Grik5 (glutamate ionotropic receptor kainate type subunit 5) - Rat Genome Database

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Gene: Grik5 (glutamate ionotropic receptor kainate type subunit 5) Rattus norvegicus
Analyze
Symbol: Grik5
Name: glutamate ionotropic receptor kainate type subunit 5
RGD ID: 2735
Description: Enables identical protein binding activity; kainate selective glutamate receptor activity; and protein domain specific binding activity. Involved in several processes, including cellular response to glucose stimulus; positive regulation of neuron apoptotic process; and protein retention in ER lumen. Located in several cellular components, including perikaryon; postsynaptic density; and terminal bouton. Is integral component of postsynaptic membrane. Part of ionotropic glutamate receptor complex. Is active in glutamatergic synapse. Is integral component of presynaptic membrane. Used to study visual epilepsy. Biomarker of temporal lobe epilepsy. Orthologous to human GRIK5 (glutamate ionotropic receptor kainate type subunit 5); PARTICIPATES IN glutamate signaling pathway; INTERACTS WITH (+)-pilocarpine; 1-naphthyl isothiocyanate; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: GluK5; glutamate receptor ionotropic, kainate 5; glutamate receptor KA-2; glutamate receptor KA2; glutamate receptor, ionotropic kainate 5; glutamate receptor, ionotropic, kainate 5; iGlu5; KA2
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
mRatBN7.2180,605,878 - 80,667,896 (-)NCBI
Rnor_6.0 Ensembl181,885,521 - 81,946,714 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0181,885,516 - 81,946,731 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0183,137,805 - 83,207,039 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4180,313,801 - 80,384,390 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1180,391,911 - 80,462,398 (-)NCBI
Celera175,051,832 - 75,112,171 (-)NCBICelera
Cytogenetic Map1q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Bettler B, etal., Neuron 1992 Feb;8(2):257-65.
2. Feligioni M, etal., J Neurochem. 2006 Oct;99(2):549-60. Epub 2006 Aug 11.
3. Garcia EP, etal., Neuron. 1998 Oct;21(4):727-39.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Jiang HX, etal., J Neurosci Res. 2007 Oct;85(13):2960-70.
7. Kim M, etal., Auton Neurosci. 2008 Feb 29;138(1-2):83-90. Epub 2007 Dec 21.
8. Lomeli H, etal., FEBS Lett 1992 Jul 28;307(2):139-43.
9. Lu CR, etal., J Comp Neurol. 2005 May 30;486(2):169-78.
10. Lucifora S, etal., Pain. 2006 Jan;120(1-2):97-105. Epub 2005 Dec 15.
11. Mathern GW, etal., Neurobiol Dis. 1998 Sep;5(3):151-76.
12. MGD data from the GO Consortium
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. Paternain AV, etal., J Neurosci. 2000 Jan 1;20(1):196-205.
15. Pipeline to import KEGG annotations from KEGG into RGD
16. Ren Z, etal., J Neurosci. 2003 Jul 23;23(16):6608-16.
17. RGD automated data pipeline
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. Sander T, etal., Am J Med Genet 1997 Jul 25;74(4):416-21.
21. Santiago AR, etal., Invest Ophthalmol Vis Sci. 2006 Sep;47(9):4130-7.
22. Schiffer HH, etal., Neuron 1997 Nov;19(5):1141-6.
23. Smolders I, etal., Nat Neurosci 2002 Aug;5(8):796-804.
24. Sussman HM, etal., J Speech Hear Res. 1975 Mar;18(1):74-81.
25. Wyneken U, etal., Neuroscience. 2001;102(1):65-74.
Additional References at PubMed
PMID:1310861   PMID:1321949   PMID:1373632   PMID:12477932   PMID:12533602   PMID:12954862   PMID:15796762   PMID:16814779   PMID:17110338   PMID:17174564   PMID:22114280   PMID:22345355  
PMID:22509486   PMID:23288040   PMID:23975096  


Genomics

Comparative Map Data
Grik5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2180,605,878 - 80,667,896 (-)NCBI
Rnor_6.0 Ensembl181,885,521 - 81,946,714 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0181,885,516 - 81,946,731 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0183,137,805 - 83,207,039 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4180,313,801 - 80,384,390 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1180,391,911 - 80,462,398 (-)NCBI
Celera175,051,832 - 75,112,171 (-)NCBICelera
Cytogenetic Map1q21NCBI
GRIK5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1941,998,321 - 42,069,498 (-)EnsemblGRCh38hg38GRCh38
GRCh381941,998,316 - 42,071,804 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371942,502,468 - 42,569,967 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361947,194,313 - 47,261,797 (-)NCBINCBI36hg18NCBI36
Build 341947,194,312 - 47,261,797NCBI
Celera1939,302,092 - 39,369,575 (-)NCBI
Cytogenetic Map19q13.2NCBI
HuRef1938,934,282 - 39,001,175 (-)NCBIHuRef
CHM1_11942,504,085 - 42,571,606 (-)NCBICHM1_1
Grik5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39724,709,274 - 24,775,421 (-)NCBIGRCm39mm39
GRCm39 Ensembl724,709,274 - 24,771,771 (-)Ensembl
GRCm38725,009,849 - 25,075,694 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl725,009,849 - 25,072,346 (-)EnsemblGRCm38mm10GRCm38
MGSCv37725,794,868 - 25,857,388 (-)NCBIGRCm37mm9NCBIm37
MGSCv36724,718,636 - 24,781,058 (-)NCBImm8
Celera719,625,658 - 19,688,340 (-)NCBICelera
Cytogenetic Map7A3NCBI
cM Map713.73NCBI
Grik5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955555812,928 - 864,874 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955555804,907 - 865,395 (+)NCBIChiLan1.0ChiLan1.0
GRIK5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11947,389,253 - 47,549,018 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1947,389,804 - 47,544,604 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01938,886,108 - 38,956,938 (-)NCBIMhudiblu_PPA_v0panPan3
GRIK5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11112,270,157 - 112,321,672 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1112,270,424 - 112,321,672 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1111,702,486 - 111,753,731 (+)NCBI
ROS_Cfam_1.01112,887,140 - 112,941,269 (+)NCBI
UMICH_Zoey_3.11112,443,154 - 112,494,596 (+)NCBI
UNSW_CanFamBas_1.01112,079,617 - 112,130,847 (+)NCBI
UU_Cfam_GSD_1.01113,005,888 - 113,057,155 (+)NCBI
Grik5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934916,062,693 - 16,121,657 (+)NCBI
SpeTri2.0NW_004936706410,806 - 469,000 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GRIK5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl649,844,879 - 49,901,186 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1649,840,671 - 49,901,656 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2645,891,687 - 45,922,679 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GRIK5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1636,199,358 - 36,273,355 (-)NCBI
ChlSab1.1 Ensembl636,199,349 - 36,269,591 (-)Ensembl
Vero_WHO_p1.0NW_02366607314,441,791 - 14,521,580 (-)NCBI
Grik5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624907653,568 - 711,358 (+)NCBI

Position Markers
D1Wox65  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0181,945,931 - 81,946,140NCBIRnor6.0
Rnor_5.0183,206,263 - 83,206,472UniSTSRnor5.0
RGSC_v3.4180,383,607 - 80,383,816UniSTSRGSC3.4
Celera175,111,416 - 75,111,597UniSTS
Cytogenetic Map1q21UniSTS
BF404569  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2180,644,005 - 80,644,105 (+)MAPPER
Rnor_6.0181,923,654 - 81,923,753NCBIRnor6.0
Rnor_5.0183,174,789 - 83,174,888UniSTSRnor5.0
RGSC_v3.4180,360,726 - 80,360,825UniSTSRGSC3.4
Celera175,089,199 - 75,089,298UniSTS
RH 3.4 Map1824.1UniSTS
Cytogenetic Map1q21UniSTS
RH139022  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2180,645,930 - 80,646,103 (+)MAPPER
Rnor_6.0181,925,579 - 81,925,751NCBIRnor6.0
Rnor_5.0183,186,701 - 83,186,873UniSTSRnor5.0
RGSC_v3.4180,363,192 - 80,363,364UniSTSRGSC3.4
Celera175,091,065 - 75,091,237UniSTS
RH 3.4 Map6791.5UniSTS
Cytogenetic Map1q21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)125439386904217Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1565577285706974Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11131448983657083Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11131448983657083Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11131448983657083Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11131448983657083Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13537750894364229Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14190724986907249Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143579208126240667Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143579208126240667Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143579208126240667Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143579208126240667Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143579208126240667Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14954732883657083Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14957857794578577Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15052271494225616Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)15385134883657083Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15385134883657083Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)157761301104391981Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)158209327103209327Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)164588516125875986Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)166113339122614963Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)16722768394201552Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)179134941113593716Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)179689548124689548Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)17968976594909507Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:230
Count of miRNA genes:141
Interacting mature miRNAs:163
Transcripts:ENSRNOT00000027578
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 22 6 6 6 73 20 33
Low 3 20 38 24 17 24 7 10 1 15 8 11 7
Below cutoff 1 13 11 2 11 1 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000027578   ⟹   ENSRNOP00000027578
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl181,885,521 - 81,946,714 (-)Ensembl
RefSeq Acc Id: NM_031508   ⟹   NP_113696
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2180,605,887 - 80,667,072 (-)NCBI
Rnor_6.0181,885,516 - 81,946,714 (-)NCBI
Rnor_5.0183,137,805 - 83,207,039 (-)NCBI
RGSC_v3.4180,313,801 - 80,384,390 (-)RGD
Celera175,051,832 - 75,112,171 (-)RGD
Sequence:
RefSeq Acc Id: XM_006228382   ⟹   XP_006228444
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2180,605,878 - 80,667,895 (-)NCBI
Rnor_6.0181,885,516 - 81,946,731 (-)NCBI
Rnor_5.0183,137,805 - 83,207,039 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008758889   ⟹   XP_008757111
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2180,605,878 - 80,667,896 (-)NCBI
Rnor_6.0181,885,516 - 81,946,731 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039095322   ⟹   XP_038951250
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2180,605,878 - 80,667,896 (-)NCBI
RefSeq Acc Id: XM_039095358   ⟹   XP_038951286
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2180,605,878 - 80,656,361 (-)NCBI
RefSeq Acc Id: XM_039095397   ⟹   XP_038951325
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2180,605,878 - 80,667,895 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_113696   ⟸   NM_031508
- Peptide Label: precursor
- UniProtKB: Q63273 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006228444   ⟸   XM_006228382
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008757111   ⟸   XM_008758889
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000027578   ⟸   ENSRNOT00000027578
RefSeq Acc Id: XP_038951250   ⟸   XM_039095322
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038951325   ⟸   XM_039095397
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038951286   ⟸   XM_039095358
- Peptide Label: isoform X4

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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2735 AgrOrtholog
Ensembl Genes ENSRNOG00000020310 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000027578 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000027578 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro ANF_lig-bd_rcpt UniProtKB/Swiss-Prot
  Glu/Gly-bd UniProtKB/Swiss-Prot
  Iono_rcpt_met UniProtKB/Swiss-Prot
  Iontro_rcpt UniProtKB/Swiss-Prot
  Peripla_BP_I UniProtKB/Swiss-Prot
KEGG Report rno:24407 UniProtKB/Swiss-Prot
NCBI Gene 24407 ENTREZGENE
Pfam ANF_receptor UniProtKB/Swiss-Prot
  Lig_chan UniProtKB/Swiss-Prot
  Lig_chan-Glu_bd UniProtKB/Swiss-Prot
PharmGKB GRIK5 RGD
PhenoGen Grik5 PhenoGen
PRINTS NMDARECEPTOR UniProtKB/Swiss-Prot
SMART Lig_chan-Glu_bd UniProtKB/Swiss-Prot
  PBPe UniProtKB/Swiss-Prot
Superfamily-SCOP SSF53822 UniProtKB/Swiss-Prot
UniProt GRIK5_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q62643 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Grik5  glutamate ionotropic receptor kainate type subunit 5  Grik5  glutamate receptor, ionotropic, kainate 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Grik5  Glutamate receptor, ionotropic, kainate 5      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease allelic variants of the gene are associated with susceptibility to juvenile absence epilepsy 625595
gene_drugs antagonists (LY377770 and LY382884 ) prevent and interrupt limbic seizures induced by intra-hippocampal pilocarpine perfusion 625595
gene_function receptor for kainic acid ( a powerful convulsant) 625595
gene_process plays a role in frequency facilitation and induction of long-term potentiation (LTP) in mossy fiber pathways and in excitatory drives of inhibitory CA1 interneurons 625595