peptide Label: isoform X1
- UniProtKB: G3V746 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447925   ⟸   XM_017592436
- Peptide Label: isoform X1
- UniProtKB: G3V746 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011697   ⟸   ENSRNOT00000011697
RefSeq Acc Id: ENSRNOP00000083097   ⟸   ENSRNOT00000108335
Protein Domains
Lig_chan-Glu_bd   PBPe

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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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
PVG/Seac (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
SBH/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: 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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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