Arhgef28 (Rho guanine nucleotide exchange factor 28) - Rat Genome Database

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Gene: Arhgef28 (Rho guanine nucleotide exchange factor 28) Rattus norvegicus
Analyze
Symbol: Arhgef28
Name: Rho guanine nucleotide exchange factor 28
RGD ID: 1307061
Description: Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in cell morphogenesis and regulation of Rho protein signal transduction. Predicted to act upstream of or within central nervous system neuron axonogenesis and neurofilament cytoskeleton organization. Predicted to be located in cytoplasm and plasma membrane. Orthologous to human ARHGEF28 (Rho guanine nucleotide exchange factor 28); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 190 kDa guanine nucleotide exchange factor; LOC361882; p190-RhoGEF; p190RhoGEF; Rgnef; rho guanine nucleotide exchange factor; Rho guanine nucleotide exchange factor (GEF) 28; Rho-guanine nucleotide exchange factor
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
mRatBN7.2229,263,886 - 29,560,595 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl229,263,886 - 29,560,672 (-)Ensembl
Rnor_6.0225,738,514 - 26,011,429 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl225,738,514 - 26,011,429 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0244,892,452 - 45,152,594 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4228,492,591 - 28,767,567 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1228,408,913 - 28,695,327 (-)NCBI
Celera225,305,647 - 25,567,110 (-)NCBICelera
Cytogenetic Map2q12NCBI
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

References

Additional References at PubMed
PMID:11058585   PMID:15378065   PMID:16236762  


Genomics

Comparative Map Data
Arhgef28
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2229,263,886 - 29,560,595 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl229,263,886 - 29,560,672 (-)Ensembl
Rnor_6.0225,738,514 - 26,011,429 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl225,738,514 - 26,011,429 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0244,892,452 - 45,152,594 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4228,492,591 - 28,767,567 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1228,408,913 - 28,695,327 (-)NCBI
Celera225,305,647 - 25,567,110 (-)NCBICelera
Cytogenetic Map2q12NCBI
ARHGEF28
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl573,626,158 - 73,941,993 (+)EnsemblGRCh38hg38GRCh38
GRCh38573,626,179 - 73,941,993 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37572,922,021 - 73,237,815 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36572,957,739 - 73,243,284 (+)NCBINCBI36hg18NCBI36
Celera568,817,282 - 69,133,144 (+)NCBI
Cytogenetic Map5q13.2NCBI
HuRef568,127,485 - 68,443,411 (+)NCBIHuRef
CHM1_1572,354,714 - 72,670,522 (+)NCBICHM1_1
Arhgef28
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391398,035,103 - 98,343,183 (-)NCBIGRCm39mm39
GRCm39 Ensembl1398,035,977 - 98,342,947 (-)Ensembl
GRCm381397,898,594 - 98,206,675 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1397,899,469 - 98,206,439 (-)EnsemblGRCm38mm10GRCm38
MGSCv371398,668,550 - 98,976,120 (-)NCBIGRCm37mm9NCBIm37
MGSCv361398,999,618 - 99,306,324 (-)NCBImm8
Celera13101,556,320 - 101,856,395 (-)NCBICelera
Cytogenetic Map13D1NCBI
cM Map1351.6NCBI
Arhgef28
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542526,690,681 - 26,989,187 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542526,690,863 - 26,987,900 (-)NCBIChiLan1.0ChiLan1.0
ARHGEF28
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1541,976,692 - 42,289,389 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl541,976,692 - 42,231,634 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0541,376,631 - 41,690,868 (-)NCBIMhudiblu_PPA_v0panPan3
ARHGEF28
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1256,427,601 - 56,700,880 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl256,464,994 - 56,700,864 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha253,390,284 - 53,679,652 (+)NCBI
ROS_Cfam_1.0256,936,539 - 57,225,573 (+)NCBI
ROS_Cfam_1.0 Ensembl256,952,119 - 57,224,714 (+)Ensembl
UMICH_Zoey_3.1254,017,700 - 54,270,546 (+)NCBI
UNSW_CanFamBas_1.0254,764,885 - 55,053,289 (+)NCBI
UU_Cfam_GSD_1.0255,657,763 - 55,946,839 (+)NCBI
Arhgef28
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213187,881,219 - 188,173,026 (+)NCBI
SpeTri2.0NW_0049365492,685,953 - 2,977,754 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ARHGEF28
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl282,761,355 - 83,102,123 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1282,760,754 - 83,102,126 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2284,347,274 - 84,533,939 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ARHGEF28
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1467,987,275 - 68,298,359 (+)NCBIChlSab1.1chlSab2
ChlSab1.1467,987,275 - 68,298,359 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl468,112,244 - 68,298,438 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604916,757,711 - 17,069,260 (+)NCBIVero_WHO_p1.0
Arhgef28
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249241,069,343 - 1,343,639 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D2Got5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2229,429,161 - 29,429,355 (+)MAPPERmRatBN7.2
Rnor_6.0225,914,984 - 25,915,177NCBIRnor6.0
Rnor_5.0245,056,178 - 45,056,371UniSTSRnor5.0
RGSC_v3.4228,657,958 - 28,658,152RGDRGSC3.4
RGSC_v3.4228,657,959 - 28,658,152UniSTSRGSC3.4
RGSC_v3.1228,578,328 - 28,578,521RGD
Celera225,469,653 - 25,469,846UniSTS
RH 3.4 Map235.4UniSTS
RH 3.4 Map235.4RGD
RH 2.0 Map2119.6RGD
Cytogenetic Map2q12UniSTS
RH144139  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2229,305,538 - 29,305,702 (+)MAPPERmRatBN7.2
Rnor_6.0225,779,909 - 25,780,072NCBIRnor6.0
Rnor_5.0244,933,689 - 44,933,852UniSTSRnor5.0
RGSC_v3.4228,534,345 - 28,534,508UniSTSRGSC3.4
Celera225,347,018 - 25,347,181UniSTS
RH 3.4 Map232.2UniSTS
Cytogenetic Map2q12UniSTS
AI232335  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2229,295,068 - 29,295,170 (+)MAPPERmRatBN7.2
Rnor_6.0225,769,439 - 25,769,540NCBIRnor6.0
Rnor_5.0244,923,219 - 44,923,320UniSTSRnor5.0
RGSC_v3.4228,523,875 - 28,523,976UniSTSRGSC3.4
Celera225,336,548 - 25,336,649UniSTS
RH 3.4 Map233.4UniSTS
Cytogenetic Map2q12UniSTS
BE097280  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2229,280,981 - 29,281,140 (+)MAPPERmRatBN7.2
Rnor_6.0225,755,610 - 25,755,768NCBIRnor6.0
Rnor_5.0244,909,543 - 44,909,701UniSTSRnor5.0
RGSC_v3.4228,509,740 - 28,509,898UniSTSRGSC3.4
Celera225,322,930 - 25,323,088UniSTS
RH 3.4 Map232.1UniSTS
Cytogenetic Map2q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22490385374786777Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22691781781754745Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
1331764Bp205Blood pressure QTL 2053.476arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22699957143154682Rat
1643006Pain1Pain QTL 13.630.005mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)22699957148268661Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22715716072157160Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:112
Count of miRNA genes:95
Interacting mature miRNAs:103
Transcripts:ENSRNOT00000065143
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 17 35 14 11
Low 2 43 40 24 18 24 8 11 57 27 8
Below cutoff 15 15 1 15

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065143   ⟹   ENSRNOP00000059196
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl229,263,886 - 29,442,183 (-)Ensembl
Rnor_6.0 Ensembl225,738,514 - 26,011,429 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115432   ⟹   ENSRNOP00000083894
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl229,263,886 - 29,560,672 (-)Ensembl
RefSeq Acc Id: NM_001108542   ⟹   NP_001102012
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2229,263,886 - 29,528,600 (-)NCBI
Rnor_6.0225,738,514 - 26,011,429 (-)NCBI
Rnor_5.0244,892,452 - 45,152,594 (-)NCBI
RGSC_v3.4228,492,591 - 28,767,567 (-)RGD
Celera225,305,647 - 25,567,110 (-)RGD
Sequence:
RefSeq Acc Id: XM_006231817   ⟹   XP_006231879
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2229,264,715 - 29,383,504 (-)NCBI
Rnor_6.0225,738,516 - 25,858,512 (-)NCBI
Rnor_5.0244,892,452 - 45,152,594 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039102531   ⟹   XP_038958459
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2229,264,715 - 29,560,590 (-)NCBI
RefSeq Acc Id: XM_039102532   ⟹   XP_038958460
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2229,264,715 - 29,560,238 (-)NCBI
RefSeq Acc Id: XM_039102533   ⟹   XP_038958461
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2229,264,715 - 29,460,167 (-)NCBI
RefSeq Acc Id: XM_039102534   ⟹   XP_038958462
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2229,271,274 - 29,560,590 (-)NCBI
RefSeq Acc Id: XM_039102535   ⟹   XP_038958463
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2229,264,715 - 29,560,164 (-)NCBI
RefSeq Acc Id: XM_039102536   ⟹   XP_038958464
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2229,264,715 - 29,457,745 (-)NCBI
RefSeq Acc Id: XM_039102537   ⟹   XP_038958465
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2229,264,715 - 29,560,595 (-)NCBI
RefSeq Acc Id: XM_039102538   ⟹   XP_038958466
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2229,264,715 - 29,433,723 (-)NCBI
RefSeq Acc Id: XM_039102539   ⟹   XP_038958467
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2229,264,912 - 29,560,587 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001102012   ⟸   NM_001108542
- Sequence:
RefSeq Acc Id: XP_006231879   ⟸   XM_006231817
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: ENSRNOP00000059196   ⟸   ENSRNOT00000065143
RefSeq Acc Id: XP_038958465   ⟸   XM_039102537
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038958459   ⟸   XM_039102531
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038958460   ⟸   XM_039102532
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038958463   ⟸   XM_039102535
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038958461   ⟸   XM_039102533
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038958464   ⟸   XM_039102536
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038958466   ⟸   XM_039102538
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038958467   ⟸   XM_039102539
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038958462   ⟸   XM_039102534
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000083894   ⟸   ENSRNOT00000115432
Protein Domains
DH   PH

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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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
2 44923891 44923892 A T snv ACI/EurMcwi (MCW), ZFDM (KyushuU), FHL/EurMcwi (MCW), GH/OmrMcwi (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), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (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), GK/Ox (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), M520/N (KNAW), MNS/Gib (KNAW), SBN/Ygl (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), BUF/MNa (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), FHH/EurMcwi (MCW)
2 44924071 44924072 G T snv COP/CrCrl (MCW & UW), SBH/Ygl (MCW), SBH/Ygl (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), NIG-III/Hok (KyushuU)
2 44933859 44933860 C T snv SR/JrHsd (KNAW), SR/JrHsd (MCW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 29295741 29295742 A T snv ACI/EurMcwi (2019), ACI/N (2020), WN/N (2020), WKY/N (2020), WKY/NCrl (2019), SS/JrHsdMcwi (2019), SR/JrHsd (2020), BUF/N (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), GK/FarMcwi (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), MWF/Hsd (2019), PVG/Seac (2019)
2 29295921 29295922 G T snv SHRSP/A3NCrl (2019), HXB31/IpcvMcwi (2019), BXH3/CubMcwi (2020), BXH2/CubMcwi (2020), SHR/OlalpcvMcwi (2019)
2 29305709 29305710 C T snv SR/JrHsd (2020)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 25770111 25770112 A T snv SR/JrHsd (2020), SS/JrHsdMcwi (2019), WKY/NCrl (2019), WKY/N (2020), WN/N (2020), CDR, CDS, ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), ACI/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), M520/N (MCW), WKY/N (MCW), WN/N (MCW), ACI/EurMcwi (RGD), BBDP/Wor (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), FHL/EurMcwi (RGD), GK/Ox (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), SBN/Ygl (RGD), SR/JrHsd (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), WKY/NHsd (RGD), ACI/EurMcwi (2019), ACI/N (2020), BUF/N (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), GK/FarMcwi (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), MWF/Hsd (2019), PVG/Seac (2019)
2 25770291 25770292 G T snv COP/CrCrl (MCW & UW), SBH/Ygl (MCW), SBH/Ygl (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), HXB31/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019)
2 25780079 25780080 C T snv SR/JrHsd (MCW), SR/JrHsd (2020), SR/JrHsd (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307061 AgrOrtholog
Ensembl Genes ENSRNOG00000016544 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000059196 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000083894 ENTREZGENE
Ensembl Transcript ENSRNOT00000065143 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000115432 ENTREZGENE
Gene3D-CATH 1.20.900.10 UniProtKB/Swiss-Prot
  2.30.29.30 UniProtKB/Swiss-Prot
InterPro ARHGEF28_PH UniProtKB/Swiss-Prot
  DBL_dom_sf UniProtKB/Swiss-Prot
  DH-domain UniProtKB/Swiss-Prot
  PE/DAG-bd UniProtKB/Swiss-Prot
  PH-like_dom_sf UniProtKB/Swiss-Prot
  PH_16 UniProtKB/Swiss-Prot
  PH_domain UniProtKB/Swiss-Prot
NCBI Gene 361882 ENTREZGENE
Pfam C1_1 UniProtKB/Swiss-Prot
  PH_16 UniProtKB/Swiss-Prot
  RhoGEF UniProtKB/Swiss-Prot
PhenoGen Arhgef28 PhenoGen
PROSITE DH_2 UniProtKB/Swiss-Prot
  PH_DOMAIN UniProtKB/Swiss-Prot
  ZF_DAG_PE_1 UniProtKB/Swiss-Prot
  ZF_DAG_PE_2 UniProtKB/Swiss-Prot
SMART RhoGEF UniProtKB/Swiss-Prot
  SM00109 UniProtKB/Swiss-Prot
  SM00233 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48065 UniProtKB/Swiss-Prot
UniProt ARG28_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-19 Arhgef28  Rho guanine nucleotide exchange factor 28  Arhgef28  Rho guanine nucleotide exchange factor (GEF) 28  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-12 Arhgef28  Rho guanine nucleotide exchange factor (GEF) 28  Rgnef  Rho-guanine nucleotide exchange factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Rgnef  Rho-guanine nucleotide exchange factor   Rgnef_predicted  Rho-guanine nucleotide exchange factor (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Rgnef_predicted  Rho-guanine nucleotide exchange factor (predicted)      Symbol and Name status set to approved 70820 APPROVED