Nek3 (NIMA-related kinase 3) - Rat Genome Database

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Gene: Nek3 (NIMA-related kinase 3) Rattus norvegicus
Analyze
Symbol: Nek3
Name: NIMA-related kinase 3
RGD ID: 1307419
Description: Predicted to enable ATP binding activity and protein kinase activity. Predicted to be involved in several processes, including neuron projection morphogenesis; protein phosphorylation; and regulation of tubulin deacetylation. Orthologous to human NEK3 (NIMA related kinase 3); INTERACTS WITH bisphenol A; diazinon; dieldrin.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC306576; NIMA (never in mitosis gene a)-related expressed kinase 3; NIMA (never in mitosis gene a)-related kinase 3; serine/threonine-protein kinase Nek3
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
mRatBN7.21669,867,020 - 69,892,477 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1669,867,047 - 69,892,508 (+)Ensembl
Rnor_6.01674,781,371 - 74,806,567 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1674,785,281 - 74,806,149 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01674,412,402 - 74,437,059 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41674,524,839 - 74,547,785 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11674,525,103 - 74,569,327 (+)NCBI
Celera1667,751,672 - 67,777,870 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
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

Biological Process

Molecular Function

References

Additional References at PubMed
PMID:15618286   PMID:19509051  


Genomics

Comparative Map Data
Nek3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21669,867,020 - 69,892,477 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1669,867,047 - 69,892,508 (+)Ensembl
Rnor_6.01674,781,371 - 74,806,567 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1674,785,281 - 74,806,149 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01674,412,402 - 74,437,059 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41674,524,839 - 74,547,785 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11674,525,103 - 74,569,327 (+)NCBI
Celera1667,751,672 - 67,777,870 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
NEK3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1352,132,639 - 52,159,861 (-)EnsemblGRCh38hg38GRCh38
GRCh381352,132,647 - 52,159,597 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371352,706,783 - 52,733,732 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361351,604,780 - 51,631,997 (-)NCBINCBI36hg18NCBI36
Build 341351,604,779 - 51,631,511NCBI
Celera1333,755,426 - 33,782,643 (-)NCBI
Cytogenetic Map13q14.3NCBI
HuRef1333,494,915 - 33,522,031 (-)NCBIHuRef
CHM1_11352,674,859 - 52,702,079 (-)NCBICHM1_1
Nek3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39822,618,299 - 22,657,009 (-)NCBIGRCm39mm39
GRCm39 Ensembl822,618,299 - 22,656,451 (-)Ensembl
GRCm38822,128,283 - 22,166,997 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl822,128,283 - 22,166,435 (-)EnsemblGRCm38mm10GRCm38
MGSCv37823,238,755 - 23,276,907 (-)NCBIGRCm37mm9NCBIm37
MGSCv36823,593,828 - 23,631,947 (-)NCBImm8
Celera823,623,168 - 23,659,067 (-)NCBICelera
Cytogenetic Map8A2NCBI
cM Map811.07NCBI
Nek3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554315,378,896 - 5,412,221 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554315,382,992 - 5,412,206 (-)NCBIChiLan1.0ChiLan1.0
NEK3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11352,003,518 - 52,030,538 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1352,003,518 - 52,030,212 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01333,261,186 - 33,288,316 (-)NCBIMhudiblu_PPA_v0panPan3
NEK3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.125118,558 - 130,901 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha25237,734 - 250,302 (-)NCBI
ROS_Cfam_1.025221,349 - 233,911 (-)NCBI
UMICH_Zoey_3.125102,210 - 114,767 (-)NCBI
UNSW_CanFamBas_1.025116,905 - 129,452 (-)NCBI
UU_Cfam_GSD_1.025184,724 - 197,292 (-)NCBI
Nek3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945161,356,381 - 161,383,259 (-)NCBI
SpeTri2.0NW_0049365654,840,416 - 4,863,349 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NEK3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1115,772,844 - 15,798,420 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11115,772,578 - 15,798,424 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21116,097,410 - 16,123,551 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NEK3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1330,018,641 - 30,048,787 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl330,018,635 - 30,045,216 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605713,765,557 - 13,795,721 (+)NCBIVero_WHO_p1.0
Nek3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247481,939,806 - 1,976,484 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH140165  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21669,892,161 - 69,892,366 (+)MAPPERmRatBN7.2
Rnor_6.01674,806,252 - 74,806,456NCBIRnor6.0
Rnor_5.01674,436,744 - 74,436,948UniSTSRnor5.0
RGSC_v3.41674,547,470 - 74,547,674UniSTSRGSC3.4
Celera1667,777,555 - 67,777,759UniSTS
RH 3.4 Map16691.1UniSTS
Cytogenetic Map16q12.5UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162515279370152793Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165571108783402471Rat
1298527Arunc2Aerobic running capacity QTL 22.9exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)166853271675029966Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:157
Count of miRNA genes:91
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000017106, ENSRNOT00000064316
Prediction methods:Microtar, 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 2 2 2 56 16 30 1
Low 3 43 55 39 19 39 8 11 18 19 11 10 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_001065115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006222274 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006222275 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006222276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006222277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006222278 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253359 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095233 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095234 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_224971 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000283 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000017106   ⟹   ENSRNOP00000017107
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1669,867,047 - 69,892,508 (+)Ensembl
Rnor_6.0 Ensembl1674,785,281 - 74,806,149 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000064316   ⟹   ENSRNOP00000061987
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1669,867,047 - 69,892,508 (+)Ensembl
Rnor_6.0 Ensembl1674,785,281 - 74,806,149 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090646   ⟹   ENSRNOP00000073909
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1669,867,047 - 69,892,508 (+)Ensembl
Rnor_6.0 Ensembl1674,785,281 - 74,806,149 (+)Ensembl
RefSeq Acc Id: XM_006253359   ⟹   XP_006253421
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21669,867,020 - 69,892,477 (+)NCBI
Rnor_6.01674,781,371 - 74,806,567 (+)NCBI
Rnor_5.01674,412,402 - 74,437,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006253360   ⟹   XP_006253422
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21669,867,033 - 69,892,477 (+)NCBI
Rnor_6.01674,781,371 - 74,806,567 (+)NCBI
Rnor_5.01674,412,402 - 74,437,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006253361   ⟹   XP_006253423
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21669,867,020 - 69,892,477 (+)NCBI
Rnor_6.01674,781,371 - 74,806,567 (+)NCBI
Rnor_5.01674,412,402 - 74,437,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006253362   ⟹   XP_006253424
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21669,867,020 - 69,892,477 (+)NCBI
Rnor_6.01674,781,371 - 74,806,567 (+)NCBI
Rnor_5.01674,412,402 - 74,437,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006253363   ⟹   XP_006253425
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21669,871,012 - 69,892,477 (+)NCBI
Rnor_6.01674,787,310 - 74,806,567 (+)NCBI
Rnor_5.01674,412,402 - 74,437,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039095233   ⟹   XP_038951161
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21669,867,020 - 69,887,917 (+)NCBI
RefSeq Acc Id: XM_039095234   ⟹   XP_038951162
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21669,867,020 - 69,887,911 (+)NCBI
RefSeq Acc Id: XM_224971   ⟹   XP_224971
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21669,867,020 - 69,892,477 (+)NCBI
Rnor_6.01674,781,371 - 74,806,567 (+)NCBI
Rnor_5.01674,412,402 - 74,437,059 (+)NCBI
RGSC_v3.41674,524,839 - 74,547,785 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: XP_224971   ⟸   XM_224971
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006253421   ⟸   XM_006253359
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006253423   ⟸   XM_006253361
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006253424   ⟸   XM_006253362
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006253422   ⟸   XM_006253360
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006253425   ⟸   XM_006253363
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000073909   ⟸   ENSRNOT00000090646
RefSeq Acc Id: ENSRNOP00000017107   ⟸   ENSRNOT00000017106
RefSeq Acc Id: ENSRNOP00000061987   ⟸   ENSRNOT00000064316
RefSeq Acc Id: XP_038951161   ⟸   XM_039095233
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038951162   ⟸   XM_039095234
- Peptide Label: isoform X6
Protein Domains
Protein kinase

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)
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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)
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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
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)
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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
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)
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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
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)
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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/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)
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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
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)
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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/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)
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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)
SS/JrHsdMcwi (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/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)
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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
WKY/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
WKY/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
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)
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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
WN/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
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
16 74416393 74416394 G A snv IS/Kyo (KyushuU), WKY/NHsd (KNAW), WKY/NCrl (KNAW), WKY/N (KNAW), WKY/Gcrc (KNAW), IS-Tlk/Kyo (KyushuU), SHR/OlaIpcvPrin (KNAW), SHR/OlaIpcv (KNAW), SHR/NHsd (KNAW), SHR/NCrlPrin (KNAW), COP/CrCrl (MCW & UW), SHRSP/Gcrc (KNAW)
16 74418412 74418413 C T snv LE/Stm (Illumina) (KNAW), BDIX.Cg-Tal/NemOda (KyushuU), BDIX/NemOda (KyushuU), F344/Jcl (KyushuU), LEC/Tj (KyushuU), F344/Stm (KyushuU), F344/NSlc (KyushuU), LE/Stm (KyushuU), F344/DuCrlCrlj (KyushuU), Crl:SD (UDEL), F344/NRrrc (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), FHL/EurMcwi (KNAW), F344/NHsd (KNAW), F344/NCrl (KNAW), F344/NRrrc (SOLiD) (KNAW), BBDP/WorN (KNAW), GH/OmrMcwi (MCW), FHL/EurMcwi (MCW)
16 74418550 74418551 G A snv LN/MavRrrc (KNAW), BUF/N (KNAW), LH/MavRrrc (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), LL/MavRrrc (KNAW), DA/BklArbNsi (KNAW), FHH/EurMcwi (KNAW), BUF/MNa (KyushuU), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), ZFDM (KyushuU), HTX/Kyo (KyushuU)
16 74427488 74427489 C A snv WN/N (KNAW), HWY/Slc (KyushuU), DOB/Oda (KyushuU)
16 74427566 74427567 C G snv WN/N (KNAW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 69871036 69871037 G A snv HXB10/IpcvMcwi (2019), HXB2/IpcvMcwi (2019), HXB4/IpcvMcwi (2020), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), WKY/NCrl (2019), WKY/N (2020)
16 69873055 69873056 C T snv LEXF2B/Stm (2019), PVG/Seac (2019), MR/N (2020), LEXF10A/StmMcwi (2020), LE/Stm (2019), LEXF4/Stm (2020), LEXF3/Stm (2020), LEXF1C/Stm (2019), LEXF1A/Stm (2019), LEXF11/Stm (2020), FXLE18/Stm (2020), FXLE16/Stm (2020), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019)
16 69873193 69873194 G A snv DA/OlaHsd (2019), SS/JrHsdMcwi (2019), BUF/N (2020), ACI/N (2020), LH/MavRrrcAek (2020), FHH/EurMcwi (2019), SR/JrHsd (2020), LN/MavRrrcAek (2020), LL/MavRrrcAek (2020), ACI/EurMcwi (2019)
16 69882611 69882612 C A snv WN/N (2020)
16 69882689 69882690 C G snv WN/N (2020)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 74785371 74785372 G A snv HXB10/IpcvMcwi (2019), WKY/NHsd (RGD), WKY/Gcrc (RGD), WKY/NCrl (RGD), SHRSP/Gcrc (RGD), SHR/NHsd (RGD), HXB2/IpcvMcwi (2019), COP/CrCrl (MCW & UW), WKY/N (2020), WKY/NCrl (2019), SHR/OlalpcvMcwi (2019), SHRSP/A3NCrl (2019), HXB4/IpcvMcwi (2020), WKY/N (MCW)
16 74787390 74787391 C T snv LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), MR/N (2020), LEXF11/Stm (2020), FXLE18/Stm (2020), FXLE16/Stm (2020), F344/Stm (2019), F344/N (2020), F344/NCrl (2019), F344/DuCrl (2019), LE/Stm (RGD), FHL/EurMcwi (RGD), PVG/Seac (2019), BBDP/Wor (RGD), F344/NRrrc (MCW), GH/OmrMcwi (MCW), FHL/EurMcwi (MCW), F344/NCrl (RGD)
16 74787528 74787529 G A snv ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), ACI/N (MCW), Buf/N (MCW), ACI/EurMcwi (RGD), FHH/EurMcwi (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), LL/MavRrrc (RGD), SR/JrHsd (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), ACI/EurMcwi (2019), ACI/N (2020), BUF/N (2020), DA/OlaHsd (2019), FHH/EurMcwi (2019), LH/MavRrrcAek (2020), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), SR/JrHsd (2020), SS/JrHsdMcwi (2019)
16 74796996 74796997 C A snv WN/N (MCW), WN/N (2020)
16 74797074 74797075 C G snv WN/N (MCW), WN/N (2020)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 74524929 74524930 G A snv SHR/OlaIpcv (ICL), SHRSP/Gcrc (MDC), WKY/N (KNAW), SHR/OlaIpcv (KNAW), COP/CrCrl (MCW & UW), WKY/NHsd (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), WKY/NCrl (ICL), WKY/Gcrc (ICL), SHR/OlaIpcv (ICL)
16 74526948 74526949 C T snv LCR/2Mco (UMich), HCR/2Mco (UMich), LCR/1Mco (UMich), LE/Stm (ICL), FHL/EurMcwi (ICL), F344/NCrl (ICL), BBDP/WorN (ICL), GH/OmrMcwi (MCW), LE/Stm (KNAW), F344/NRrrc (KNAW), FHL/EurMcwi (MCW)
16 74527086 74527087 G A snv LL/MavRrrc (ICL), ACI/EurMcwi (MCW), SR/JrHsd (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), HCR/1Mco (UMich), DA/BklArbNsi (ICAHN), LN/MavRrrc (ICL), LH/MavRrrc (ICL), FHH/EurMcwi (ICL), ACI/EurMcwi (ICL), BUF/N (KNAW), ACI/N (KNAW), SS/JrHsdMcwi (MDC), FHH/EurMcwi (MDC), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW)
16 74537919 74537920 C A snv WN/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307419 AgrOrtholog
Ensembl Genes ENSRNOG00000012757 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000017107 UniProtKB/TrEMBL
  ENSRNOP00000061987 UniProtKB/TrEMBL
  ENSRNOP00000073909 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017106 UniProtKB/TrEMBL
  ENSRNOT00000064316 UniProtKB/TrEMBL
  ENSRNOT00000090646 UniProtKB/TrEMBL
InterPro Kinase-like_dom UniProtKB/TrEMBL
  Prot_kinase_cat_dom UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/TrEMBL
  Ser/Thr_prot_kinase_AS UniProtKB/TrEMBL
NCBI Gene 306576 ENTREZGENE
Pfam Pkinase UniProtKB/TrEMBL
PhenoGen Nek3 PhenoGen
PROSITE PROTEIN_KINASE_ATP UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/TrEMBL
  PROTEIN_KINASE_ST UniProtKB/TrEMBL
SMART S_TKc UniProtKB/TrEMBL
Superfamily-SCOP Kinase_like UniProtKB/TrEMBL
UniProt A0A0G2K6R1_RAT UniProtKB/TrEMBL
  D3ZCU1_RAT UniProtKB/TrEMBL
  D3ZTD6_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-11-21 Nek3  NIMA-related kinase 3  Nek3  NIMA (never in mitosis gene a)-related kinase 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Nek3  NIMA (never in mitosis gene a)-related kinase 3  Nek3  NIMA (never in mitosis gene a)-related expressed kinase 3   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Nek3  NIMA (never in mitosis gene a)-related expressed kinase 3   Nek3_predicted  NIMA (never in mitosis gene a)-related expressed kinase 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Nek3_predicted  NIMA (never in mitosis gene a)-related expressed kinase 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED