Gria4 (glutamate ionotropic receptor AMPA type subunit 4) - Rat Genome Database

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Gene: Gria4 (glutamate ionotropic receptor AMPA type subunit 4) Rattus norvegicus
Analyze
Symbol: Gria4
Name: glutamate ionotropic receptor AMPA type subunit 4
RGD ID: 61863
Description: Enables AMPA glutamate receptor activity and identical protein binding activity. Involved in chemical synaptic transmission; positive regulation of glutamatergic synaptic transmission; and response to fungicide. Located in several cellular components, including dendritic spine; glutamatergic synapse; and postsynaptic density. Is integral component of postsynaptic density membrane. Part of AMPA glutamate receptor complex and kainate selective glutamate receptor complex. Human ortholog(s) of this gene implicated in schizophrenia. Orthologous to human GRIA4 (glutamate ionotropic receptor AMPA type subunit 4); PARTICIPATES IN glutamate signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: AMPA-selective glutamate receptor 4; GluA4; GluR-D; Glur4; glutamate receptor 4; glutamate receptor ionotropic AMPA4 (alpha 4); glutamate receptor, ionotrophic, AMPA 4; glutamate receptor, ionotropic, 4; glutamate receptor, ionotropic, AMPA 4; glutamate receptor, ionotropic, AMPA4; glutamate receptor, ionotropic, AMPA4 (alpha 4)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.281,562,118 - 2,035,035 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl81,562,119 - 2,034,979 (-)Ensembl
Rnor_6.081,548,145 - 2,045,874 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl81,548,146 - 2,045,817 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.081,676,489 - 2,069,626 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.081,542,036 - 1,606,502 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48956,325 - 1,438,314 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18957,189 - 1,438,021 (-)NCBI
Celera81,445,037 - 1,902,161 (-)NCBICelera
Cytogenetic Map8q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Birdsey-Benson A, etal., J Neurosci. 2010 Jan 27;30(4):1463-70. doi: 10.1523/JNEUROSCI.4558-09.2010.
3. Boehm J and Malinow R, Biochem Soc Trans. 2005 Dec;33(Pt 6):1354-6.
4. Correia SS, etal., J Biol Chem. 2003 Feb 21;278(8):6307-13. Epub 2002 Dec 5.
5. Dutta A, etal., Structure. 2012 Nov 7;20(11):1838-49. doi: 10.1016/j.str.2012.08.012. Epub 2012 Sep 6.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Gill A, etal., Biochemistry. 2008 Dec 30;47(52):13831-41. doi: 10.1021/bi8013196.
8. GOA data from the GO Consortium
9. Gonzalez J, etal., Proc Natl Acad Sci U S A. 2010 May 25;107(21):9891-6. doi: 10.1073/pnas.0911854107. Epub 2010 May 10.
10. Herguedas B, etal., Science. 2016 Apr 29;352(6285):aad3873. doi: 10.1126/science.aad3873. Epub 2016 Mar 10.
11. Hirbec H, etal., J Biol Chem. 2002 May 3;277(18):15221-4. Epub 2002 Mar 12.
12. Jouppila A, etal., Eur J Biochem 2002 Dec;269(24):6261-70.
13. Kato AS, etal., Neuron. 2008 Sep 25;59(6):986-96. doi: 10.1016/j.neuron.2008.07.034.
14. Keinanen K, etal., Science 1990 Aug 3;249(4968):556-60.
15. Lu CR, etal., J Comp Neurol. 2005 May 30;486(2):169-78.
16. Madden DR Nat Rev Neurosci. 2002 Feb;3(2):91-101.
17. Makino C, etal., Am J Med Genet B Neuropsychiatr Genet 2003 Jan 1;116(1):17-22.
18. McPhie P, Biochemistry. 1975 Dec 2;14(24):5253-6.
19. MGD data from the GO Consortium
20. Nakatsu Y, etal., Toxicol Appl Pharmacol. 2009 Oct 15;240(2):292-8. Epub 2009 Jul 7.
21. NCBI rat LocusLink and RefSeq merged data July 26, 2002
22. Pipeline to import KEGG annotations from KEGG into RGD
23. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
24. RGD automated import pipeline for gene-chemical interactions
25. Rossmann M, etal., EMBO J. 2011 Mar 2;30(5):959-71. doi: 10.1038/emboj.2011.16. Epub 2011 Feb 11.
26. Schwenk J, etal., Science. 2009 Mar 6;323(5919):1313-9. doi: 10.1126/science.1167852.
27. Sommer B, etal., Science 1990 Sep 28;249(4976):1580-5.
28. Soto D, etal., Nat Neurosci. 2009 Mar;12(3):277-85. doi: 10.1038/nn.2266. Epub 2009 Feb 22.
29. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
30. Thomas GM, etal., EMBO J. 2008 Jan 23;27(2):361-72. doi: 10.1038/sj.emboj.7601969. Epub 2008 Jan 10.
31. Wyszynski M, etal., Neuron 2002 Mar 28;34(1):39-52.
32. Zhao WQ, etal., J Biol Chem. 2010 Mar 5;285(10):7619-32. doi: 10.1074/jbc.M109.057182. Epub 2009 Dec 23.
33. Zhu JJ, etal., Nat Neurosci. 2000 Nov;3(11):1098-106.
Additional References at PubMed
PMID:1309749   PMID:1372042   PMID:7992055   PMID:8889548   PMID:10027300   PMID:10688364   PMID:12477932   PMID:12574408   PMID:12911624   PMID:14706873   PMID:15883194   PMID:17873364  
PMID:18765917   PMID:19052206   PMID:19200070   PMID:19439609   PMID:20131911   PMID:21172611   PMID:21700703   PMID:21857658   PMID:22632720   PMID:23296627   PMID:23375774   PMID:24769233  
PMID:27157711   PMID:27714514  


Genomics

Comparative Map Data
Gria4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.281,562,118 - 2,035,035 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl81,562,119 - 2,034,979 (-)Ensembl
Rnor_6.081,548,145 - 2,045,874 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl81,548,146 - 2,045,817 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.081,676,489 - 2,069,626 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.081,542,036 - 1,606,502 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48956,325 - 1,438,314 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18957,189 - 1,438,021 (-)NCBI
Celera81,445,037 - 1,902,161 (-)NCBICelera
Cytogenetic Map8q11NCBI
GRIA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11105,609,994 - 105,982,092 (+)EnsemblGRCh38hg38GRCh38
GRCh3811105,609,540 - 105,982,090 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711105,480,800 - 105,852,817 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3611104,986,010 - 105,358,029 (+)NCBINCBI36hg18NCBI36
Build 3411104,986,934 - 105,355,676NCBI
Celera11102,645,046 - 103,017,070 (+)NCBI
Cytogenetic Map11q22.3NCBI
HuRef11101,412,072 - 101,783,915 (+)NCBIHuRef
CHM1_111105,364,023 - 105,735,685 (+)NCBICHM1_1
Gria4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3994,417,893 - 4,796,250 (-)NCBIGRCm39mm39
GRCm39 Ensembl94,417,896 - 4,796,234 (-)Ensembl
GRCm3894,417,893 - 4,796,234 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl94,417,896 - 4,796,234 (-)EnsemblGRCm38mm10GRCm38
MGSCv3794,417,893 - 4,796,234 (-)NCBIGRCm37mm9NCBIm37
MGSCv3694,417,896 - 4,796,142 (-)NCBImm8
Celera3117,909,944 - 118,286,524 (+)NCBICelera
Cytogenetic Map9A1NCBI
cM Map92.46NCBI
Gria4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554128,307,091 - 8,644,598 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554128,306,187 - 8,644,156 (+)NCBIChiLan1.0ChiLan1.0
GRIA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111103,982,785 - 104,357,629 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11103,983,862 - 104,355,280 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v011100,498,632 - 100,873,764 (+)NCBIMhudiblu_PPA_v0panPan3
GRIA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1526,272,008 - 26,642,819 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl526,272,970 - 26,642,100 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha526,197,215 - 26,574,534 (-)NCBI
ROS_Cfam_1.0526,300,625 - 26,678,461 (-)NCBI
UMICH_Zoey_3.1526,351,009 - 26,721,522 (-)NCBI
UNSW_CanFamBas_1.0526,236,451 - 26,607,672 (-)NCBI
UU_Cfam_GSD_1.0526,386,039 - 26,759,919 (-)NCBI
Gria4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494788,776,461 - 89,111,029 (+)NCBI
SpeTri2.0NW_0049365512,426,840 - 2,760,042 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GRIA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl935,441,999 - 35,805,361 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1935,442,060 - 35,803,989 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2939,465,051 - 39,839,043 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GRIA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1197,003,564 - 97,377,850 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl197,004,515 - 97,378,597 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604328,501,572 - 28,878,171 (-)NCBIVero_WHO_p1.0
Gria4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624784428,295 - 792,593 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D8Rat228  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.081,751,561 - 1,751,680NCBIRnor5.0
RGSC_v3.481,127,280 - 1,127,498RGDRGSC3.4
RGSC_v3.481,127,281 - 1,127,498UniSTSRGSC3.4
RGSC_v3.181,127,280 - 1,127,498RGD
SHRSP x BN Map81.0UniSTS
SHRSP x BN Map81.0RGD
FHH x ACI Map81.11RGD
Cytogenetic Map8q11UniSTS
D8Got3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.281,798,512 - 1,798,770 (+)MAPPERmRatBN7.2
Rnor_6.081,813,140 - 1,813,397NCBIRnor6.0
Rnor_5.081,834,282 - 1,834,539UniSTSRnor5.0
RGSC_v3.481,194,468 - 1,194,725RGDRGSC3.4
RGSC_v3.481,194,469 - 1,194,726UniSTSRGSC3.4
RGSC_v3.181,194,468 - 1,194,725RGD
Celera81,680,170 - 1,680,427UniSTS
RH 2.0 Map80.0RGD
Cytogenetic Map8q11UniSTS
AW531802  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.281,921,117 - 1,921,268 (+)MAPPERmRatBN7.2
mRatBN7.2154,615,370 - 4,615,517 (-)MAPPERmRatBN7.2
Rnor_6.081,933,354 - 1,933,504NCBIRnor6.0
Rnor_5.081,956,740 - 1,956,890UniSTSRnor5.0
Celera81,800,389 - 1,800,539UniSTS
Celera15250 - 399UniSTS
RH 3.4 Map1568.9UniSTS
Cytogenetic Map15p16UniSTS
Cytogenetic Map8q11UniSTS
UniSTS:25220  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.281,645,744 - 1,645,780 (+)MAPPERmRatBN7.2
mRatBN7.21670,197,622 - 70,198,235 (+)MAPPERmRatBN7.2
Rnor_6.081,631,735 - 1,631,770NCBIRnor6.0
Rnor_6.01675,193,146 - 75,193,758NCBIRnor6.0
Rnor_5.081,656,117 - 1,656,153NCBIRnor5.0
Rnor_5.01674,810,871 - 74,811,403NCBIRnor5.0
RGSC_v3.41674,874,971 - 74,875,583UniSTSRGSC3.4
RGSC_v3.481,039,345 - 1,039,380UniSTSRGSC3.4
Celera81,527,912 - 1,527,947UniSTS
Celera1668,076,960 - 68,077,572UniSTS
Cytogenetic Map8q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
71120Niddm21Non-insulin dependent diabetes mellitus QTL 213.73blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)813402289Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:101
Count of miRNA genes:77
Interacting mature miRNAs:92
Transcripts:ENSRNOT00000009542
Prediction methods:Miranda, 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 62 9
Low 4 16 8 8 8 8 10 10 23 2 8
Below cutoff 2 36 30 22 17 22 3 2 17 9 6

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001113184 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001113185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_017263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595510 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595511 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595512 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595513 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC107267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC128948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY158020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC093608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF390245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF390683 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF413680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB761818 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474089 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK598329 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DV726151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000188 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M36421 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M38063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M85037 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000009542   ⟹   ENSRNOP00000009542
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl81,562,119 - 2,034,979 (-)Ensembl
Rnor_6.0 Ensembl81,548,146 - 2,045,817 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078765   ⟹   ENSRNOP00000068876
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl81,623,212 - 2,034,979 (-)Ensembl
Rnor_6.0 Ensembl81,609,205 - 2,045,817 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081171   ⟹   ENSRNOP00000068940
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl81,562,119 - 2,034,979 (-)Ensembl
Rnor_6.0 Ensembl81,548,146 - 2,045,817 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111725   ⟹   ENSRNOP00000081710
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl81,625,181 - 2,034,979 (-)Ensembl
RefSeq Acc Id: NM_001113184   ⟹   NP_001106655
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.281,562,118 - 2,034,979 (-)NCBI
Rnor_6.081,548,145 - 2,045,817 (-)NCBI
Rnor_5.081,542,036 - 1,606,502 (-)NCBI
Rnor_5.081,676,489 - 2,069,626 (-)NCBI
RGSC_v3.48956,325 - 1,438,314 (-)RGD
Celera81,445,037 - 1,902,161 (-)RGD
Sequence:
RefSeq Acc Id: NM_001113185   ⟹   NP_001106656
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.281,623,211 - 2,034,979 (-)NCBI
Rnor_6.081,609,204 - 2,045,817 (-)NCBI
Rnor_5.081,542,036 - 1,606,502 (-)NCBI
Rnor_5.081,676,489 - 2,069,626 (-)NCBI
RGSC_v3.48956,325 - 1,438,314 (-)RGD
Celera81,505,395 - 1,902,161 (-)NCBI
Sequence:
RefSeq Acc Id: NM_017263   ⟹   NP_058959
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.281,562,118 - 2,034,979 (-)NCBI
Rnor_6.081,548,145 - 2,045,817 (-)NCBI
Rnor_5.081,542,036 - 1,606,502 (-)NCBI
Rnor_5.081,676,489 - 2,069,626 (-)NCBI
RGSC_v3.48956,325 - 1,438,314 (-)RGD
Celera81,445,037 - 1,902,161 (-)RGD
Sequence:
RefSeq Acc Id: XM_017595510   ⟹   XP_017450999
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.281,563,111 - 2,035,035 (-)NCBI
Rnor_6.081,549,189 - 2,045,872 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595511   ⟹   XP_017451000
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.281,563,111 - 2,035,035 (-)NCBI
Rnor_6.081,549,189 - 2,045,872 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039080969   ⟹   XP_038936897
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.281,585,908 - 2,035,034 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_058959   ⟸   NM_017263
- Peptide Label: isoform 1 precursor
- UniProtKB: P19493 (UniProtKB/Swiss-Prot),   A0A0G2JU28 (UniProtKB/TrEMBL),   Q566D4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001106655   ⟸   NM_001113184
- Peptide Label: isoform 2 precursor
- UniProtKB: P19493 (UniProtKB/Swiss-Prot),   G3V6W1 (UniProtKB/TrEMBL),   Q566D4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001106656   ⟸   NM_001113185
- Peptide Label: isoform 3 precursor
- UniProtKB: Q566D4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451000   ⟸   XM_017595511
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017450999   ⟸   XM_017595510
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000009542   ⟸   ENSRNOT00000009542
RefSeq Acc Id: ENSRNOP00000068940   ⟸   ENSRNOT00000081171
RefSeq Acc Id: ENSRNOP00000068876   ⟸   ENSRNOT00000078765
RefSeq Acc Id: XP_038936897   ⟸   XM_039080969
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000081710   ⟸   ENSRNOT00000111725
Protein Domains
ANF_receptor   Lig_chan-Glu_bd   PBPe

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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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/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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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/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:61863 AgrOrtholog
BIND 144347
Ensembl Genes ENSRNOG00000006957 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009542 UniProtKB/TrEMBL
  ENSRNOP00000068876 UniProtKB/TrEMBL
  ENSRNOP00000068940 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009542 UniProtKB/TrEMBL
  ENSRNOT00000078765 UniProtKB/TrEMBL
  ENSRNOT00000081171 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:29629 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 29629 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 Gria4 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 TC233174
UniProt A0A0G2JU28 ENTREZGENE, UniProtKB/TrEMBL
  G3V6W1 ENTREZGENE, UniProtKB/TrEMBL
  GRIA4_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q566D4 ENTREZGENE, UniProtKB/TrEMBL
  Q80ZF6_RAT UniProtKB/TrEMBL
UniProt Secondary Q64241 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Gria4  glutamate ionotropic receptor AMPA type subunit 4  Gria4  glutamate receptor, ionotropic, AMPA 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-16 Gria4  glutamate receptor, ionotropic, AMPA 4  Gria4  glutamate receptor, ionotrophic, AMPA 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-18 Gria4  glutamate receptor, ionotropic, AMPA4   Gria4  glutamate receptor, ionotropic, 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Gria4  glutamate receptor, ionotropic, 4      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference