Rapgef3 (Rap guanine nucleotide exchange factor 3) - Rat Genome Database

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Gene: Rapgef3 (Rap guanine nucleotide exchange factor 3) Rattus norvegicus
Analyze
Symbol: Rapgef3
Name: Rap guanine nucleotide exchange factor 3
RGD ID: 621869
Description: Enables cAMP binding activity and transmembrane transporter binding activity. Involved in several processes, including animal organ development; positive regulation of cation transmembrane transport; and positive regulation of nitrogen compound metabolic process. Located in several cellular components, including basolateral part of cell; brush border membrane; and distal axon. Colocalizes with cortical actin cytoskeleton and plasma membrane. Orthologous to human RAPGEF3 (Rap guanine nucleotide exchange factor 3); PARTICIPATES IN adenosine signaling pathway; long term potentiation; INTERACTS WITH (S)-nicotine; 17alpha-ethynylestradiol; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cAMP-GEFI; cAMP-regulated guanine nucleotide exchange factor I (cAMP-GEFI); Epac; epac 1; exchange factor directly activated by cAMP 1; exchange protein directly activated by cAMP 1; MGC124613; Rap guanine nucleotide exchange factor (GEF) 3
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
mRatBN7.27128,875,772 - 128,898,203 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl7139,232,251 - 139,254,551 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07139,232,263 - 139,254,668 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07139,423,916 - 139,445,945 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47136,452,945 - 136,474,659 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17136,529,382 - 136,551,096 (-)NCBI
Celera7125,367,430 - 125,389,118 (-)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
angiogenesis  (IEA)
artery development  (IEP)
brain development  (IEP)
cellular response to cAMP  (IEA,ISO,ISS)
cellular response to L-dopa  (IEP)
cellular response to organic cyclic compound  (IEP)
cellular response to transforming growth factor beta stimulus  (IEP)
cellular response to xenobiotic stimulus  (IEP)
dorsal root ganglion development  (IEP)
establishment of endothelial barrier  (IEA,ISO,ISS)
liver regeneration  (IEP)
negative regulation of cardiac muscle cell apoptotic process  (IMP)
negative regulation of collagen biosynthetic process  (IMP)
negative regulation of syncytium formation by plasma membrane fusion  (IEA,ISO)
positive regulation of actin cytoskeleton reorganization  (IMP)
positive regulation of angiogenesis  (IEA,ISO,ISS)
positive regulation of calcium ion transmembrane transport  (IMP)
positive regulation of cell size  (IMP)
positive regulation of GTP binding  (IMP)
positive regulation of GTPase activity  (IEA,ISO,ISS)
positive regulation of peptidyl-serine phosphorylation  (IEA,ISO)
positive regulation of potassium:proton exchanging ATPase activity  (IMP)
positive regulation of protein acetylation  (IEA,ISO)
positive regulation of protein export from nucleus  (IEA,ISO)
positive regulation of protein phosphorylation  (IMP)
positive regulation of smooth muscle cell migration  (IMP)
positive regulation of stress fiber assembly  (IEA,ISO,ISS)
positive regulation of syncytium formation by plasma membrane fusion  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IMP)
Rap protein signal transduction  (IEA,ISO,ISS)
regulation of actin cytoskeleton reorganization  (IEA,ISO,ISS)
regulation of catalytic activity  (IEA)
regulation of histone H3-K9 acetylation  (ISO)
response to nicotine  (IEP)
small GTPase mediated signal transduction  (IEA)
spinal cord development  (IEP)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Borland G, etal., Mol Pharmacol. 2006 Jan;69(1):374-84. Epub 2005 Oct 21.
2. Broecker-Preuss M, etal., Horm Metab Res. 2015 Mar;47(3):200-8. doi: 10.1055/s-0034-1390484. Epub 2014 Nov 5.
3. Chen X, etal., Am J Med Genet B Neuropsychiatr Genet. 2004 Aug 15;129B(1):116-9.
4. Colombo G, etal., Brain Behav Immun. 2008 Aug;22(6):817-23. doi: 10.1016/j.bbi.2007.11.009. Epub 2008 Jan 4.
5. GOA data from the GO Consortium
6. Hochbaum D, etal., J Biol Chem. 2011 Jan 7;286(1):859-66. doi: 10.1074/jbc.M110.163816. Epub 2010 Nov 3.
7. Joshi R, etal., Mol Cell Endocrinol. 2014 Aug 5;393(1-2):152-63. doi: 10.1016/j.mce.2014.06.012. Epub 2014 Jun 25.
8. Kawasaki H, etal., Science 1998 Dec 18;282(5397):2275-9.
9. Konu O, etal., Brain Res. 2001 Aug 3;909(1-2):194-203.
10. Kwak HJ, etal., Cell Signal. 2008 May;20(5):803-14. doi: 10.1016/j.cellsig.2007.12.011. Epub 2007 Dec 28.
11. Laroche-Joubert N, etal., J Biol Chem 2002 May 24;277(21):18598-604.
12. Laurent AC, etal., Cardiovasc Res. 2015 Jan 1;105(1):55-64. doi: 10.1093/cvr/cvu242. Epub 2014 Nov 19.
13. Li JW, etal., J Genet. 2011 Dec;90(3):435-42.
14. Li Y, etal., Am J Physiol Renal Physiol. 2008 Aug;295(2):F525-33. Epub 2008 May 21.
15. Magiera MM, etal., Biochem J. 2004 Sep 15;382(Pt 3):803-10.
16. Metrich M, etal., Circ Res. 2008 Apr 25;102(8):959-65. doi: 10.1161/CIRCRESAHA.107.164947. Epub 2008 Mar 6.
17. MGD data from the GO Consortium
18. Miller CL, etal., Basic Res Cardiol. 2011 Nov;106(6):1023-39. doi: 10.1007/s00395-011-0228-2. Epub 2011 Oct 20.
19. Monceau V, etal., Radiother Oncol. 2014 Apr;111(1):63-71. doi: 10.1016/j.radonc.2014.01.025. Epub 2014 Apr 7.
20. Murray AJ and Shewan DA, Mol Cell Neurosci. 2008 Aug;38(4):578-88. doi: 10.1016/j.mcn.2008.05.006. Epub 2008 May 20.
21. NCBI rat LocusLink and RefSeq merged data July 26, 2002
22. Olmedo I, etal., Toxicol Appl Pharmacol. 2013 Oct 15;272(2):414-22. doi: 10.1016/j.taap.2013.06.022. Epub 2013 Jul 8.
23. Park KH, etal., J Neurosci Res. 2014 Dec;92(12):1746-56. doi: 10.1002/jnr.23450. Epub 2014 Jul 12.
24. Pereira L, etal., J Mol Cell Cardiol. 2012 Jan;52(1):283-91. doi: 10.1016/j.yjmcc.2011.10.016. Epub 2011 Oct 29.
25. Pietrobon M, etal., J Neurosci. 2011 Jun 8;31(23):8395-405. doi: 10.1523/JNEUROSCI.6722-10.2011.
26. Pipeline to import KEGG annotations from KEGG into RGD
27. Pipeline to import SMPDB annotations from SMPDB into RGD
28. Purves GI, etal., J Physiol. 2009 Jul 15;587(Pt 14):3639-50. doi: 10.1113/jphysiol.2009.173534.
29. RGD automated data pipeline
30. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
31. RGD automated import pipeline for gene-chemical interactions
32. Ruiz-Hurtado G, etal., J Mol Cell Cardiol. 2012 Nov;53(5):617-25. doi: 10.1016/j.yjmcc.2012.08.004. Epub 2012 Aug 19.
33. Shimomura H, etal., Arch Biochem Biophys. 2004 Nov 1;431(1):124-8.
34. Whitaker CM and Cooper NG, Neuroscience. 2009 Oct 31.
35. Yokoyama U, etal., Am J Physiol Heart Circ Physiol. 2008 Oct;295(4):H1547-55. doi: 10.1152/ajpheart.01317.2007. Epub 2008 Aug 8.
36. Yokoyama U, etal., J Biol Chem. 2008 Oct 17;283(42):28702-9. Epub 2008 Aug 11.
Additional References at PubMed
PMID:12477932   PMID:14622088   PMID:14712229   PMID:15133061   PMID:15334074   PMID:15545605   PMID:16076873   PMID:16123333   PMID:16207818   PMID:16684923   PMID:17234888   PMID:17702820  
PMID:17725712   PMID:17895835   PMID:18021770   PMID:18063584   PMID:18178724   PMID:18202100   PMID:18434542   PMID:18550542   PMID:18685024   PMID:19056867   PMID:19244230   PMID:19279233  
PMID:19592485   PMID:19661162   PMID:19666481   PMID:20007468   PMID:20585956   PMID:20640531   PMID:21393242   PMID:21454546   PMID:21840392   PMID:22076955   PMID:23080165   PMID:23376036  
PMID:23867755   PMID:24349260   PMID:24469067   PMID:24586073   PMID:24733293   PMID:25593293   PMID:25719403   PMID:26219954   PMID:26269639   PMID:26462734   PMID:26466753   PMID:26553454  
PMID:26854595   PMID:27142830   PMID:27385722   PMID:27789473   PMID:27984207   PMID:27995459   PMID:28039940   PMID:28216156   PMID:29037982   PMID:30225708   PMID:30551377  


Genomics

Comparative Map Data
Rapgef3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27128,875,772 - 128,898,203 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl7139,232,251 - 139,254,551 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07139,232,263 - 139,254,668 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07139,423,916 - 139,445,945 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47136,452,945 - 136,474,659 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17136,529,382 - 136,551,096 (-)NCBI
Celera7125,367,430 - 125,389,118 (-)NCBICelera
Cytogenetic Map7q36NCBI
RAPGEF3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1247,734,363 - 47,771,040 (-)EnsemblGRCh38hg38GRCh38
GRCh381247,734,363 - 47,758,880 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371248,128,146 - 48,152,663 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361246,417,293 - 46,438,952 (-)NCBINCBI36hg18NCBI36
Build 341246,417,293 - 46,438,822NCBI
Celera1246,925,923 - 46,950,362 (-)NCBI
Cytogenetic Map12q13.11NCBI
HuRef1245,159,564 - 45,184,005 (-)NCBIHuRef
CHM1_11248,094,358 - 48,118,798 (-)NCBICHM1_1
Rapgef3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391597,637,886 - 97,666,300 (-)NCBIGRCm39mm39
GRCm39 Ensembl1597,642,651 - 97,665,853 (-)Ensembl
GRCm381597,744,770 - 97,768,419 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1597,744,770 - 97,767,972 (-)EnsemblGRCm38mm10GRCm38
MGSCv371597,575,201 - 97,598,097 (-)NCBIGRCm37mm9NCBIm37
MGSCv361597,572,987 - 97,595,706 (-)NCBImm8
Celera1599,871,753 - 99,894,632 (-)NCBICelera
Cytogenetic Map15F1NCBI
Rapgef3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555006,655,056 - 6,674,311 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555006,655,056 - 6,674,311 (-)NCBIChiLan1.0ChiLan1.0
RAPGEF3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11241,836,354 - 41,873,252 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1241,848,785 - 41,873,252 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01240,974,756 - 40,999,471 (+)NCBIMhudiblu_PPA_v0panPan3
RAPGEF3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1276,993,452 - 7,030,372 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl276,993,452 - 7,017,316 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2739,291,724 - 39,314,353 (-)NCBI
ROS_Cfam_1.0277,060,331 - 7,082,948 (+)NCBI
UMICH_Zoey_3.1276,997,147 - 7,019,732 (+)NCBI
UNSW_CanFamBas_1.0277,032,603 - 7,055,256 (+)NCBI
UU_Cfam_GSD_1.02739,580,125 - 39,602,733 (-)NCBI
LOC101973720
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494567,505,399 - 67,557,201 (+)NCBI
SpeTri2.0NW_0049365125,636,197 - 5,659,606 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RAPGEF3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl578,101,289 - 78,134,103 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1578,101,286 - 78,134,150 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
RAPGEF3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11143,954,517 - 43,979,068 (-)NCBI
ChlSab1.1 Ensembl1143,957,425 - 43,978,047 (-)Ensembl
Vero_WHO_p1.0NW_023666037202,402,390 - 202,425,041 (+)NCBI
Rapgef3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248164,496,848 - 4,519,782 (+)NCBI


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:95
Count of miRNA genes:77
Interacting mature miRNAs:88
Transcripts:ENSRNOT00000067767
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 1 20 8 6 42 35 27 11
Low 2 23 49 41 13 41 8 11 32 14 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000078644   ⟹   ENSRNOP00000072633
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7139,232,251 - 139,254,149 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000083182   ⟹   ENSRNOP00000069952
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7139,232,830 - 139,254,551 (-)Ensembl
RefSeq Acc Id: NM_021690   ⟹   NP_067722
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27128,875,848 - 128,897,719 (-)NCBI
Rnor_6.07139,232,326 - 139,254,196 (-)NCBI
Rnor_5.07139,423,916 - 139,445,945 (-)NCBI
RGSC_v3.47136,452,945 - 136,474,659 (-)RGD
Celera7125,367,430 - 125,389,118 (-)RGD
Sequence:
RefSeq Acc Id: XM_039079828   ⟹   XP_038935756
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27128,875,772 - 128,897,757 (-)NCBI
RefSeq Acc Id: XM_039079829   ⟹   XP_038935757
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27128,875,785 - 128,898,203 (-)NCBI
RefSeq Acc Id: XM_039079830   ⟹   XP_038935758
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27128,875,772 - 128,896,526 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_067722   ⟸   NM_021690
- Sequence:
RefSeq Acc Id: ENSRNOP00000069952   ⟸   ENSRNOT00000083182
RefSeq Acc Id: ENSRNOP00000072633   ⟸   ENSRNOT00000078644
RefSeq Acc Id: XP_038935756   ⟸   XM_039079828
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038935758   ⟸   XM_039079830
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038935757   ⟸   XM_039079829
- Peptide Label: isoform X2
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)
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)
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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)
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)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621869 AgrOrtholog
Ensembl Genes ENSRNOG00000059961 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000069952 UniProtKB/TrEMBL
  ENSRNOP00000072633 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000078644 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000083182 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.10.840.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.60.120.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7936411 IMAGE-MGC_LOAD
InterPro cNMP-bd-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  cNMP-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DEP_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ras-like_GEF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ras-like_Gua-exchang_fac_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ras_G-nucl-exch_fac_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ras_GEF_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RASGEF_cat_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RASGEF_cat_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RmlC-like_jellyroll UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:59326 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124613 IMAGE-MGC_LOAD
NCBI Gene 59326 ENTREZGENE
PANTHER PTHR23113 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam cNMP_binding UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DEP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RasGEF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RasGEF_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rapgef3 PhenoGen
PROSITE CNMP_BINDING_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DEP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RASGEF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RASGEF_CAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RASGEF_NTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART cNMP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DEP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RasGEF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RasGEFN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF48366 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF51206 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54236 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JWN8_RAT UniProtKB/TrEMBL
  Q3B7C8_RAT UniProtKB/TrEMBL
  Q9Z1C8 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-20 Rapgef3  Rap guanine nucleotide exchange factor 3  Rapgef3  Rap guanine nucleotide exchange factor (GEF) 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Rapgef3  Rap guanine nucleotide exchange factor (GEF) 3    cAMP-regulated guanine nucleotide exchange factor I (cAMP-GEFI)  Name updated 1299863 APPROVED
2004-09-10 Rapgef3  cAMP-regulated guanine nucleotide exchange factor I (cAMP-GEFI)  Epac    Symbol and Name updated 1299863 APPROVED
2002-08-07 Epac  cAMP-regulated guanine nucleotide exchange factor I (cAMP-GEFI)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression mRNA is expressed in the neonatal brain including the septum and thalamus 632397
gene_process activates Ras and Ras-like small G-proteins 632397
gene_protein protein has binding sites for calcium, diacylglyserol and Rap-specific GEF 632397