Nek3 (NIMA-related kinase 3) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Nek3 (NIMA-related kinase 3) Rattus norvegicus
Analyze
Symbol: Nek3
Name: NIMA-related kinase 3
RGD ID: 1307419
Description: Predicted to have ATP binding activity and protein kinase activity. Predicted to be involved in several processes, including establishment of cell polarity; neuron projection morphogenesis; 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21669,867,020 - 69,892,477 (+)NCBI
Rnor_6.0 Ensembl1674,785,281 - 74,806,149 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01674,781,371 - 74,806,567 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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 (+)NCBI
Rnor_6.0 Ensembl1674,785,281 - 74,806,149 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01674,781,371 - 74,806,567 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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
GRCh371352,706,779 - 52,733,996 (-)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
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
Nek3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1330,018,641 - 30,048,787 (-)NCBI
ChlSab1.1 Ensembl330,018,635 - 30,045,216 (-)Ensembl
Nek3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247481,939,806 - 1,976,484 (+)NCBI

Position Markers
RH140165  
Rat AssemblyChrPosition (strand)SourceJBrowse
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 (Rnor_6.0)
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)16109005486162972Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)162075555680316424Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163900002184000021Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164151271086512710Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164151271086512710Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164655818890668790Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165781635790668790Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165781635790668790Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165781635790668790Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165928577589248943Rat
1298527Arunc2Aerobic running capacity QTL 22.9exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)167321963880115794Rat

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


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017106   ⟹   ENSRNOP00000017107
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1674,785,281 - 74,806,149 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000064316   ⟹   ENSRNOP00000061987
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1674,785,281 - 74,806,149 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090646   ⟹   ENSRNOP00000073909
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1674,785,281 - 74,806,149 (+)Ensembl
RefSeq Acc Id: XM_001065115   ⟹   XP_001065115
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1667,751,672 - 67,777,870 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006222274   ⟹   XP_006222336
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1667,751,672 - 67,777,870 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006222275   ⟹   XP_006222337
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1667,751,672 - 67,777,870 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006222276   ⟹   XP_006222338
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1667,751,672 - 67,777,870 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006222277   ⟹   XP_006222339
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1667,751,672 - 67,777,870 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006222278   ⟹   XP_006222340
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1667,757,610 - 67,777,870 (+)NCBI
Sequence:
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_001065115   ⟸   XM_001065115
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_224971   ⟸   XM_224971
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006222336   ⟸   XM_006222274
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006222338   ⟸   XM_006222276
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006222339   ⟸   XM_006222277
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006222337   ⟸   XM_006222275
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006222340   ⟸   XM_006222278
- Peptide Label: isoform X5
- 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 (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 (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/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 (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)
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
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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)
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
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/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
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 (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
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
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
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
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
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 (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
SBH/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: 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
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 (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 (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
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 (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 (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 (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 SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), IS-Tlk/Kyo (KyushuU), IS/Kyo (KyushuU), COP/CrCrl (MCW & UW), SHR/OlaIpcv (KNAW), WKY/NCrl (KNAW), WKY/N (KNAW), WKY/Gcrc (KNAW), SHRSP/Gcrc (KNAW), SHR/OlaIpcvPrin (KNAW), WKY/NHsd (KNAW)
16 74418412 74418413 C T snv FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), 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), LE/Stm (SOLiD) (KNAW), LE/Stm (Illumina) (KNAW), FHL/EurMcwi (KNAW), F344/NHsd (KNAW), F344/NCrl (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NRrrc (Illumina) (KNAW), BBDP/WorN (KNAW)
16 74418550 74418551 G A snv SS/JrHsdMcwi (KNAW), SS/Jr (KNAW), HTX/Kyo (KyushuU), ZFDM (KyushuU), ACI/N (KNAW), FHH/EurMcwi (KNAW), BUF/MNa (KyushuU), FHH/EurMcwi (MCW), DA/BklArbNsi (KNAW), BUF/N (KNAW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), ACI/EurMcwi (MCW), LN/MavRrrc (KNAW), SR/JrHsd (KNAW), ACI/EurMcwi (KNAW)
16 74427488 74427489 C A snv DOB/Oda (KyushuU), HWY/Slc (KyushuU), WN/N (KNAW)
16 74427566 74427567 C G snv WN/N (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 74785371 74785372 G A snv COP/CrCrl (MCW & UW), WKY/Gcrc (RGD), WKY/NCrl (RGD), SHRSP/Gcrc (RGD), SHR/NHsd (RGD), WKY/N (MCW), WKY/NHsd (RGD)
16 74787390 74787391 C T snv GH/OmrMcwi (MCW), F344/NCrl (RGD), BBDP/Wor (RGD), F344/NRrrc (MCW), FHL/EurMcwi (RGD), FHL/EurMcwi (MCW), LE/Stm (RGD)
16 74787528 74787529 G A snv LL/MavRrrc (RGD), SS/Jr (RGD), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), LN/MavRrrc (RGD), LH/MavRrrc (RGD), FHH/EurMcwi (RGD), ACI/EurMcwi (RGD), SR/JrHsd (RGD), ACI/EurMcwi (MCW), ACI/N (MCW), Buf/N (MCW), SS/JrHsdMcwi (RGD), FHH/EurMcwi (MCW)
16 74796996 74796997 C A snv WN/N (MCW)
16 74797074 74797075 C G snv WN/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 74524929 74524930 G A snv SHRSP/Gcrc (MDC), COP/CrCrl (MCW & UW), SHR/OlaIpcv (ICL), WKY/NHsd (ICL), WKY/Gcrc (ICL), SHR/OlaIpcv (KNAW), SHR/OlaIpcv (ICL), WKY/NCrl (ICL), WKY/N (KNAW), SHR/NHsd (ICL), SHRSP/Gcrc (ICL)
16 74526948 74526949 C T snv FHL/EurMcwi (MCW), LE/Stm (KNAW), F344/NRrrc (KNAW), F344/NCrl (ICL), LCR/2Mco (UMich), HCR/2Mco (UMich), LCR/1Mco (UMich), FHL/EurMcwi (ICL), LE/Stm (ICL), BBDP/WorN (ICL), GH/OmrMcwi (MCW)
16 74527086 74527087 G A snv FHH/EurMcwi (ICL), SR/JrHsd (MCW), LH/MavRrrc (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), ACI/EurMcwi (MCW), HCR/1Mco (UMich), BUF/N (KNAW), SR/JrHsd (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), FHH/EurMcwi (MDC), DA/BklArbNsi (ICAHN), SS/JrHsdMcwi (MDC), ACI/EurMcwi (ICL), ACI/N (KNAW), FHH/EurMcwi (MCW), SS/JrHsdMcwi (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, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000017107 ENTREZGENE, 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