Gria3 (glutamate ionotropic receptor AMPA type subunit 3) - Rat Genome Database
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Gene: Gria3 (glutamate ionotropic receptor AMPA type subunit 3) Rattus norvegicus
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Symbol: Gria3
Name: glutamate ionotropic receptor AMPA type subunit 3
RGD ID: 70958
Description: Exhibits AMPA glutamate receptor activity; PDZ domain binding activity; and amyloid-beta binding activity. Involved in regulation of receptor recycling; response to fungicide; and response to lithium ion. Localizes to several cellular components, including dendrite; integral component of plasma membrane; and perikaryon. Human ortholog(s) of this gene implicated in syndromic X-linked intellectual disability 94. Orthologous to human GRIA3 (glutamate ionotropic receptor AMPA type subunit 3); PARTICIPATES IN glutamate signaling pathway; long term depression; INTERACTS WITH (+)-pilocarpine; 1-nitropropane; 17beta-estradiol.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: AMPA-selective glutamate receptor 3; GluA3; GluR-3; GluR-C; GluR-K3; GLUR3; glutamate receptor 3; glutamate receptor, ionotrophic, AMPA 3; glutamate receptor, ionotropic, AMPA 3; glutamate receptor, ionotropic, AMPA3 (alpha 3)
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
mRatBN7.2X120,238,515 - 120,504,106 (+)NCBI
Rnor_6.0 EnsemblX127,562,660 - 127,829,753 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X127,561,843 - 127,829,763 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X127,655,758 - 127,922,244 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X3,452,523 - 3,718,486 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X3,460,084 - 3,724,042 (-)NCBI
CeleraX119,369,614 - 119,631,774 (+)NCBICelera
Cytogenetic MapXq35NCBI
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  (ISO)
1-nitropropane  (EXP)
17beta-estradiol  (EXP)
2,3,4,7,8-Pentachlorodibenzofuran  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-diaminotoluene  (EXP)
2,6-diaminotoluene  (EXP)
2-acetamidofluorene  (EXP,ISO)
2-nitro-p-phenylenediamine  (EXP)
2-nitrofluorene  (EXP)
2-nitropropane  (EXP)
3,4-methylenedioxymethamphetamine  (EXP)
3-(5-fluorouracil-1-yl)-L-alanine  (ISO)
3-methylcholanthrene  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-acetylaminofluorene  (EXP)
4-nitro-1,2-phenylenediamine  (EXP)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
aldrin  (ISO)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (EXP)
anthracen-2-amine  (EXP)
arsenite(3-)  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
benzoates  (EXP)
bisphenol A  (EXP)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
cefaloridine  (EXP)
celecoxib  (ISO)
chlorpyrifos  (EXP,ISO)
choline  (ISO)
cisplatin  (ISO)
citalopram  (ISO)
Citreoviridin  (ISO)
cocaine  (EXP,ISO)
crocidolite asbestos  (ISO)
decabromodiphenyl ether  (EXP)
Diacetoxyscirpenol  (ISO)
dichloroacetic acid  (ISO)
diethyl maleate  (EXP)
dorsomorphin  (ISO)
endosulfan  (EXP)
ethanol  (EXP,ISO)
etoposide  (ISO)
flutamide  (EXP)
folic acid  (ISO)
geldanamycin  (ISO)
Heliotrine  (EXP)
kainic acid  (EXP,ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
lithium atom  (EXP)
lithium hydride  (EXP)
mercury dibromide  (ISO)
methamphetamine  (EXP)
methylmercury chloride  (ISO)
mitomycin C  (ISO)
morphine  (EXP)
N-nitrosodiethylamine  (EXP,ISO)
nickel atom  (ISO)
olanzapine  (EXP)
orphenadrine  (EXP)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
phenobarbital  (EXP,ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
quercetin 3-O-beta-D-glucofuranoside  (EXP)
quercetin 3-O-beta-D-glucopyranoside  (EXP)
rotenone  (EXP)
SB 431542  (ISO)
senecionine  (EXP)
Senkirkine  (EXP)
sulforaphane  (ISO)
testosterone  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
tremolite asbestos  (ISO)
tributylstannane  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
valproic acid  (EXP,ISO)
venlafaxine hydrochloride  (EXP)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Aicher SA, etal., Brain Res 2002 Dec 27;958(2):454-8.
2. Dev KK, etal., Neuropharmacology. 1999 May;38(5):635-44.
3. Du J, etal., J Neurosci. 2004 Jul 21;24(29):6578-89.
4. Feligioni M, etal., J Neurochem. 2006 Oct;99(2):549-60. Epub 2006 Aug 11.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. GOA data from the GO Consortium
7. Herguedas B, etal., Science. 2016 Apr 29;352(6285):aad3873. doi: 10.1126/science.aad3873. Epub 2016 Mar 10.
8. Hirbec H, etal., J Biol Chem. 2002 May 3;277(18):15221-4. Epub 2002 Mar 12.
9. Kato AS, etal., Neuron. 2008 Sep 25;59(6):986-96. doi: 10.1016/j.neuron.2008.07.034.
10. Keinanen K, etal., Science 1990 Aug 3;249(4968):556-60.
11. Kurschner C, etal., Mol Cell Neurosci. 1998 Jun;11(3):161-72.
12. Levy RB and Aoki C, J Neurosci. 2002 Jun 15;22(12):5001-15.
13. Lu CR, etal., J Comp Neurol. 2005 May 30;486(2):169-78.
14. Madden DR Nat Rev Neurosci. 2002 Feb;3(2):91-101.
15. MGD Curation, June 12, 2002
16. MGD data from the GO Consortium
17. Moga DE, etal., J Comp Neurol. 2003 Jul 14;462(1):15-28. doi: 10.1002/cne.10710.
18. Nakanishi N, etal., Neuron 1990 Nov;5(5):569-81.
19. Nakatsu Y, etal., Toxicol Appl Pharmacol. 2009 Oct 15;240(2):292-8. Epub 2009 Jul 7.
20. NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. Nishimune A, etal., Neuron. 1998 Jul;21(1):87-97.
22. Nishizaki T and Matsumura T, Brain Res Mol Brain Res 2002 Jan 31;98(1-2):130-4.
23. OMIM Disease Annotation Pipeline
24. Pipeline to import KEGG annotations from KEGG into RGD
25. Radley JJ, etal., Brain Res. 2007 Feb 23;1134(1):87-94. Epub 2007 Jan 17.
26. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
27. RGD automated import pipeline for gene-chemical interactions
28. Schwenk J, etal., Science. 2009 Mar 6;323(5919):1313-9. doi: 10.1126/science.1167852.
29. Shi S, etal., Cell. 2001 May 4;105(3):331-43.
30. Sommer B, etal., Science 1990 Sep 28;249(4976):1580-5.
31. Sutton MA, etal., Nature 2003 Jan 2;421(6918):70-5.
32. Xia J, etal., Neuron 1999 Jan;22(1):179-87.
33. Zhao WQ, etal., J Biol Chem. 2010 Mar 5;285(10):7619-32. doi: 10.1074/jbc.M109.057182. Epub 2009 Dec 23.
Additional References at PubMed
PMID:2168579   PMID:7992055   PMID:8889548   PMID:9069286   PMID:10414981   PMID:10688364   PMID:12477932   PMID:12665613   PMID:14706873   PMID:14969735   PMID:15260958   PMID:15610164  
PMID:16436610   PMID:17093100   PMID:17256974   PMID:17873364   PMID:19020286   PMID:19063943   PMID:19200070   PMID:20869354   PMID:21141507   PMID:21172611   PMID:22044924   PMID:22632720  
PMID:22871113   PMID:23212166   PMID:23296627   PMID:23375774   PMID:23884930   PMID:25524891   PMID:27641494   PMID:28103481   PMID:28951554  


Genomics

Comparative Map Data
Gria3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X120,238,515 - 120,504,106 (+)NCBI
Rnor_6.0 EnsemblX127,562,660 - 127,829,753 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X127,561,843 - 127,829,763 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X127,655,758 - 127,922,244 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X3,452,523 - 3,718,486 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X3,460,084 - 3,724,042 (-)NCBI
CeleraX119,369,614 - 119,631,774 (+)NCBICelera
Cytogenetic MapXq35NCBI
GRIA3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX123,184,153 - 123,490,915 (+)EnsemblGRCh38hg38GRCh38
GRCh38X123,184,278 - 123,490,915 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X122,318,131 - 122,624,766 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X122,145,777 - 122,452,447 (+)NCBINCBI36hg18NCBI36
Build 34X122,043,692 - 122,064,066NCBI
CeleraX122,704,041 - 123,010,712 (+)NCBI
Cytogenetic MapXq25NCBI
HuRefX111,704,466 - 112,009,621 (+)NCBIHuRef
CHM1_1X122,228,980 - 122,535,894 (+)NCBICHM1_1
Gria3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X40,489,351 - 40,767,478 (+)NCBIGRCm39mm39
GRCm39 EnsemblX40,489,731 - 40,767,478 (+)Ensembl
GRCm38X41,400,819 - 41,678,601 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX41,400,854 - 41,678,601 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X38,754,481 - 39,031,778 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X37,646,141 - 37,923,227 (+)NCBImm8
CeleraX28,988,899 - 29,264,344 (+)NCBICelera
Cytogenetic MapXA4NCBI
cM MapX23.19NCBI
Gria3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547311,281,379 - 11,574,907 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495547311,283,642 - 11,574,836 (-)NCBIChiLan1.0ChiLan1.0
GRIA3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X122,562,571 - 122,870,130 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX122,562,330 - 122,870,130 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X112,380,229 - 112,687,740 (+)NCBIMhudiblu_PPA_v0panPan3
GRIA3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblX94,730,943 - 95,004,279 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X94,729,828 - 95,006,244 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Gria3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364797,050,018 - 7,323,047 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GRIA3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX100,827,461 - 101,109,209 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X100,827,293 - 101,109,213 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X115,591,526 - 115,873,477 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GRIA3
(Chlorocebus sabaeus - African green monkey)
No map positions available.
Gria3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247971,775,105 - 2,167,651 (+)NCBI

Position Markers
DXGot55  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X127,612,051 - 127,612,247NCBIRnor6.0
Rnor_5.0X127,705,805 - 127,706,001UniSTSRnor5.0
RGSC_v3.4X3,668,948 - 3,669,157RGDRGSC3.4
RGSC_v3.4X3,668,949 - 3,669,157UniSTSRGSC3.4
RGSC_v3.1X3,674,504 - 3,674,713RGD
CeleraX119,418,712 - 119,418,919UniSTS
Cytogenetic MapXq11UniSTS
RH143176  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X127,761,592 - 127,761,704NCBIRnor6.0
Rnor_5.0X127,854,198 - 127,854,310UniSTSRnor5.0
RGSC_v3.4X3,521,277 - 3,521,389UniSTSRGSC3.4
CeleraX119,564,585 - 119,564,697UniSTS
RH 3.4 Map5717.3UniSTS
Cytogenetic MapXq11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X70352120127888215Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X82930791127930791Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X101333032146333032Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX107886746152409805Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X110957467155957467Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X110957467155957467Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X118715462159970021Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX120045041143145818Rat
5685004Bss104Bone structure and strength QTL 1043.9tibia area (VT:1000281)tibia area measurement (CMO:0001382)X121442246134627946Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1672
Count of miRNA genes:341
Interacting mature miRNAs:487
Transcripts:ENSRNOT00000010367, ENSRNOT00000029031
Prediction methods:Microtar, Miranda, Pita, Pita,Targetscan, 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 24 15 9 60 28 11
Low 3 19 28 27 10 27 7 7 14 34 13 7
Below cutoff 12 12 12 1 4 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001112742 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_032990 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257496 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257498 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601950 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601951 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005497951 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF201350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC091324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF559208 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BQ205510 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB713194 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473991 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DV723256 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EV762496 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000458 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M36420 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M38062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M85036 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X54656 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000010367   ⟹   ENSRNOP00000010367
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX127,562,660 - 127,829,753 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000029031   ⟹   ENSRNOP00000031170
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX127,562,660 - 127,829,753 (+)Ensembl
RefSeq Acc Id: NM_001112742   ⟹   NP_001106213
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X120,238,988 - 120,504,106 (+)NCBI
Rnor_6.0X127,562,660 - 127,829,763 (+)NCBI
Rnor_5.0X127,655,758 - 127,922,244 (+)NCBI
RGSC_v3.4X3,452,523 - 3,718,486 (-)RGD
CeleraX119,369,614 - 119,631,774 (+)RGD
Sequence:
RefSeq Acc Id: NM_032990   ⟹   NP_116785
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X120,238,988 - 120,504,106 (+)NCBI
Rnor_6.0X127,562,660 - 127,829,763 (+)NCBI
Rnor_5.0X127,655,758 - 127,922,244 (+)NCBI
RGSC_v3.4X3,452,523 - 3,718,486 (-)RGD
CeleraX119,369,614 - 119,631,774 (+)RGD
Sequence:
RefSeq Acc Id: XM_006257496   ⟹   XP_006257558
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X120,238,524 - 120,504,106 (+)NCBI
Rnor_6.0X127,561,874 - 127,829,763 (+)NCBI
Rnor_5.0X127,655,758 - 127,922,244 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257498   ⟹   XP_006257560
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X120,238,524 - 120,504,106 (+)NCBI
Rnor_6.0X127,561,843 - 127,829,763 (+)NCBI
Rnor_5.0X127,655,758 - 127,922,244 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257499   ⟹   XP_006257561
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X127,562,531 - 127,819,864 (+)NCBI
Rnor_5.0X127,655,758 - 127,922,244 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257501   ⟹   XP_006257563
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X120,238,517 - 120,504,106 (+)NCBI
Rnor_6.0X127,561,852 - 127,829,763 (+)NCBI
Rnor_5.0X127,655,758 - 127,922,244 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601950   ⟹   XP_017457439
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X120,238,833 - 120,504,106 (+)NCBI
Rnor_6.0X127,562,531 - 127,829,763 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601951   ⟹   XP_017457440
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X120,238,515 - 120,504,106 (+)NCBI
Rnor_6.0X127,561,852 - 127,829,763 (+)NCBI
Sequence:
RefSeq Acc Id: XR_001842597
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X127,562,531 - 127,779,024 (+)NCBI
Sequence:
RefSeq Acc Id: XR_005497951
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X120,238,831 - 120,496,821 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_116785   ⟸   NM_032990
- Peptide Label: isoform 1 precursor
- UniProtKB: P19492 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001106213   ⟸   NM_001112742
- Peptide Label: isoform 2 precursor
- UniProtKB: P19492 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006257560   ⟸   XM_006257498
- Peptide Label: isoform X2
- UniProtKB: G3V8Y9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257563   ⟸   XM_006257501
- Peptide Label: isoform X1
- UniProtKB: G3V6Z5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257558   ⟸   XM_006257496
- Peptide Label: isoform X1
- UniProtKB: G3V6Z5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257561   ⟸   XM_006257499
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017457440   ⟸   XM_017601951
- Peptide Label: isoform X2
- UniProtKB: G3V8Y9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457439   ⟸   XM_017601950
- Peptide Label: isoform X1
- UniProtKB: G3V6Z5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000031170   ⟸   ENSRNOT00000029031
RefSeq Acc Id: ENSRNOP00000010367   ⟸   ENSRNOT00000010367
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)
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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)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (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/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 127803894 127803895 T C snv ACI/N (MCW), Buf/N (MCW), WKY/N (MCW), M520/N (MCW), MR/N (MCW), F344/NRrrc (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:70958 AgrOrtholog
BIND 144355
Ensembl Genes ENSRNOG00000007682 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000010367 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000031170 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000010367 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000029031 ENTREZGENE, UniProtKB/TrEMBL
InterPro ANF_lig-bd_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glu/Gly-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Iono_rcpt_met UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Iontro_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peripla_BP_I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29628 UniProtKB/Swiss-Prot
NCBI Gene 29628 ENTREZGENE
Pfam ANF_receptor UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lig_chan UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lig_chan-Glu_bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB GRIA3 RGD
PhenoGen Gria3 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 G3V6Z5 ENTREZGENE, UniProtKB/TrEMBL
  G3V8Y9 ENTREZGENE, UniProtKB/TrEMBL
  GRIA3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Gria3  glutamate ionotropic receptor AMPA type subunit 3  Gria3  glutamate receptor, ionotropic, AMPA 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-16 Gria3  glutamate receptor, ionotropic, AMPA 3  Gria3  glutamate receptor, ionotrophic, AMPA 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-24 Gria3  glutamate receptor, ionotrophic, AMPA 3  Gria3  glutamate receptor, ionotropic, AMPA3 (alpha 3)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-07-09 Gria3  glutamate receptor, ionotropic, AMPA3 (alpha 3)      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_regulation 2-pyrrolidinone potentiation of AMPA receptor activity may occur via inhibition of calcium/calmodulin-dependent protein kinase (CaMKII) 728843