Eya1 (EYA transcriptional coactivator and phosphatase 1) - Rat Genome Database

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Gene: Eya1 (EYA transcriptional coactivator and phosphatase 1) Rattus norvegicus
Analyze
Symbol: Eya1
Name: EYA transcriptional coactivator and phosphatase 1
RGD ID: 1584849
Description: Predicted to enable RNA binding activity and protein tyrosine phosphatase activity. Predicted to be involved in several processes, including cellular protein modification process; mesodermal cell fate specification; and positive regulation of nucleobase-containing compound metabolic process. Predicted to act upstream of or within several processes, including animal organ development; positive regulation of cell population proliferation; and regulation of signal transduction. Predicted to be located in cytoplasm and nuclear body. Predicted to be part of protein-DNA complex. Human ortholog(s) of this gene implicated in branchiootorenal syndrome and branchiootorenal syndrome 1. Orthologous to human EYA1 (EYA transcriptional coactivator and phosphatase 1); PARTICIPATES IN ataxia telangiectasia-mutated (ATM) signaling pathway; INTERACTS WITH acrylamide; bisphenol A; indole-3-methanol.
Type: protein-coding
RefSeq Status: MODEL
Also known as: eyes absent 1; eyes absent 1 homolog; eyes absent 1 homolog (Drosophila); eyes absent homolog 1; eyes absent homolog 1 (Drosophila); LOC108350919; LOC502935; similar to eyes absent 1 isoform a; uncharacterized LOC108350919
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
mRatBN7.254,863,501 - 5,101,483 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl54,955,543 - 5,101,483 (+)Ensembl
Rnor_6.054,275,728 - 4,495,525 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl54,373,626 - 4,513,142 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.054,252,745 - 4,487,853 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.454,132,825 - 4,276,837 (+)NCBIRGSC3.4rn4RGSC3.4
Celera54,454,356 - 4,554,997 (+)NCBICelera
Celera54,581,829 - 4,692,568 (+)NCBICelera
Cytogenetic Map5q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure development  (IBA,ISO)
animal organ morphogenesis  (ISO)
aorta morphogenesis  (ISO)
biological_process  (ND)
branching involved in ureteric bud morphogenesis  (ISO)
cell differentiation  (IBA)
cell fate commitment  (ISO)
cellular protein localization  (ISO)
cochlea morphogenesis  (ISO)
double-strand break repair  (ISO)
embryonic skeletal system morphogenesis  (ISO)
establishment of mitotic spindle orientation  (ISO)
establishment or maintenance of apical/basal cell polarity  (ISO)
histone dephosphorylation  (IBA,ISO)
inner ear morphogenesis  (ISO)
lung epithelial cell differentiation  (ISO)
mesodermal cell fate specification  (ISO)
metanephros development  (ISO)
middle ear morphogenesis  (ISO)
negative regulation of extrinsic apoptotic signaling pathway in absence of ligand  (IBA,ISO)
neuron fate specification  (ISO)
otic vesicle development  (ISO)
otic vesicle morphogenesis  (ISO)
outer ear morphogenesis  (ISO)
outflow tract morphogenesis  (ISO)
pattern specification process  (ISO)
peptidyl-tyrosine dephosphorylation  (IEA)
pharyngeal system development  (ISO)
positive regulation of DNA repair  (IBA,ISO)
positive regulation of epithelial cell proliferation  (ISO)
positive regulation of Notch signaling pathway  (ISO)
positive regulation of secondary heart field cardioblast proliferation  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of transcription, DNA-templated  (ISO)
protein dephosphorylation  (ISO)
protein sumoylation  (ISO)
regulation of neuron differentiation  (ISO)
response to ionizing radiation  (ISO)
semicircular canal morphogenesis  (ISO)
striated muscle tissue development  (ISO)
ureteric bud development  (ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10072433   PMID:10471511   PMID:12070080   PMID:12783782   PMID:14628052   PMID:15496442   PMID:15817220   PMID:16018995   PMID:16024294   PMID:16530750   PMID:16916509   PMID:16990542  
PMID:17098221   PMID:17785448   PMID:19234442   PMID:19497856   PMID:21364285   PMID:21936910   PMID:22513373  


Genomics

Comparative Map Data
Eya1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.254,863,501 - 5,101,483 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl54,955,543 - 5,101,483 (+)Ensembl
Rnor_6.054,275,728 - 4,495,525 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl54,373,626 - 4,513,142 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.054,252,745 - 4,487,853 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.454,132,825 - 4,276,837 (+)NCBIRGSC3.4rn4RGSC3.4
Celera54,454,356 - 4,554,997 (+)NCBICelera
Celera54,581,829 - 4,692,568 (+)NCBICelera
Cytogenetic Map5q11NCBI
EYA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl871,197,433 - 71,592,025 (-)EnsemblGRCh38hg38GRCh38
GRCh38871,197,433 - 71,548,104 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37872,109,668 - 72,460,329 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36872,272,222 - 72,437,021 (-)NCBINCBI36hg18NCBI36
Build 34872,272,221 - 72,437,021NCBI
Celera868,106,627 - 68,271,433 (-)NCBI
Cytogenetic Map8q13.3NCBI
HuRef867,603,371 - 67,768,504 (-)NCBIHuRef
CHM1_1872,164,260 - 72,329,031 (-)NCBICHM1_1
Eya1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39114,239,177 - 14,381,259 (-)NCBIGRCm39mm39
GRCm39 Ensembl114,239,178 - 14,380,459 (-)Ensembl
GRCm38114,168,953 - 14,311,035 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl114,168,954 - 14,310,235 (-)EnsemblGRCm38mm10GRCm38
MGSCv37114,159,039 - 14,300,280 (-)NCBIGRCm37mm9NCBIm37
MGSCv36114,154,172 - 14,295,413 (-)NCBImm8
Celera114,109,695 - 14,251,151 (-)NCBICelera
Cytogenetic Map1A3NCBI
cM Map14.31NCBI
Eya1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554448,495,530 - 8,655,100 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554448,336,071 - 8,655,041 (+)NCBIChiLan1.0ChiLan1.0
EYA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1869,387,769 - 69,551,829 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl869,387,769 - 69,551,829 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0867,728,057 - 68,060,069 (-)NCBIMhudiblu_PPA_v0panPan3
EYA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12920,176,306 - 20,595,131 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2920,177,014 - 20,525,653 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2920,436,698 - 20,855,121 (-)NCBI
ROS_Cfam_1.02920,275,380 - 20,693,971 (-)NCBI
UMICH_Zoey_3.12920,325,900 - 20,743,158 (-)NCBI
UNSW_CanFamBas_1.02920,378,421 - 20,796,035 (-)NCBI
UU_Cfam_GSD_1.02920,660,077 - 21,078,705 (-)NCBI
Eya1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530358,739,647 - 59,053,061 (+)NCBI
SpeTri2.0NW_004936648395,526 - 546,705 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
EYA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl463,970,511 - 64,328,105 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1463,970,939 - 64,328,107 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2469,915,648 - 69,943,761 (-)NCBISscrofa10.2Sscrofa10.2susScr3
EYA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1866,902,961 - 67,238,149 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl866,902,972 - 67,060,567 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603974,161,305 - 74,511,047 (+)NCBIVero_WHO_p1.0
Eya1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474419,782,174 - 19,975,496 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH131160  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.255,101,167 - 5,101,387 (+)MAPPERmRatBN7.2
Rnor_6.054,514,798 - 4,515,017NCBIRnor6.0
Rnor_5.054,487,538 - 4,487,757UniSTSRnor5.0
RGSC_v3.454,278,492 - 4,278,711UniSTSRGSC3.4
Celera54,692,253 - 4,692,472UniSTS
Cytogenetic Map5q11UniSTS
BE118841  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.255,087,195 - 5,087,397 (+)MAPPERmRatBN7.2
Rnor_6.054,501,555 - 4,501,756NCBIRnor6.0
Rnor_5.054,474,004 - 4,474,205UniSTSRnor5.0
RGSC_v3.454,261,648 - 4,261,849UniSTSRGSC3.4
Celera54,677,816 - 4,678,017UniSTS
RH 3.4 Map50.0UniSTS
Cytogenetic Map5q11UniSTS
Eya1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.255,013,761 - 5,014,209 (+)MAPPERmRatBN7.2
Rnor_6.054,424,872 - 4,425,319NCBIRnor6.0
Rnor_5.054,401,233 - 4,401,680UniSTSRnor5.0
Celera54,604,211 - 4,604,658UniSTS
Cytogenetic Map5q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
631551Vetf1Vascular elastic tissue fragility QTL 150.0001aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)522822265904428Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:53
Count of miRNA genes:50
Interacting mature miRNAs:52
Transcripts:ENSRNOT00000064946
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 1 2 4 11 16 9 2
Low 43 21 6 11 6 6 7 63 19 31 9 6
Below cutoff 1 11 11 7 11 1 2

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_006225171 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225174 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225175 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775886 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593674 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593675 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593676 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110907 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110908 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110911 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110912 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110913 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110914 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110916 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001843561 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001843562 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473984 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000157 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000064946   ⟹   ENSRNOP00000063439
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl54,955,543 - 5,101,483 (+)Ensembl
Rnor_6.0 Ensembl54,373,626 - 4,513,142 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082717   ⟹   ENSRNOP00000070005
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl54,961,075 - 5,101,483 (+)Ensembl
Rnor_6.0 Ensembl54,393,472 - 4,513,142 (+)Ensembl
RefSeq Acc Id: XM_039110905   ⟹   XP_038966833
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,863,501 - 5,101,483 (+)NCBI
RefSeq Acc Id: XM_039110906   ⟹   XP_038966834
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,863,506 - 5,101,483 (+)NCBI
RefSeq Acc Id: XM_039110907   ⟹   XP_038966835
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,863,501 - 5,101,483 (+)NCBI
RefSeq Acc Id: XM_039110908   ⟹   XP_038966836
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,863,505 - 5,101,483 (+)NCBI
RefSeq Acc Id: XM_039110909   ⟹   XP_038966837
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,863,504 - 5,101,483 (+)NCBI
RefSeq Acc Id: XM_039110910   ⟹   XP_038966838
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,960,849 - 5,101,483 (+)NCBI
RefSeq Acc Id: XM_039110911   ⟹   XP_038966839
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,955,650 - 5,101,483 (+)NCBI
RefSeq Acc Id: XM_039110912   ⟹   XP_038966840
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,960,842 - 5,101,483 (+)NCBI
RefSeq Acc Id: XM_039110913   ⟹   XP_038966841
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,955,487 - 5,101,483 (+)NCBI
RefSeq Acc Id: XM_039110914   ⟹   XP_038966842
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,983,203 - 5,101,483 (+)NCBI
RefSeq Acc Id: XM_039110916   ⟹   XP_038966844
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,983,203 - 5,101,483 (+)NCBI
Reference Sequences
RefSeq Acc Id: ENSRNOP00000070005   ⟸   ENSRNOT00000082717
RefSeq Acc Id: ENSRNOP00000063439   ⟸   ENSRNOT00000064946
RefSeq Acc Id: XP_038966833   ⟸   XM_039110905
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038966835   ⟸   XM_039110907
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038966837   ⟸   XM_039110909
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038966836   ⟸   XM_039110908
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038966834   ⟸   XM_039110906
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038966841   ⟸   XM_039110913
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038966839   ⟸   XM_039110911
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038966840   ⟸   XM_039110912
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038966838   ⟸   XM_039110910
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038966842   ⟸   XM_039110914
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038966844   ⟸   XM_039110916
- Peptide Label: isoform X9

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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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:1584849 AgrOrtholog
Ensembl Genes ENSRNOG00000007590 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000063439 UniProtKB/TrEMBL
  ENSRNOP00000070005 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064946 UniProtKB/TrEMBL
  ENSRNOT00000082717 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.12350 UniProtKB/TrEMBL
InterPro EYA_dom UniProtKB/TrEMBL
  EYA_dom_metazoan UniProtKB/TrEMBL
  EYA_dom_sf UniProtKB/TrEMBL
  EYA_fam UniProtKB/TrEMBL
  Eyes_absent_h1 UniProtKB/TrEMBL
NCBI Gene 502935 ENTREZGENE
PANTHER PTHR10190 UniProtKB/TrEMBL
  PTHR10190:SF11 UniProtKB/TrEMBL
PhenoGen Eya1 PhenoGen
TIGRFAMs EYA-cons_domain UniProtKB/TrEMBL
UniProt A0A0G2JWT3_RAT UniProtKB/TrEMBL
  D3ZVI5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Eya1  EYA transcriptional coactivator and phosphatase 1  LOC108350919  uncharacterized LOC108350919  Data Merged 737654 PROVISIONAL
2016-08-02 LOC108350919  uncharacterized LOC108350919      Symbol and Name status set to provisional 70820 PROVISIONAL
2014-06-25 Eya1  EYA transcriptional coactivator and phosphatase 1  Eya1  eyes absent homolog 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-29 Eya1  eyes absent homolog 1 (Drosophila)  Eya1  eyes absent 1 homolog (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Eya1  eyes absent 1 homolog (Drosophila)  LOC502935  similar to eyes absent 1 isoform a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC502935  similar to eyes absent 1 isoform a      Symbol and Name status set to provisional 70820 PROVISIONAL