Grik1 (glutamate ionotropic receptor kainate type subunit 1) - Rat Genome Database

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Gene: Grik1 (glutamate ionotropic receptor kainate type subunit 1) Rattus norvegicus
Analyze
Symbol: Grik1
Name: glutamate ionotropic receptor kainate type subunit 1
RGD ID: 2732
Description: Exhibits extracellular ligand-gated ion channel activity; glutamate binding activity; and identical protein binding activity. Involved in ionotropic glutamate receptor signaling pathway; modulation of chemical synaptic transmission; and nervous system development. Localizes to several cellular components, including glutamatergic synapse; integral component of plasma membrane; and neuronal cell body. Used to study status epilepticus. Human ortholog(s) of this gene implicated in childhood absence epilepsy. Orthologous to human GRIK1 (glutamate ionotropic receptor kainate type subunit 1); PARTICIPATES IN long term potentiation; glutamate signaling pathway; INTERACTS WITH (+)-pilocarpine; 17beta-estradiol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: GluK1; GluR-5; GluR5; glutamate receptor 5; glutamate receptor ionotropic kainate 1; glutamate receptor ionotropic, kainate 1; glutamate receptor, ionotropic kainate 1; glutamate receptor, ionotropic, kainate 1
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
mRatBN7.21127,169,739 - 27,571,131 (-)NCBI
Rnor_6.0 Ensembl1127,811,957 - 27,971,359 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01127,811,954 - 28,213,940 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01131,426,627 - 31,828,737 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41127,703,874 - 28,106,450 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11127,703,874 - 28,106,450 (-)NCBI
Celera1126,906,345 - 27,304,585 (-)NCBICelera
Cytogenetic Map11q11NCBI
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 1990 Nov;5(5):583-95.
2. Bortolotto ZA, etal., Nature. 1999 Nov 18;402(6759):297-301.
3. Braga MF, etal., J Neurosci. 2003 Jan 15;23(2):442-52.
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. Gryder DS and Rogawski MA, J Neurosci 2003 Aug 6;23(18):7069-74.
7. Guo W, etal., Eur J Pharmacol 2002 Oct 11;452(3):309-18.
8. Lu CR, etal., J Comp Neurol. 2005 May 30;486(2):169-78.
9. Lucifora S, etal., Pain. 2006 Jan;120(1-2):97-105. Epub 2005 Dec 15.
10. Mayer ML, etal., J Neurosci. 2006 Mar 15;26(11):2852-61.
11. MGD data from the GO Consortium
12. NCBI rat LocusLink and RefSeq merged data July 26, 2002
13. Online Mendelian Inheritance in Man, OMIM (TM).
14. Paternain AV, etal., J Neurosci. 2000 Jan 1;20(1):196-205.
15. Pipeline to import KEGG annotations from KEGG into RGD
16. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. RGD automated import pipeline for gene-chemical interactions
18. Rogawski MA, etal., Ann N Y Acad Sci. 2003 Apr;985:150-62.
19. Salinas GD, etal., J Biol Chem. 2006 Dec 29;281(52):40164-73. Epub 2006 Oct 24.
20. Sallert M, etal., Neuropharmacology. 2007 May;52(6):1354-65. Epub 2007 Feb 4.
21. Sander T, etal., Am J Med Genet 1997 Jul 25;74(4):416-21.
22. Shibata H, etal., Psychiatr Genet. 2001 Sep;11(3):139-44.
23. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
Additional References at PubMed
PMID:1322826   PMID:1373382   PMID:8889548   PMID:9069287   PMID:9335499   PMID:10516295   PMID:11069933   PMID:11144357   PMID:11985817   PMID:12223554   PMID:14715943   PMID:14724198  
PMID:15014126   PMID:15458844   PMID:15483117   PMID:15509753   PMID:15513934   PMID:15537878   PMID:15673679   PMID:15928066   PMID:17174564   PMID:17245443   PMID:17569736   PMID:18046310  
PMID:18678878   PMID:19043593   PMID:19123252   PMID:20848775   PMID:21734292   PMID:22279215   PMID:24069373   PMID:28100490   PMID:30421168   PMID:30451858  


Genomics

Comparative Map Data
Grik1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21127,169,739 - 27,571,131 (-)NCBI
Rnor_6.0 Ensembl1127,811,957 - 27,971,359 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01127,811,954 - 28,213,940 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01131,426,627 - 31,828,737 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41127,703,874 - 28,106,450 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11127,703,874 - 28,106,450 (-)NCBI
Celera1126,906,345 - 27,304,585 (-)NCBICelera
Cytogenetic Map11q11NCBI
GRIK1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2129,536,933 - 29,940,033 (-)EnsemblGRCh38hg38GRCh38
GRCh382129,536,933 - 29,939,996 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372130,909,254 - 31,312,314 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362129,831,125 - 30,234,153 (-)NCBINCBI36hg18NCBI36
Build 342129,831,126 - 30,234,153NCBI
Celera2116,092,373 - 16,495,412 (-)NCBI
Cytogenetic Map21q21.3NCBI
HuRef2116,317,387 - 16,721,110 (-)NCBIHuRef
CHM1_12130,470,770 - 30,873,809 (-)NCBICHM1_1
Grik1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391687,692,789 - 88,087,751 (-)NCBIGRCm39mm39
GRCm39 Ensembl1687,692,788 - 88,087,153 (-)Ensembl
GRCm381687,895,901 - 88,290,863 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1687,895,900 - 88,290,265 (-)EnsemblGRCm38mm10GRCm38
MGSCv371687,896,142 - 88,290,503 (-)NCBIGRCm37mm9NCBIm37
MGSCv361687,784,754 - 88,179,102 (-)NCBImm8
Celera1688,093,673 - 88,486,750 (-)NCBICelera
Cytogenetic Map16C3.3NCBI
cM Map1650.23NCBI
Grik1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540728,899,899 - 29,308,470 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540728,899,643 - 29,308,936 (-)NCBIChiLan1.0ChiLan1.0
GRIK1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12129,363,972 - 29,743,940 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2129,364,269 - 29,743,379 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02115,976,931 - 16,357,578 (-)NCBIMhudiblu_PPA_v0panPan3
GRIK1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13124,477,319 - 24,839,502 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3124,478,696 - 24,839,434 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3124,471,425 - 24,648,177 (-)NCBI
ROS_Cfam_1.03124,592,133 - 24,768,924 (-)NCBI
UMICH_Zoey_3.13124,542,198 - 24,719,018 (-)NCBI
UNSW_CanFamBas_1.03124,544,158 - 24,720,948 (-)NCBI
UU_Cfam_GSD_1.03125,015,707 - 25,192,582 (-)NCBI
Grik1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497124,931,282 - 25,310,559 (-)NCBI
SpeTri2.0NW_00493650012,157,215 - 12,536,555 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GRIK1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13192,877,618 - 193,294,952 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113192,877,707 - 193,296,954 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213203,411,219 - 203,897,606 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GRIK1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1262,286,828 - 62,692,061 (+)NCBI
Vero_WHO_p1.0NW_0236660714,856,919 - 5,276,564 (+)NCBI
Grik1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474517,592,587 - 17,986,863 (-)NCBI

Position Markers
RH132302  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21127,169,788 - 27,169,979 (+)MAPPER
Rnor_6.01127,812,004 - 27,812,194NCBIRnor6.0
Rnor_5.01131,426,677 - 31,426,867UniSTSRnor5.0
RGSC_v3.41127,703,924 - 27,704,114UniSTSRGSC3.4
Celera1126,906,395 - 26,906,585UniSTS
RH 3.4 Map11137.5UniSTS
Cytogenetic Map11q11UniSTS
D10S224  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21127,188,185 - 27,189,584 (+)MAPPER
Rnor_6.01127,830,716 - 27,832,114NCBIRnor6.0
Rnor_5.01131,445,389 - 31,446,787UniSTSRnor5.0
RGSC_v3.41127,722,321 - 27,723,719UniSTSRGSC3.4
Celera1126,924,740 - 26,926,138UniSTS
Cytogenetic Map11q11UniSTS
UniSTS:478959  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21127,413,001 - 27,413,216 (+)MAPPER
Rnor_6.01128,056,384 - 28,056,598NCBIRnor6.0
Rnor_5.01131,671,205 - 31,671,419UniSTSRnor5.0
RGSC_v3.41127,948,442 - 27,948,656UniSTSRGSC3.4
Celera1127,149,365 - 27,149,579UniSTS
Cytogenetic Map8q24UniSTS
Cytogenetic Map11q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11133867429Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11172720192Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)1132503169342559Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11935127454351274Rat
2290451Scl58Serum cholesterol level QTL 583.48blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)111136730644444347Rat
724517Uae18Urinary albumin excretion QTL 183.7urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)111632197346583360Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111947517979734728Rat
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)112194422966944229Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)112194422966944229Rat
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)112204314944444112Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112540112970401129Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112572003870720038Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112572003870720038Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:110
Count of miRNA genes:67
Interacting mature miRNAs:70
Transcripts:ENSRNOT00000042581, ENSRNOT00000050073, ENSRNOT00000051060
Prediction methods:Microtar, Miranda, Rnahybrid
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 46 2
Low 8 2 2 2 22 18 29
Below cutoff 1 14 9 6 10 6 3 3 6 5 7 1 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001111114 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001111117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_017241 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248054 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597946 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005491017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AI145540 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473989 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M83560 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M83561 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Z11712 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Z11713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Z11714 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000042581   ⟹   ENSRNOP00000050263
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1127,811,957 - 27,971,359 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000050073   ⟹   ENSRNOP00000045594
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1127,812,235 - 27,971,359 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000051060   ⟹   ENSRNOP00000046164
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1127,811,957 - 27,971,359 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081066   ⟹   ENSRNOP00000074448
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1127,812,751 - 27,971,359 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085629   ⟹   ENSRNOP00000069424
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1127,811,957 - 27,971,359 (-)Ensembl
RefSeq Acc Id: NM_001111114   ⟹   NP_001104584
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21127,169,739 - 27,570,273 (-)NCBI
Rnor_6.01127,811,954 - 28,213,539 (-)NCBI
Rnor_5.01131,426,627 - 31,828,737 (-)NCBI
RGSC_v3.41127,703,874 - 28,106,450 (-)RGD
Celera1126,906,345 - 27,304,585 (-)RGD
Sequence:
RefSeq Acc Id: NM_001111117   ⟹   NP_001104587
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21127,169,739 - 27,570,273 (-)NCBI
Rnor_6.01127,811,954 - 28,213,539 (-)NCBI
Rnor_5.01131,426,627 - 31,828,737 (-)NCBI
RGSC_v3.41127,703,874 - 28,106,450 (-)RGD
Celera1126,906,345 - 27,304,585 (-)RGD
Sequence:
RefSeq Acc Id: NM_017241   ⟹   NP_058937
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21127,169,739 - 27,570,273 (-)NCBI
Rnor_6.01127,811,954 - 28,213,539 (-)NCBI
Rnor_5.01131,426,627 - 31,828,737 (-)NCBI
RGSC_v3.41127,703,874 - 28,106,450 (-)RGD
Celera1126,906,345 - 27,304,585 (-)RGD
Sequence:
RefSeq Acc Id: XM_006248053   ⟹   XP_006248115
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21127,170,020 - 27,570,088 (-)NCBI
Rnor_6.01127,811,954 - 28,213,940 (-)NCBI
Rnor_5.01131,426,627 - 31,828,737 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248054   ⟹   XP_006248116
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21127,187,281 - 27,570,119 (-)NCBI
Rnor_6.01127,828,400 - 28,213,940 (-)NCBI
Rnor_5.01131,426,627 - 31,828,737 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597946   ⟹   XP_017453435
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01127,811,954 - 28,192,653 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597947   ⟹   XP_017453436
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21127,169,739 - 27,341,648 (-)NCBI
Rnor_6.01127,811,954 - 27,984,741 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597948   ⟹   XP_017453437
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01127,811,954 - 27,999,076 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597949   ⟹   XP_017453438
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01127,811,954 - 28,213,214 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039088252   ⟹   XP_038944180
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21127,187,370 - 27,570,088 (-)NCBI
RefSeq Acc Id: XM_039088253   ⟹   XP_038944181
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21127,200,581 - 27,571,131 (-)NCBI
RefSeq Acc Id: XR_005491017
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21127,170,034 - 27,570,119 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_058937   ⟸   NM_017241
- Peptide Label: isoform 2
- UniProtKB: P22756 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001104584   ⟸   NM_001111114
- Peptide Label: isoform 3
- UniProtKB: P22756 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001104587   ⟸   NM_001111117
- Peptide Label: isoform 1 precursor
- UniProtKB: P22756 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006248115   ⟸   XM_006248053
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006248116   ⟸   XM_006248054
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017453438   ⟸   XM_017597949
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017453435   ⟸   XM_017597946
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453437   ⟸   XM_017597948
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017453436   ⟸   XM_017597947
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000069424   ⟸   ENSRNOT00000085629
RefSeq Acc Id: ENSRNOP00000046164   ⟸   ENSRNOT00000051060
RefSeq Acc Id: ENSRNOP00000050263   ⟸   ENSRNOT00000042581
RefSeq Acc Id: ENSRNOP00000074448   ⟸   ENSRNOT00000081066
RefSeq Acc Id: ENSRNOP00000045594   ⟸   ENSRNOT00000050073
RefSeq Acc Id: XP_038944180   ⟸   XM_039088252
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038944181   ⟸   XM_039088253
- Peptide Label: isoform X5
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2732 AgrOrtholog
Ensembl Genes ENSRNOG00000001575 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000045594 UniProtKB/TrEMBL
  ENSRNOP00000046164 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000050263 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069424 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074448 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000042581 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000050073 UniProtKB/TrEMBL
  ENSRNOT00000051060 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000081066 UniProtKB/TrEMBL
  ENSRNOT00000085629 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:29559 UniProtKB/Swiss-Prot
NCBI Gene 29559 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
PhenoGen Grik1 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
TIGR TC221180
UniProt A0A0G2JVC0_RAT UniProtKB/TrEMBL
  A0A0G2K830_RAT UniProtKB/TrEMBL
  A0A140TAF9_RAT UniProtKB/TrEMBL
  A0A140TAG6_RAT UniProtKB/TrEMBL
  F1M7M9_RAT UniProtKB/TrEMBL
  GRIK1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Grik1  glutamate ionotropic receptor kainate type subunit 1  Grik1  glutamate receptor, ionotropic, kainate 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Grik1  Glutamate receptor, ionotropic, kainate 1      Symbol and Name status set to approved 70586 APPROVED