Grin2a (glutamate ionotropic receptor NMDA type subunit 2A) - Rat Genome Database

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Gene: Grin2a (glutamate ionotropic receptor NMDA type subunit 2A) Rattus norvegicus
Analyze
Symbol: Grin2a
Name: glutamate ionotropic receptor NMDA type subunit 2A
RGD ID: 2737
Description: Exhibits several functions, including enzyme binding activity; glutamate binding activity; and ligand-gated ion channel activity. Contributes to cation channel activity and extracellularly glutamate-gated ion channel activity. Involved in several processes, including cellular response to metal ion; central nervous system development; and modulation of chemical synaptic transmission. Localizes to several cellular components, including NMDA selective glutamate receptor complex; parallel fiber to Purkinje cell synapse; and synaptic membrane. Used to study hyperhomocysteinemia. Biomarker of cognitive disorder; placental insufficiency; and status epilepticus. Human ortholog(s) of this gene implicated in Huntington's disease; bipolar disorder; and schizophrenia. Orthologous to human GRIN2A (glutamate ionotropic receptor NMDA type subunit 2A); PARTICIPATES IN excitatory synaptic transmission pathway; long term depression; long term potentiation; INTERACTS WITH (+)-pilocarpine; (25R)-cholest-5-ene-3beta,26-diol; (R)-lipoic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: GluN2A; glutamate [NMDA] receptor subunit epsilon-1; glutamate receptor ionotropic, NMDA 2A; glutamate receptor, ionotropic, N-methyl D-aspartate 2A; N-methyl D-aspartate receptor subtype 2A; N-methyl-D-aspartate receptor subunit 2A; NMDAR2A; NR2A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2105,630,684 - 6,043,341 (+)NCBI
Rnor_6.0 Ensembl105,930,298 - 6,119,990 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0105,707,806 - 6,123,568 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0104,523,233 - 4,940,912 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4105,588,229 - 6,004,780 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1105,588,940 - 6,006,076 (+)NCBI
Celera104,645,710 - 5,048,399 (+)NCBICelera
Cytogenetic Map10q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-pilocarpine  (EXP)
(25R)-cholest-5-ene-3beta,26-diol  (EXP)
(R)-lipoic acid  (EXP)
17beta-estradiol  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (EXP,ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
26-hydroxycholesterol  (EXP)
3',5'-cyclic AMP  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-[1-hydroxy-2-[4-(phenylmethyl)-1-piperidinyl]propyl]phenol  (EXP)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
allopurinol  (EXP)
Amaranth  (EXP)
ammonium acetate  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
Brilliant Blue  (EXP)
celecoxib  (ISO)
chaetocin  (EXP)
chlorpyrifos  (EXP)
choline  (EXP)
clozapine  (EXP)
cocaine  (EXP,ISO)
curcumin  (EXP)
dextromethorphan  (EXP)
Diacetoxyscirpenol  (ISO)
diazepam  (ISO)
diazinon  (EXP)
dinitrogen oxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
excitatory amino acid agonist  (ISO)
felbamate  (EXP)
fluoxetine  (EXP)
folic acid  (EXP)
formaldehyde  (ISO)
furan  (EXP)
genistein  (EXP)
haloperidol  (EXP)
hydrogen peroxide  (ISO)
indigo carmine  (EXP)
kainic acid  (ISO)
ketamine  (EXP,ISO)
L-ascorbic acid  (ISO)
lead diacetate  (EXP,ISO)
lead nitrate  (ISO)
leflunomide  (ISO)
lipoic acid  (EXP)
lipoteichoic acid  (ISO)
lithium atom  (EXP)
lithium hydride  (EXP)
manganese atom  (EXP)
manganese(0)  (EXP)
manganese(II) chloride  (EXP)
mercury dibromide  (ISO)
methamphetamine  (EXP)
methapyrilene  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (EXP)
midazolam  (ISO)
minocycline  (EXP)
morphine  (ISO)
N-methyl-N-nitrosourea  (EXP)
nickel atom  (ISO)
nobiletin  (EXP)
Nor-9-carboxy-delta9-THC  (ISO)
ochratoxin A  (EXP)
oxybenzone  (EXP)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paraquat  (EXP,ISO)
PCB138  (ISO)
pentobarbital  (EXP,ISO)
phencyclidine  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
poly(cytidylic acid)  (EXP)
profenofos  (EXP)
propofol  (ISO)
prostaglandin E2  (ISO)
rimonabant  (ISO)
SB 431542  (ISO)
sevoflurane  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (EXP,ISO)
sulfur dioxide  (EXP)
Sunset Yellow FCF  (EXP)
T-2 toxin  (ISO)
tadalafil  (ISO)
tartrazine  (EXP)
tetrodotoxin  (ISO)
thioacetamide  (ISO)
titanium dioxide  (ISO)
toluene  (EXP,ISO)
tributylstannane  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
urethane  (ISO)
valproic acid  (EXP,ISO)
venlafaxine hydrochloride  (EXP)
zinc atom  (EXP)
zinc dichloride  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
action potential  (IMP)
calcium ion transmembrane import into cytosol  (IEA,ISO,ISS)
calcium ion transport  (ISO)
calcium-mediated signaling  (IEA)
cellular response to amino acid stimulus  (IMP)
cellular response to amyloid-beta  (ISO)
cellular response to dsRNA  (IEP)
cellular response to growth factor stimulus  (IEP)
cellular response to lipid  (IEP)
cellular response to magnesium ion  (IEP)
cellular response to manganese ion  (IEP)
cellular response to zinc ion  (IMP)
cerebral cortex development  (IEP)
chemical synaptic transmission  (IMP,ISO)
dendritic spine organization  (IMP)
detection of mechanical stimulus involved in sensory perception of pain  (ISO)
directional locomotion  (IEA,ISO)
dopamine metabolic process  (IEA,ISO)
excitatory postsynaptic potential  (IBA,IEA,IMP,ISO)
hippocampus development  (IEP)
ionotropic glutamate receptor signaling pathway  (IDA,IEA)
learning  (ISO)
learning or memory  (ISO)
locomotion  (ISO)
long-term synaptic potentiation  (IBA,IEA,ISO)
memory  (IDA,IEA,ISO)
modulation of chemical synaptic transmission  (ISO)
negative regulation of protein catabolic process  (IEA,ISO)
neurogenesis  (IEA,ISO)
positive regulation of apoptotic process  (IEA,ISO)
positive regulation of cell death  (IDA)
positive regulation of excitatory postsynaptic potential  (IDA)
protein localization to postsynaptic membrane  (IEA,ISO)
regulation of long-term neuronal synaptic plasticity  (IMP)
regulation of membrane potential  (ISO)
regulation of NMDA receptor activity  (IMP)
regulation of postsynaptic membrane potential  (ISO)
regulation of presynaptic membrane potential  (IEA)
regulation of synaptic plasticity  (ISO)
response to amine  (IEP)
response to ammonium ion  (IEP)
response to amphetamine  (IEA,ISO)
response to calcium ion  (IEP)
response to carbohydrate  (IEP)
response to cocaine  (IEP)
response to drug  (IEA,IEP,ISO)
response to ethanol  (IEA,IEP,IMP,ISO)
response to fungicide  (IEP)
response to light stimulus  (IEP)
response to manganese ion  (IEP)
response to methylmercury  (IEP)
response to organic cyclic compound  (IEP)
response to other organism  (IEP)
response to wounding  (IEA,ISO)
rhythmic process  (IDA)
sensory perception of pain  (IEA,ISO)
serotonin metabolic process  (IEA,ISO)
sleep  (IEA,ISO)
spinal cord development  (IEP)
startle response  (IEA,ISO)
visual learning  (IEA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
alfentanil pharmacodynamics pathway  (ISO)
Alzheimer's disease pathway  (IEA)
amyotrophic lateral sclerosis pathway  (IEA)
bupivacaine pharmacodynamics pathway  (ISO)
buprenorphine pharmacodynamics pathway  (ISO)
calcium/calcium-mediated signaling pathway  (IEA)
calcium/calmodulin dependent kinase 2 signaling pathway  (ISO)
chloroprocaine pharmacodynamics pathway  (ISO)
citalopram pharmacodynamics pathway  (ISO)
cocaine pharmacodynamics pathway  (ISO)
codeine and morphine pharmacodynamics pathway  (ISO)
desipramine pharmacodynamics pathway  (ISO)
diphenoxylate pharmacodynamics pathway  (ISO)
escitalopram pharmacodynamics pathway  (ISO)
ethylmorphine pharmacodynamics pathway  (ISO)
excitatory synaptic transmission pathway  (IDA)
fentanyl pharmacodynamics pathway  (ISO)
fluoxetine pharmacodynamics pathway  (ISO)
glutamate signaling pathway  (IEA)
heroin pharmacodynamics pathway  (ISO)
hydrocodone pharmacodynamics pathway  (ISO)
hydromorphone pharmacodynamics pathway  (ISO)
imipramine pharmacodynamics pathway  (ISO)
levacetylmethadol pharmacodynamics pathway  (ISO)
levobupivacaine phgarmacodynamics pathway  (ISO)
levorphanol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
long term depression  (IMP)
long term potentiation  (IEA,IMP)
mepivacaine pharmacodynamics pathway  (ISO)
methadone pharmacodynamics pathway  (ISO)
methadone pharmacokinetics pathway  (ISO)
nalbuphine pharmacodynamics pathway  (ISO)
naloxone pharmacodynamics pathway  (ISO)
naltrexone pharmacodynamics pathway  (ISO)
nicotine pharmacodynamics pathway  (ISO)
oxybuprocaine pharmacodynamics pathway  (ISO)
oxycodone pharmacodynamics pathway  (ISO)
oxymorphone pharmacodynamics pathway  (ISO)
pentazocine pharmacodynamics pathway  (ISO)
prilocaine pharmacodynamics pathway  (ISO)
procaine pharmacodynamics pathway  (ISO)
Reelin signaling pathway  (ISO,TAS)
remifentanil pharmacodynamics pathway  (ISO)
ropivacaine pharmacodynamics pathway  (ISO)
systemic lupus erythematosus pathway  (IEA)
tramadol pharmacodynamics pathway  (ISO)

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
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Additional References at PubMed
PMID:1374164   PMID:1377365   PMID:7816096   PMID:7929101   PMID:8699248   PMID:8840015   PMID:8987814   PMID:9003035   PMID:9147327   PMID:9427357   PMID:9458051   PMID:9512392  
PMID:9556603   PMID:9647694   PMID:9694864   PMID:9712642   PMID:9718984   PMID:9822733   PMID:9892651   PMID:10480938   PMID:10694228   PMID:10771345   PMID:11160393   PMID:11160454  
PMID:11487658   PMID:11488959   PMID:11530236   PMID:11588171   PMID:11929923   PMID:12103442   PMID:12147342   PMID:12242020   PMID:12391275   PMID:12427824   PMID:12486601   PMID:12579524  
PMID:12676993   PMID:12695509   PMID:12711087   PMID:12746457   PMID:12754515   PMID:12764094   PMID:12859686   PMID:12890763   PMID:12941447   PMID:14503841   PMID:14622577   PMID:14645471  
PMID:14732708   PMID:14750973   PMID:14760703   PMID:14985927   PMID:15016095   PMID:15143284   PMID:15201510   PMID:15317856   PMID:15356193   PMID:15574735   PMID:15580338   PMID:15610162  
PMID:15649985   PMID:15731593   PMID:15737435   PMID:15790561   PMID:15804717   PMID:15888440   PMID:15908129   PMID:15924861   PMID:15967799   PMID:16045501   PMID:16190898   PMID:16281028  
PMID:16540573   PMID:16709630   PMID:16710293   PMID:16814779   PMID:16901514   PMID:16927803   PMID:16980547   PMID:17114649   PMID:17124177   PMID:17156360   PMID:17229826   PMID:17234586  
PMID:17255096   PMID:17451646   PMID:17455306   PMID:17459877   PMID:17486105   PMID:17545075   PMID:17670980   PMID:17717018   PMID:17803966   PMID:17853656   PMID:17854777   PMID:17962329  
PMID:17986236   PMID:18048007   PMID:18054859   PMID:18230675   PMID:18445116   PMID:18468585   PMID:18538939   PMID:18688011   PMID:18720514   PMID:18765272   PMID:18927268   PMID:19088076  
PMID:19376094   PMID:19490087   PMID:19533626   PMID:19587283   PMID:19626270   PMID:19726645   PMID:19771923   PMID:19772634   PMID:19934647   PMID:20107120   PMID:20145658   PMID:20418887  
PMID:20441772   PMID:20448042   PMID:20581725   PMID:20661302   PMID:20831617   PMID:20844142   PMID:20850419   PMID:20884369   PMID:20887777   PMID:20974938   PMID:21114966   PMID:21162311  
PMID:21470075   PMID:21554958   PMID:21558424   PMID:21608225   PMID:21664258   PMID:21669274   PMID:21719075   PMID:21862938   PMID:21883149   PMID:21883211   PMID:22055014   PMID:22089426  
PMID:22108330   PMID:22291020   PMID:22335236   PMID:22362014   PMID:22366650   PMID:22375001   PMID:22474321   PMID:22493505   PMID:22681877   PMID:22870316   PMID:22891278   PMID:23022504  
PMID:23049922   PMID:23113297   PMID:23212166   PMID:23221411   PMID:23352316   PMID:23383317   PMID:23431156   PMID:23611155   PMID:23621516   PMID:23672716   PMID:23676200   PMID:23760273  
PMID:23839940   PMID:24029697   PMID:24076085   PMID:24278457   PMID:24388786   PMID:24607230   PMID:24761931   PMID:24981431   PMID:25319628   PMID:25393018   PMID:25496357   PMID:25521238  
PMID:25544544   PMID:25772108   PMID:25829490   PMID:26088419   PMID:26220171   PMID:26370091   PMID:26548659   PMID:26609151   PMID:26627310   PMID:26682524   PMID:26875626   PMID:27457929  
PMID:27497478   PMID:27807032   PMID:27839871   PMID:27857196   PMID:28042872   PMID:28160495   PMID:28823933   PMID:29335819   PMID:29339324   PMID:30269991   PMID:30500536   PMID:31080121  
PMID:31167782   PMID:31277281   PMID:31936514   PMID:31978422   PMID:32015122   PMID:32032749   PMID:32070042   PMID:32197489   PMID:32320718   PMID:32929031  


Genomics

Comparative Map Data
Grin2a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2105,630,684 - 6,043,341 (+)NCBI
Rnor_6.0 Ensembl105,930,298 - 6,119,990 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0105,707,806 - 6,123,568 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0104,523,233 - 4,940,912 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4105,588,229 - 6,004,780 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1105,588,940 - 6,006,076 (+)NCBI
Celera104,645,710 - 5,048,399 (+)NCBICelera
Cytogenetic Map10q11NCBI
GRIN2A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl169,753,404 - 10,182,928 (-)EnsemblGRCh38hg38GRCh38
GRCh38169,753,404 - 10,182,928 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37169,847,261 - 10,276,765 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36169,762,923 - 10,184,112 (-)NCBINCBI36hg18NCBI36
Build 34169,762,922 - 10,184,112NCBI
Celera1610,014,039 - 10,444,548 (-)NCBI
Cytogenetic Map16p13.2NCBI
HuRef169,767,577 - 9,952,307 (-)NCBIHuRef
HuRef1610,193,124 - 10,195,907 (-)NCBIHuRef
CHM1_1169,847,229 - 10,277,115 (-)NCBICHM1_1
Grin2a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39169,385,765 - 9,813,744 (-)NCBIGRCm39mm39
GRCm39 Ensembl169,385,762 - 9,813,424 (-)Ensembl
GRCm38169,567,901 - 9,996,083 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl169,567,898 - 9,995,560 (-)EnsemblGRCm38mm10GRCm38
MGSCv37169,577,803 - 9,992,626 (-)NCBIGRCm37mm9NCBIm37
MGSCv36169,491,265 - 9,906,111 (-)NCBImm8
Celera1610,217,398 - 10,625,063 (-)NCBICelera
Cytogenetic Map16A1NCBI
cM Map165.28NCBI
Grin2a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554428,174,232 - 8,562,059 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554428,171,114 - 8,565,187 (+)NCBIChiLan1.0ChiLan1.0
GRIN2A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1169,909,406 - 10,339,147 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl169,919,143 - 10,336,167 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0168,682,169 - 9,105,581 (-)NCBIMhudiblu_PPA_v0panPan3
GRIN2A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1632,132,070 - 32,678,319 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl632,303,121 - 32,668,960 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha633,514,238 - 34,067,205 (+)NCBI
ROS_Cfam_1.0632,315,346 - 32,865,008 (+)NCBI
UMICH_Zoey_3.1632,128,354 - 32,680,283 (+)NCBI
UNSW_CanFamBas_1.0632,000,797 - 32,549,532 (+)NCBI
UU_Cfam_GSD_1.0632,426,676 - 32,972,580 (+)NCBI
Grin2a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344110,432,891 - 110,765,991 (-)NCBI
SpeTri2.0NW_0049365308,286,101 - 8,612,183 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GRIN2A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl332,752,351 - 33,143,499 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1332,749,329 - 33,149,350 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2333,810,701 - 33,913,481 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GRIN2A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.159,233,028 - 9,707,322 (-)NCBI
ChlSab1.1 Ensembl59,286,775 - 9,462,828 (-)Ensembl
Vero_WHO_p1.0NW_02366606820,460,991 - 20,885,559 (+)NCBI
Grin2a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248247,128,169 - 7,513,360 (-)NCBI

Position Markers
D10Got12  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2105,801,990 - 5,802,227 (+)MAPPER
Rnor_6.0105,877,536 - 5,877,770NCBIRnor6.0
Rnor_5.0104,695,640 - 4,695,874UniSTSRnor5.0
RGSC_v3.4105,761,138 - 5,761,372RGDRGSC3.4
RGSC_v3.4105,761,139 - 5,761,373UniSTSRGSC3.4
RGSC_v3.1105,761,138 - 5,761,372RGD
Celera104,812,755 - 4,813,001UniSTS
RH 3.4 Map1060.5UniSTS
RH 3.4 Map1060.5RGD
RH 2.0 Map100.0RGD
Cytogenetic Map10q11UniSTS
D10Got164  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2105,933,009 - 5,933,133 (+)MAPPER
Rnor_6.0106,009,414 - 6,009,537NCBIRnor6.0
Rnor_5.0104,827,340 - 4,827,463UniSTSRnor5.0
RGSC_v3.4105,894,189 - 5,894,313RGDRGSC3.4
RGSC_v3.4105,894,190 - 5,894,313UniSTSRGSC3.4
RGSC_v3.1105,894,189 - 5,894,313RGD
Celera104,938,649 - 4,938,772UniSTS
RH 2.0 Map100.0RGD
Cytogenetic Map10q11UniSTS
D10Got9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2105,684,047 - 5,684,259 (+)MAPPER
Rnor_6.0105,760,565 - 5,760,774NCBIRnor6.0
Rnor_5.0104,578,252 - 4,578,461UniSTSRnor5.0
RGSC_v3.4105,641,331 - 5,641,541RGDRGSC3.4
RGSC_v3.4105,641,332 - 5,641,541UniSTSRGSC3.4
RGSC_v3.1105,641,332 - 5,641,541RGD
Celera104,696,381 - 4,696,598UniSTS
RH 3.4 Map1066.7UniSTS
RH 3.4 Map1066.7RGD
RH 2.0 Map100.0RGD
Cytogenetic Map10q11UniSTS
D10Ulb1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2221,143,394 - 21,144,889 (+)MAPPER
mRatBN7.2105,796,328 - 5,796,484 (+)MAPPER
Rnor_6.0105,872,003 - 5,872,158NCBIRnor6.0
Rnor_6.0218,873,175 - 18,874,669NCBIRnor6.0
Rnor_5.0104,690,107 - 4,690,262UniSTSRnor5.0
Rnor_5.0218,748,955 - 18,750,449UniSTSRnor5.0
RGSC_v3.4220,104,168 - 20,105,662UniSTSRGSC3.4
RGSC_v3.4105,755,479 - 5,755,634UniSTSRGSC3.4
Celera104,807,109 - 4,807,263UniSTS
Celera217,271,726 - 17,273,220UniSTS
Cytogenetic Map2q12UniSTS
Cytogenetic Map10q11UniSTS
Grin2a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2106,042,978 - 6,043,203 (+)MAPPER
Rnor_6.0106,119,535 - 6,119,759NCBIRnor6.0
Rnor_5.0104,936,511 - 4,936,735UniSTSRnor5.0
RGSC_v3.4106,004,418 - 6,004,642UniSTSRGSC3.4
Celera105,048,037 - 5,048,261UniSTS
Cytogenetic Map10q11UniSTS
BE120369  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2105,670,580 - 5,670,760 (+)MAPPER
Rnor_6.0105,747,098 - 5,747,277NCBIRnor6.0
Rnor_5.0104,564,785 - 4,564,964UniSTSRnor5.0
RGSC_v3.4105,627,865 - 5,628,044UniSTSRGSC3.4
Celera104,682,926 - 4,683,105UniSTS
RH 3.4 Map1085.81UniSTS
Cytogenetic Map10q11UniSTS
BF413021  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2105,629,039 - 5,629,155 (+)MAPPER
Rnor_6.0105,706,163 - 5,706,278NCBIRnor6.0
Rnor_5.0104,523,319 - 4,523,434UniSTSRnor5.0
RGSC_v3.4105,586,586 - 5,586,701UniSTSRGSC3.4
Celera104,644,067 - 4,644,182UniSTS
RH 3.4 Map1067.3UniSTS
Cytogenetic Map10q11UniSTS
ha2303  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2105,783,618 - 5,784,012 (+)MAPPER
Rnor_6.0105,859,293 - 5,859,686NCBIRnor6.0
Rnor_5.0104,677,397 - 4,677,790UniSTSRnor5.0
RGSC_v3.4105,742,769 - 5,743,162UniSTSRGSC3.4
Celera104,794,399 - 4,794,792UniSTS
Cytogenetic Map10q11UniSTS
Grin2a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2106,041,709 - 6,042,108 (+)MAPPER
Rnor_6.0106,118,266 - 6,118,664NCBIRnor6.0
Rnor_5.0104,935,242 - 4,935,640UniSTSRnor5.0
Celera105,046,768 - 5,047,166UniSTS
Cytogenetic Map10q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10129592136Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135538813Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138594330Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142669970Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)10144902893Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1076442166221621Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10483563820170031Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10521719917555534Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10521719919591669Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10546011921524070Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10546011921524070Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10546011921524070Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10546011921524070Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10546011921524070Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10587753664401490Rat

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir132rno-miR-132-3pMirtarbaseexternal_infoWestern blotFunctional MTI19958814

Predicted Target Of
Summary Value
Count of predictions:28
Count of miRNA genes:24
Interacting mature miRNAs:27
Transcripts:ENSRNOT00000044626
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 21
Low 1 41 2 1
Below cutoff 2 20 23 19 10 19 7 7 12 15 35 7 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000044626   ⟹   ENSRNOP00000042235
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl105,930,298 - 6,119,990 (+)Ensembl
RefSeq Acc Id: NM_012573   ⟹   NP_036705
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2105,630,684 - 6,043,341 (+)NCBI
Rnor_6.0105,707,806 - 6,119,897 (+)NCBI
Rnor_5.0104,523,233 - 4,940,912 (+)NCBI
RGSC_v3.4105,588,229 - 6,004,780 (+)RGD
Celera104,645,710 - 5,048,399 (+)RGD
Sequence:
RefSeq Acc Id: XM_017596984   ⟹   XP_017452473
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0105,709,597 - 6,123,568 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596985   ⟹   XP_017452474
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0105,708,813 - 6,123,568 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036705   ⟸   NM_012573
- Peptide Label: precursor
- UniProtKB: Q00959 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017452474   ⟸   XM_017596985
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017452473   ⟸   XM_017596984
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000042235   ⟸   ENSRNOT00000044626
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 (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/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)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2737 AgrOrtholog
Ensembl Genes ENSRNOG00000033942 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000042235 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044626 ENTREZGENE, UniProtKB/TrEMBL
InterPro ANF_lig-bd_rcpt UniProtKB/Swiss-Prot
  Glu/Gly-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Iono_rcpt_met UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Iontro_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NMDAR2_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peripla_BP_I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24409 UniProtKB/Swiss-Prot
NCBI Gene 24409 ENTREZGENE
Pfam ANF_receptor UniProtKB/Swiss-Prot
  Lig_chan UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lig_chan-Glu_bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NMDAR2_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Grin2a PhenoGen
PRINTS NMDARECEPTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Lig_chan-Glu_bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PBPe UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53822 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V9C5_RAT UniProtKB/TrEMBL
  NMDE1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q8CGM3_RAT UniProtKB/TrEMBL
UniProt Secondary O08948 UniProtKB/Swiss-Prot
  Q63728 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Grin2a  glutamate ionotropic receptor NMDA type subunit 2A  Grin2a  glutamate receptor, ionotropic, N-methyl D-aspartate 2A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Grin2a  glutamate receptor, ionotropic, N-methyl D-aspartate 2A      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression colocalized with cdk 5 in cerebral cortex, hipppocampus 69667
gene_expression expressed in majority of gonadotrophin releasing hormone (GnRH) neurons 625682
gene_expression expressed abundantly in hypothalamus in females of all ages 625682
gene_function N-methyl-D-aspartate (NMDA) class, glutamate receptor subunit 69667
gene_process modulates neuronal function of N-methyl-D-aspartate (NMDA) 69667
gene_process may play a role in synaptic transmission 69667
gene_process receptor for glutamate that influences reproductive physiology in females 625682
gene_regulation phosphorylated by various kinases such as PKC, cdk5 and Fyn (a tyrosine kinase) 69667