Cckar (cholecystokinin A receptor) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Cckar (cholecystokinin A receptor) Rattus norvegicus
Analyze
Symbol: Cckar
Name: cholecystokinin A receptor
RGD ID: 2289
Description: Enables cholecystokinin receptor activity. Involved in several processes, including positive regulation of somatostatin secretion; reduction of food intake in response to dietary excess; and regulation of metal ion transport. Located in several cellular components, including endosome; lysosome; and terminal bouton. Used to study obesity and type 2 diabetes mellitus. Biomarker of pancreatic cancer. Human ortholog(s) of this gene implicated in obesity. Orthologous to human CCKAR (cholecystokinin A receptor); PARTICIPATES IN calcium/calcium-mediated signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3H-1,2-dithiole-3-thione; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CCK-A receptor; Cck-ar; CCK1-R; cholecystokinin receptor type A; cholecystokinin-1 receptor
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: QTLs:   Niddm28  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21457,292,397 - 57,300,747 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1457,292,397 - 57,300,747 (+)Ensembl
Rnor_6.01459,610,939 - 59,619,786 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1459,611,434 - 59,619,783 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01459,691,504 - 59,747,723 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41462,052,510 - 62,057,201 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11462,054,843 - 62,064,735 (+)NCBI
Celera1456,400,364 - 56,408,663 (+)NCBICelera
RH 3.4 Map14455.67RGD
Cytogenetic Map14q11NCBI
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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Bellissimo N and Anderson GH, J Nutr. 2003 Jul;133(7):2319-25.
2. Bi S and Moran TH, Physiol Behav. 2003 Sep;79(4-5):655-61.
3. Bourassa J, etal., Biochem Biophys Res Commun. 1999 Jul 14;260(3):820-8.
4. De Jonghe BC, etal., Am J Physiol Gastrointest Liver Physiol. 2006 Oct;291(4):G640-9. Epub 2006 May 25.
5. Ding X, etal., Hepatobiliary Pancreat Dis Int. 2005 May;4(2):295-8.
6. El-Kouhen K and Morisset J, Pancreas. 2010 Mar;39(2):127-34.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. GOA data from the GO Consortium
9. Griesbacher T, etal., Pancreatology. 2006;6(1-2):65-75; discussion 75-6. Epub 2005 Dec 2.
10. Gunther R, etal., Pancreatology. 2003;3(1):47-54.
11. Hajnal A, etal., Am J Physiol Regul Integr Comp Physiol. 2005 Dec;289(6):R1675-86. Epub 2005 Aug 4.
12. Hashimoto H, etal., Auton Neurosci. 2005 Aug 31;121(1-2):16-25.
13. Hernandez-Gomez AM, etal., Amino Acids 2002;23(1-3):283-90.
14. Herness S, etal., J Neurosci. 2002 Nov 15;22(22):10018-29.
15. Hill DR, etal., Brain Res. 1988 Jun 28;454(1-2):101-5.
16. Inoue H, etal., Genomics 1997 Jun 1;42(2):331-5.
17. Jaworek J, etal., J Physiol Pharmacol. 2007 Jun;58(2):287-302.
18. Kiehne K, etal., Regul Pept. 2002 May 15;105(2):131-7.
19. Ko ES, etal., Peptides. 2006 Jul;27(7):1841-5. Epub 2006 Feb 10.
20. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
21. Leray V, etal., Peptides. 2003 Dec;24(12):1929-34.
22. MGD data from the GO Consortium
23. Miyasaka K, etal., J Pharmacol Sci. 2006 Aug;101(4):280-5. Epub 2006 Aug 5.
24. Moonka R, etal., J Gastrointest Surg. 1999 Mar-Apr;3(2):134-40.
25. Moran TH and Bi S, Philos Trans R Soc Lond B Biol Sci. 2006 Jul 29;361(1471):1211-8.
26. Moran TH, etal., Am J Physiol. 1998 Mar;274(3 Pt 2):R618-25.
27. Nakamura H, etal., J Gastroenterol. 1998 Oct;33(5):702-9.
28. NCBI rat LocusLink and RefSeq merged data July 26, 2002
29. Nomoto S, etal., Am J Physiol Regul Integr Comp Physiol. 2004 Sep;287(3):R556-61. Epub 2004 Jun 3.
30. Pipeline to import KEGG annotations from KEGG into RGD
31. Reidelberger RD, etal., Am J Physiol Regul Integr Comp Physiol 2003 Feb;284(2):R389-98.
32. Reidelberger RD, etal., Am J Physiol Regul Integr Comp Physiol 2003 Jan;284(1):R66-75.
33. Reubi JC, etal., Gastroenterology. 2003 Jul;125(1):98-106.
34. RGD automated data pipeline
35. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
36. RGD automated import pipeline for gene-chemical interactions
37. Rosewicz S, etal., Am J Physiol. 1994 Nov;267(5 Pt 1):G772-7.
38. Sorimachi M, etal., Neurosci Lett. 2001 Mar 9;300(2):91-4.
39. Sternini C, etal., Gastroenterology. 1999 Nov;117(5):1136-46.
40. Takiguchi S, etal., Gene 1997 Sep 15;197(1-2):169-75.
41. Tapia JA, etal., Biochim Biophys Acta 2002 Dec 16;1593(1):99-113.
42. Tarasova NI, etal., J Biol Chem. 1997 Jun 6;272(23):14817-24.
43. Wang J, etal., Pharmacogenetics. 2003 Jun;13(6):365-9.
44. Wank SA, etal., Proc Natl Acad Sci U S A 1992 Sep 15;89(18):8691-5.
45. Wei J and Hemmings GP, Eur Psychiatry 1999 Apr;14(2):67-70.
46. Weinberg DS, etal., J Clin Invest. 1997 Aug 1;100(3):597-603.
47. Wu SV, etal., Am J Physiol Gastrointest Liver Physiol. 2008 Sep;295(3):G641-7.
48. Yang X, etal., Sheng Li Xue Bao. 2006 Jun 25;58(3):275-80.
49. Zhou W, etal., Carcinogenesis. 1993 Oct;14(10):2189-92.
Additional References at PubMed
PMID:1313582   PMID:7654260   PMID:8024583   PMID:8503909   PMID:12016125   PMID:12457239   PMID:12562931   PMID:12651850   PMID:12800239   PMID:12855414   PMID:12916469   PMID:12932815  
PMID:14607104   PMID:14698681   PMID:14700745   PMID:14988658   PMID:15117731   PMID:15123537   PMID:15152034   PMID:15358606   PMID:16099824   PMID:16112401   PMID:16289472   PMID:16491099  
PMID:16556659   PMID:17505309   PMID:19026634   PMID:19111529   PMID:19533109   PMID:19887078   PMID:19940076   PMID:20001102   PMID:20347877   PMID:20624386   PMID:20843811   PMID:20953702  
PMID:21109591   PMID:21728335   PMID:21984583   PMID:22981453   PMID:23545074   PMID:24564397   PMID:24978951   PMID:32699194  


Genomics

Comparative Map Data
Cckar
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21457,292,397 - 57,300,747 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1457,292,397 - 57,300,747 (+)Ensembl
Rnor_6.01459,610,939 - 59,619,786 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1459,611,434 - 59,619,783 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01459,691,504 - 59,747,723 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41462,052,510 - 62,057,201 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11462,054,843 - 62,064,735 (+)NCBI
Celera1456,400,364 - 56,408,663 (+)NCBICelera
RH 3.4 Map14455.67RGD
Cytogenetic Map14q11NCBI
CCKAR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl426,481,396 - 26,490,484 (-)EnsemblGRCh38hg38GRCh38
GRCh38426,481,396 - 26,490,484 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37426,483,018 - 26,492,106 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36426,092,116 - 26,101,140 (-)NCBINCBI36hg18NCBI36
Build 34426,159,286 - 26,168,311NCBI
Celera426,934,075 - 26,943,099 (-)NCBI
Cytogenetic Map4p15.2NCBI
HuRef425,821,291 - 25,830,315 (-)NCBIHuRef
CHM1_1426,484,379 - 26,493,404 (-)NCBICHM1_1
Cckar
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39553,855,827 - 53,865,046 (-)NCBIGRCm39mm39
GRCm39 Ensembl553,855,118 - 53,865,047 (-)Ensembl
GRCm38553,698,485 - 53,707,704 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl553,697,776 - 53,707,705 (-)EnsemblGRCm38mm10GRCm38
MGSCv37554,089,724 - 54,098,943 (-)NCBIGRCm37mm9NCBIm37
MGSCv36553,986,735 - 53,996,350 (-)NCBImm8
Celera551,081,684 - 51,090,889 (-)NCBICelera
Cytogenetic Map5C1NCBI
cM Map529.52NCBI
Cckar
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544318,737,974 - 18,748,727 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544318,738,029 - 18,748,684 (+)NCBIChiLan1.0ChiLan1.0
CCKAR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1426,157,702 - 26,166,773 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl426,157,702 - 26,166,773 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0420,881,340 - 20,890,986 (-)NCBIMhudiblu_PPA_v0panPan3
CCKAR
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1384,010,700 - 84,019,066 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl384,010,205 - 84,021,293 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha386,523,114 - 86,531,436 (+)NCBI
ROS_Cfam_1.0384,979,595 - 84,989,334 (+)NCBI
UMICH_Zoey_3.1384,102,638 - 84,110,963 (+)NCBI
UNSW_CanFamBas_1.0384,222,497 - 84,230,820 (+)NCBI
UU_Cfam_GSD_1.0384,607,068 - 84,615,397 (+)NCBI
Cckar
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528549,605,282 - 49,613,370 (+)NCBI
SpeTri2.0NW_0049364773,306,898 - 3,314,659 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCKAR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl820,186,189 - 20,199,477 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1820,187,324 - 20,200,273 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2820,563,652 - 20,574,944 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CCKAR
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12723,855,766 - 23,866,104 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2723,856,705 - 23,865,367 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604770,369,554 - 70,378,492 (+)NCBIVero_WHO_p1.0
Cckar
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247556,122,181 - 6,132,623 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D14Wox26  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21457,294,664 - 57,294,870 (+)MAPPERmRatBN7.2
Rnor_6.01459,613,700 - 59,613,905NCBIRnor6.0
Rnor_5.01459,740,309 - 59,740,514UniSTSRnor5.0
RGSC_v3.41462,054,776 - 62,054,981UniSTSRGSC3.4
Celera1456,402,622 - 56,402,827UniSTS
Cytogenetic Map14q11UniSTS
D14Wox24  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21457,292,079 - 57,292,360 (+)MAPPERmRatBN7.2
Rnor_6.01459,611,115 - 59,611,397NCBIRnor6.0
Rnor_5.01459,737,724 - 59,738,006UniSTSRnor5.0
RGSC_v3.41462,052,193 - 62,052,473UniSTSRGSC3.4
Celera1456,400,067 - 56,400,327UniSTS
Cytogenetic Map14q11UniSTS
D14Wox25  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21457,293,870 - 57,293,950 (+)MAPPERmRatBN7.2
Rnor_6.01459,612,906 - 59,612,985NCBIRnor6.0
Rnor_5.01459,739,515 - 59,739,594UniSTSRnor5.0
RGSC_v3.41462,053,982 - 62,054,061UniSTSRGSC3.4
Celera1456,401,822 - 56,401,907UniSTS
Cytogenetic Map14q11UniSTS
PMC129753P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21457,293,392 - 57,293,524 (+)MAPPERmRatBN7.2
Rnor_6.01459,612,428 - 59,612,559NCBIRnor6.0
Rnor_5.01459,739,037 - 59,739,168UniSTSRnor5.0
RGSC_v3.41462,053,504 - 62,053,635UniSTSRGSC3.4
Celera1456,401,344 - 56,401,475UniSTS
Cytogenetic Map14q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143999825175582726Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:50
Count of miRNA genes:44
Interacting mature miRNAs:47
Transcripts:ENSRNOT00000065366
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 1 26 7 6 8 6 47 9 9 2
Below cutoff 1 24 17 3 17 2 2 21 18 10 8 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065366   ⟹   ENSRNOP00000063137
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1457,292,397 - 57,300,747 (+)Ensembl
Rnor_6.0 Ensembl1459,611,434 - 59,619,783 (+)Ensembl
RefSeq Acc Id: NM_012688   ⟹   NP_036820
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21457,292,397 - 57,300,747 (+)NCBI
Rnor_6.01459,611,434 - 59,619,783 (+)NCBI
Rnor_5.01459,691,504 - 59,747,723 (+)NCBI
RGSC_v3.41462,052,510 - 62,057,201 (+)RGD
Celera1456,400,364 - 56,408,663 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_036820 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA40899 (Get FASTA)   NCBI Sequence Viewer  
  BAA09170 (Get FASTA)   NCBI Sequence Viewer  
  BAA22847 (Get FASTA)   NCBI Sequence Viewer  
  EDL99868 (Get FASTA)   NCBI Sequence Viewer  
  P30551 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_036820   ⟸   NM_012688
- UniProtKB: P30551 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000063137   ⟸   ENSRNOT00000065366
Protein Domains
G_PROTEIN_RECEP_F1_2

Transcriptome

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

Promoters
RGD ID:13699328
Promoter ID:EPDNEW_R9853
Type:single initiation site
Name:Cckar_1
Description:cholecystokinin A receptor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01459,611,405 - 59,611,465EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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)
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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)
FHL/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
FXLE16/Stm (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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)
GK/FarMcwi (2019)
Visual CSV TAB Printer
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)
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
LEW/Crl (2019)
Visual CSV TAB Printer
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)
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
LEW/NCrlBR (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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
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)
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
MNS/Gib (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
MR/N (2020)
Visual CSV TAB Printer
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)
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
MWF/Hsd (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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: 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)
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: 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)
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/OlalpcvMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
SR/JrHsd (2020)
Visual CSV TAB Printer
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)
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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
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)
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/RijCrl (2020)
Visual CSV TAB Printer
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)
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
WKY/N (2020)
Visual CSV TAB Printer
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)
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
WKY/NCrl (2019)
Visual CSV TAB Printer
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)
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
WKY/NHsd (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
WN/N (2020)
Visual CSV TAB Printer
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)
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 59746322 59746323 C T snv ACI/EurMcwi (MCW), KFRS3B/Kyo (KyushuU), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), WN/N (KNAW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MHS/Gib (KNAW), MR/N (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), BUF/N (KNAW), DA/BklArbNsi (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), M520/N (KNAW), MNS/Gib (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), COP/CrCrl (MCW & UW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 57300677 57300678 C T snv ACI/EurMcwi (2019), WN/N (2020), BUF/N (2020), BXH3/CubMcwi (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), HXB20/IpcvMcwi (2020), HXB31/IpcvMcwi (2019), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LH/MavRrrcAek (2020), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SHR/OlalpcvMcwi (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), ACI/N (2020)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 59619713 59619714 C T snv CDR, CDS, ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), ACI/EurMcwi (RGD), BBDP/Wor (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), FHL/EurMcwi (RGD), LE/Stm (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), LL/MavRrrc (RGD), MHS/Gib (RGD), MNS/Gib (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), SHR/NHsd (RGD), SR/JrHsd (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WAG/Rij (RGD), WKY/Gcrc (RGD), ACI/EurMcwi (2019), ACI/N (2020), BUF/N (2020), BXH3/CubMcwi (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), HXB20/IpcvMcwi (2020), HXB31/IpcvMcwi (2019), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LH/MavRrrcAek (2020), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SHR/OlalpcvMcwi (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WN/N (2020)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2289 AgrOrtholog
Ensembl Genes ENSRNOG00000043124 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000063137 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065366 UniProtKB/TrEMBL
Gene3D-CATH 4.10.670.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Cholcskin_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cholcy_rcpt_A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CholecystokininA_recpt_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CholecystokininA_recpt_N_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Gastrin_rcpt UniProtKB/TrEMBL
  GPCR_Rhodpsn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCR_Rhodpsn_7TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24889 UniProtKB/Swiss-Prot
NCBI Gene 24889 ENTREZGENE
Pfam 7tm_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CholecysA-Rec_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cckar PhenoGen
PRINTS CCYSTOKININR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CCYSTOKNINAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GASTRINR UniProtKB/TrEMBL
  GPCRRHODOPSN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  G_PROTEIN_RECEP_F1_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART 7TM_GPCR_Srsx UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CCKAR_RAT UniProtKB/Swiss-Prot
  F1LQR7_RAT UniProtKB/TrEMBL
  P30551 ENTREZGENE
  V9H0R3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Cckar  Cholecystokinin A receptor      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease deletion in gene may be associated with hyperglycemia, hyperinsulinemia and mild obesity 634705
gene_expression expressed in pancreatic acinar cells 631304
gene_expression expressed in the peripheral region of the blood-brain barrier 631304
gene_function binds sulfated cholecystokinin peptides 631304
gene_function binds sulfated cholecystokinin peptides 634707
gene_process inhibits gastric emptying 628552
gene_process may be involved in inhibiting food intake 634706
gene_process may be involved in duodenal nutrient-induced inhibition of gastric emptying 628552
gene_process activation results in the tyrosine phosphorylation of PKC delta 631304
gene_product member of G protein coupled heptahelical superfamily 631304
gene_regulation binds and is activated by a carboxy-terminal octapeptide of cholecystokinin 631304