Epha3 (Eph receptor A3) - Rat Genome Database

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Gene: Epha3 (Eph receptor A3) Rattus norvegicus
Analyze
Symbol: Epha3
Name: Eph receptor A3
RGD ID: 68389
Description: Predicted to enable GPI-linked ephrin receptor activity; growth factor binding activity; and transmembrane-ephrin receptor activity. Involved in fever generation; response to cytokine; and response to lipopolysaccharide. Predicted to be located in several cellular components, including actin cytoskeleton; early endosome; and nucleus. Predicted to be part of receptor complex. Predicted to be active in GABA-ergic synapse; neuron projection; and presynapse. Predicted to be integral component of plasma membrane. Human ortholog(s) of this gene implicated in pancreatic cancer. Orthologous to human EPHA3 (EPH receptor A3); PARTICIPATES IN altered ephrin - ephrin receptor bidirectional signaling pathway; ephrin - ephrin receptor bidirectional signaling axis; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: EK4; EPH-like kinase 4; ephrin type-A receptor 3; rEK4; tyrosine-protein kinase receptor REK4; tyrosine-protein kinase TYRO4
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
mRatBN7.2111,138,485 - 1,474,102 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl111,140,985 - 1,473,900 (-)Ensembl
Rnor_6.011421,253 - 783,037 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl11421,135 - 782,954 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.011420,518 - 782,868 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.411696,185 - 1,033,287 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.111696,200 - 1,033,287 (-)NCBI
Celera111,134,161 - 1,466,533 (-)NCBICelera
Cytogenetic Map11p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
(S)-nicotine  (ISO)
1,2-dichloroethane  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-naphthylamine  (ISO)
acetamide  (EXP)
acrylamide  (ISO)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antimycin A  (ISO)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP)
bucladesine  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
cocaine  (EXP)
DDD  (ISO)
DDE  (ISO)
DDT  (ISO)
dibutyl phthalate  (EXP)
dieldrin  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
endrin  (ISO)
entinostat  (ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
gamma-hexachlorocyclohexane  (ISO)
genistein  (EXP,ISO)
Licochalcone B  (ISO)
medroxyprogesterone acetate  (ISO)
methoxychlor  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
nicotine  (ISO)
ozone  (EXP)
panobinostat  (ISO)
permethrin  (EXP)
phenylmercury acetate  (ISO)
picoxystrobin  (ISO)
pioglitazone  (ISO)
ponatinib  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
rofecoxib  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sunitinib  (ISO)
temozolomide  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
valproic acid  (ISO)
XL147  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11870224   PMID:11877430   PMID:15145949   PMID:17046737   PMID:17910947   PMID:18403711   PMID:19505147   PMID:21135139   PMID:21791286   PMID:22275477   PMID:23242526   PMID:27721017  


Genomics

Comparative Map Data
Epha3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2111,138,485 - 1,474,102 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl111,140,985 - 1,473,900 (-)Ensembl
Rnor_6.011421,253 - 783,037 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl11421,135 - 782,954 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.011420,518 - 782,868 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.411696,185 - 1,033,287 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.111696,200 - 1,033,287 (-)NCBI
Celera111,134,161 - 1,466,533 (-)NCBICelera
Cytogenetic Map11p12NCBI
EPHA3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl389,107,621 - 89,482,134 (+)EnsemblGRCh38hg38GRCh38
GRCh38389,107,621 - 89,482,134 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37389,156,771 - 89,531,284 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36389,239,364 - 89,613,974 (+)NCBINCBI36hg18NCBI36
Build 34389,239,501 - 89,532,185NCBI
Celera389,910,744 - 90,285,017 (+)NCBI
Cytogenetic Map3p11.1NCBI
HuRef389,169,906 - 89,544,877 (+)NCBIHuRef
CHM1_1389,109,505 - 89,484,203 (+)NCBICHM1_1
Epha3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391663,363,895 - 63,684,538 (-)NCBIGRCm39mm39
GRCm39 Ensembl1663,363,897 - 63,684,538 (-)Ensembl
GRCm381663,543,532 - 63,864,175 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1663,543,534 - 63,864,175 (-)EnsemblGRCm38mm10GRCm38
MGSCv371663,545,044 - 63,863,983 (-)NCBIGRCm37mm9NCBIm37
MGSCv361663,487,420 - 63,806,359 (-)NCBImm8
Celera1663,844,890 - 64,154,791 (-)NCBICelera
Cytogenetic Map16C1.3NCBI
Epha3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554074,138,362 - 4,500,688 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554074,135,671 - 4,500,900 (-)NCBIChiLan1.0ChiLan1.0
EPHA3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1391,369,233 - 91,737,300 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl391,369,239 - 91,739,056 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0389,261,166 - 89,629,010 (+)NCBIMhudiblu_PPA_v0panPan3
EPHA3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.133770,234 - 1,092,063 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl33769,423 - 1,115,986 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha33949,355 - 1,298,894 (+)NCBI
ROS_Cfam_1.033810,080 - 1,159,494 (+)NCBI
UMICH_Zoey_3.133779,847 - 1,129,604 (+)NCBI
UNSW_CanFamBas_1.033811,416 - 1,161,165 (+)NCBI
UU_Cfam_GSD_1.0331,284,819 - 1,381,967 (+)NCBI
Epha3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404971462,842 - 799,414 (-)NCBI
SpeTri2.0NW_004936610462,842 - 799,466 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
EPHA3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13166,591,686 - 166,942,767 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113166,592,492 - 166,942,791 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213177,406,602 - 177,539,843 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Sscrofa10.213177,670,369 - 177,810,115 (-)NCBISscrofa10.2Sscrofa10.2susScr3
EPHA3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12287,480,220 - 87,840,628 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2287,480,126 - 87,838,512 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604178,860,955 - 79,218,698 (+)NCBIVero_WHO_p1.0
Epha3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247895,534,011 - 5,925,592 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
Epha3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2111,140,949 - 1,141,092 (+)MAPPERmRatBN7.2
Rnor_6.011423,718 - 423,860NCBIRnor6.0
Rnor_5.011422,983 - 423,125UniSTSRnor5.0
RGSC_v3.411696,150 - 696,292UniSTSRGSC3.4
Celera111,134,126 - 1,134,268UniSTS
Cytogenetic Map11p12UniSTS
UniSTS:498373  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2111,161,712 - 1,161,779 (+)MAPPERmRatBN7.2
Rnor_6.011444,421 - 444,487NCBIRnor6.0
Rnor_5.011443,716 - 443,782UniSTSRnor5.0
RGSC_v3.411716,927 - 716,993UniSTSRGSC3.4
Celera111,154,834 - 1,154,900UniSTS
Cytogenetic Map11p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)11121836709Rat
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11135331169Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:35
Count of miRNA genes:31
Interacting mature miRNAs:34
Transcripts:ENSRNOT00000040065
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 48 16 16 5
Low 43 38 27 9 27 4 4 26 11 23 6 4
Below cutoff 2 19 14 8 14 4 4 8 2 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000040065   ⟹   ENSRNOP00000043263
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl111,140,985 - 1,473,900 (-)Ensembl
Rnor_6.0 Ensembl11423,753 - 782,954 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000090197   ⟹   ENSRNOP00000068593
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl111,140,985 - 1,459,294 (-)Ensembl
Rnor_6.0 Ensembl11421,135 - 768,644 (-)Ensembl
RefSeq Acc Id: NM_031564   ⟹   NP_113752
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2111,140,985 - 1,473,900 (-)NCBI
Rnor_6.011423,753 - 782,954 (-)NCBI
Rnor_5.011420,518 - 782,868 (-)NCBI
RGSC_v3.411696,185 - 1,033,287 (-)RGD
Celera111,134,161 - 1,466,533 (-)RGD
Sequence:
RefSeq Acc Id: XM_006247976   ⟹   XP_006248038
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2111,138,485 - 1,474,100 (-)NCBI
Rnor_6.011421,253 - 783,037 (-)NCBI
Rnor_5.011420,518 - 782,868 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006247977   ⟹   XP_006248039
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2111,138,485 - 1,459,324 (-)NCBI
Rnor_6.011421,253 - 769,783 (-)NCBI
Rnor_5.011420,518 - 782,868 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039088234   ⟹   XP_038944162
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2111,138,485 - 1,474,102 (-)NCBI
RefSeq Acc Id: XM_039088235   ⟹   XP_038944163
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2111,138,485 - 1,459,191 (-)NCBI
RefSeq Acc Id: XM_039088236   ⟹   XP_038944164
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2111,138,485 - 1,398,187 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_113752   ⟸   NM_031564
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_006248038   ⟸   XM_006247976
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006248039   ⟸   XM_006247977
- Peptide Label: isoform X2
- UniProtKB: A0A0G2JT71 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068593   ⟸   ENSRNOT00000090197
RefSeq Acc Id: ENSRNOP00000043263   ⟸   ENSRNOT00000040065
RefSeq Acc Id: XP_038944162   ⟸   XM_039088234
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038944163   ⟸   XM_039088235
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038944164   ⟸   XM_039088236
- Peptide Label: isoform X4
Protein Domains
Eph LBD   Fibronectin type-III   Protein kinase   SAM

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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:68389 AgrOrtholog
Ensembl Genes ENSRNOG00000030285 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000043263 UniProtKB/TrEMBL
  ENSRNOP00000068593 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000040065 UniProtKB/TrEMBL
  ENSRNOT00000090197 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Eph_TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EphA3_rcpt_lig-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ephrin_rcpt_lig-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Galactose-bd-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Growth_fac_rcpt_cys_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kinase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot_kinase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM/pointed_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ser-Thr/Tyr_kinase_cat_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr-kin_ephrin_A/B_rcpt-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_cat_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_ephrin_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_rcpt_V_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29210 UniProtKB/Swiss-Prot
NCBI Gene 29210 ENTREZGENE
Pfam EphA2_TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ephrin_lbd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ephrin_rec_like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  fn3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pkinase_Tyr UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Epha3 PhenoGen
PIRSF TyrPK_ephrin_receptor UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS TYRKINASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE EGF_2 UniProtKB/Swiss-Prot
  EPH_LBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_TYR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RECEPTOR_TYR_KIN_V_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RECEPTOR_TYR_KIN_V_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART EPH_lbd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TyrKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47769 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49265 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57184 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JT71 ENTREZGENE, UniProtKB/TrEMBL
  EPHA3_RAT UniProtKB/Swiss-Prot
  G3V9D5_RAT UniProtKB/TrEMBL
  O08680 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Epha3  Eph receptor A3       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in leukemia cells, thymocytes from the subcapsulary region, cortex, and medulla and in epithelial cells of the thymic medulla 625721
gene_homology aa sequence for predicted gene shares 90-98% homology with human EPHA3, chick EphA3, and mouse EphA3 68243