Pcnt (pericentrin) - Rat Genome Database

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Gene: Pcnt (pericentrin) Rattus norvegicus
Analyze
Symbol: Pcnt
Name: pericentrin
RGD ID: 1595865
Description: Predicted to enable molecular adaptor activity. Predicted to be involved in microtubule cytoskeleton organization and positive regulation of intracellular protein transport. Predicted to act upstream of or within several processes, including animal organ development; mitotic spindle organization; and neuron migration. Predicted to be located in several cellular components, including cis-Golgi network; intercellular bridge; and microtubule organizing center. Human ortholog(s) of this gene implicated in microcephalic osteodysplastic primordial dwarfism type II. Orthologous to human PCNT (pericentrin); PARTICIPATES IN protein kinase C (PKC) signaling pathway; INTERACTS WITH aconitine; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC309692; similar to pericentrin
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
mRatBN7.22012,190,597 - 12,278,723 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2012,191,648 - 12,278,710 (+)Ensembl
Rnor_6.02012,943,523 - 13,038,615 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2012,944,786 - 13,038,431 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02015,102,765 - 15,195,221 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42012,608,650 - 12,694,390 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2013,689,491 - 13,776,410 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8124707   PMID:11555636   PMID:15037549   PMID:15280373   PMID:15337773   PMID:17600711   PMID:17920017   PMID:18955030   PMID:19543530   PMID:19946888   PMID:20096683   PMID:20186884  
PMID:21399614   PMID:22031837   PMID:22797915   PMID:22851319   PMID:24145165   PMID:24421332   PMID:25088364   PMID:25220058   PMID:27137183  


Genomics

Comparative Map Data
Pcnt
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22012,190,597 - 12,278,723 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2012,191,648 - 12,278,710 (+)Ensembl
Rnor_6.02012,943,523 - 13,038,615 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2012,944,786 - 13,038,431 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02015,102,765 - 15,195,221 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42012,608,650 - 12,694,390 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2013,689,491 - 13,776,410 (+)NCBICelera
Cytogenetic Map20p12NCBI
PCNT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2146,324,141 - 46,445,769 (+)EnsemblGRCh38hg38GRCh38
GRCh382146,324,122 - 46,445,769 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372147,744,070 - 47,865,682 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362146,568,483 - 46,690,110 (+)NCBINCBI36hg18NCBI36
Build 342146,568,482 - 46,690,106NCBI
Celera2132,857,810 - 32,978,856 (+)NCBI
Cytogenetic Map21q22.3NCBI
HuRef2133,126,870 - 33,245,591 (+)NCBIHuRef
CHM1_12147,304,775 - 47,426,531 (+)NCBICHM1_1
Pcnt
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391076,187,088 - 76,279,988 (-)NCBIGRCm39mm39
GRCm39 Ensembl1076,187,097 - 76,278,620 (-)Ensembl
GRCm381076,351,254 - 76,442,912 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1076,351,263 - 76,442,786 (-)EnsemblGRCm38mm10GRCm38
MGSCv371075,813,999 - 75,905,657 (-)NCBIGRCm37mm9NCBIm37
MGSCv361075,794,980 - 75,886,622 (-)NCBImm8
Celera1077,395,555 - 77,487,301 (-)NCBICelera
Cytogenetic Map10C1NCBI
Pcnt
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540742,735,188 - 42,835,465 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540742,735,078 - 42,835,851 (+)NCBIChiLan1.0ChiLan1.0
LOC100976159
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12145,914,665 - 46,042,990 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2145,914,665 - 46,042,990 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02132,665,361 - 32,741,592 (+)NCBIMhudiblu_PPA_v0panPan3
DIP2A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13139,695,620 - 39,778,527 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3139,686,465 - 39,777,484 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3138,915,968 - 39,008,744 (+)NCBI
ROS_Cfam_1.03139,329,446 - 39,422,224 (+)NCBI
ROS_Cfam_1.0 Ensembl3139,329,161 - 39,422,110 (+)Ensembl
UMICH_Zoey_3.13139,191,013 - 39,283,507 (+)NCBI
UNSW_CanFamBas_1.03139,151,916 - 39,244,318 (+)NCBI
UU_Cfam_GSD_1.03139,669,833 - 39,762,599 (+)NCBI
Pcnt
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497138,882,745 - 38,980,366 (+)NCBI
SpeTri2.0NW_004936778149,844 - 248,905 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCNT
(Sus scrofa - pig)
No map positions available.
PCNT
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1289,934,888 - 90,046,767 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl289,936,210 - 90,046,328 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605418,328,339 - 18,445,620 (+)NCBIVero_WHO_p1.0
Pcnt
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474531,402,791 - 31,516,522 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D20Uwm4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22012,267,086 - 12,267,284 (+)MAPPERmRatBN7.2
Rnor_6.02013,026,489 - 13,026,686NCBIRnor6.0
Rnor_5.02015,183,601 - 15,183,798UniSTSRnor5.0
RGSC_v3.42012,682,772 - 12,682,969UniSTSRGSC3.4
Celera2013,764,327 - 13,764,524UniSTS
Cytogenetic Map20p12UniSTS
RH137318  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22012,278,439 - 12,278,621 (+)MAPPERmRatBN7.2
Rnor_6.02013,037,842 - 13,038,023NCBIRnor6.0
Rnor_5.02015,194,954 - 15,195,135UniSTSRnor5.0
RGSC_v3.42012,694,123 - 12,694,304UniSTSRGSC3.4
Celera2013,775,637 - 13,775,818UniSTS
RH 3.4 Map20179.22UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20669170617489458Rat
1581577Pur15Proteinuria QTL 154.380.0002total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20804241017617956Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20903971913461775Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:144
Count of miRNA genes:89
Interacting mature miRNAs:95
Transcripts:ENSRNOT00000048218, ENSRNOT00000074737
Prediction methods:Microtar, 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 19 13 4 17 4 7 10 37 28 41 11 7
Low 2 24 44 37 2 37 1 1 37 7 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_002728936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003753471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006223854 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256312 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772930 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008774937 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588047 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601880 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601881 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099203 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099204 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099205 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099206 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099207 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099208 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099209 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099210 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099211 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099212 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC098763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000048218   ⟹   ENSRNOP00000039329
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2012,191,648 - 12,278,710 (+)Ensembl
Rnor_6.0 Ensembl2012,944,786 - 13,038,431 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000097925   ⟹   ENSRNOP00000095505
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2012,194,328 - 12,278,710 (+)Ensembl
RefSeq Acc Id: XM_002728936   ⟹   XP_002728982
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,190,597 - 12,278,723 (+)NCBI
Rnor_6.02012,943,524 - 13,038,615 (+)NCBI
Rnor_5.02015,102,765 - 15,195,221 (+)NCBI
RGSC_v3.42012,608,650 - 12,694,390 (+)RGD
Sequence:
RefSeq Acc Id: XM_006256312   ⟹   XP_006256374
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,190,597 - 12,278,723 (+)NCBI
Rnor_6.02012,943,524 - 13,038,615 (+)NCBI
Rnor_5.02015,102,765 - 15,195,221 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601880   ⟹   XP_017457369
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,190,597 - 12,278,723 (+)NCBI
Rnor_6.02012,943,523 - 13,038,615 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099203   ⟹   XP_038955131
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,190,597 - 12,278,723 (+)NCBI
RefSeq Acc Id: XM_039099204   ⟹   XP_038955132
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,190,597 - 12,278,723 (+)NCBI
RefSeq Acc Id: XM_039099205   ⟹   XP_038955133
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,190,597 - 12,278,723 (+)NCBI
RefSeq Acc Id: XM_039099206   ⟹   XP_038955134
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,190,597 - 12,278,723 (+)NCBI
RefSeq Acc Id: XM_039099207   ⟹   XP_038955135
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,190,597 - 12,278,723 (+)NCBI
RefSeq Acc Id: XM_039099208   ⟹   XP_038955136
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,190,597 - 12,278,723 (+)NCBI
RefSeq Acc Id: XM_039099209   ⟹   XP_038955137
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,190,597 - 12,278,723 (+)NCBI
RefSeq Acc Id: XM_039099210   ⟹   XP_038955138
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,190,597 - 12,278,723 (+)NCBI
RefSeq Acc Id: XM_039099211   ⟹   XP_038955139
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,221,960 - 12,278,723 (+)NCBI
RefSeq Acc Id: XM_039099212   ⟹   XP_038955140
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,190,597 - 12,278,723 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_002728982   ⟸   XM_002728936
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_006256374   ⟸   XM_006256312
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_017457369   ⟸   XM_017601880
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: ENSRNOP00000039329   ⟸   ENSRNOT00000048218
RefSeq Acc Id: XP_038955131   ⟸   XM_039099203
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955136   ⟸   XM_039099208
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038955137   ⟸   XM_039099209
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038955138   ⟸   XM_039099210
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038955133   ⟸   XM_039099205
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955134   ⟸   XM_039099206
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038955132   ⟸   XM_039099204
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955135   ⟸   XM_039099207
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038955140   ⟸   XM_039099212
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038955139   ⟸   XM_039099211
- Peptide Label: isoform X10
RefSeq Acc Id: ENSRNOP00000095505   ⟸   ENSRNOT00000097925
Protein Domains
PACT_coil_coil

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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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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
20 15105096 15105097 G A snv ACI/EurMcwi (MCW), WKY/NHsd (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), GK/Ox (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), MNS/Gib (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), COP/CrCrl (MCW & UW)
20 15127956 15127957 C T snv ZFDM (KyushuU)
20 15148781 15148782 G A snv SHR/OlaIpcv (KNAW), SDLEF7/Barth (UDEL), ZFDM (KyushuU), HTX/Kyo (KyushuU), BUF/MNa (KyushuU), Crl:SD (UDEL), WKY/NHsd (KNAW), WKY/NCrl (KNAW), WKY/N (KNAW), WKY/Gcrc (KNAW), SHRSP/Gcrc (KNAW), SHR/OlaIpcvPrin (KNAW), SHR/NHsd (KNAW), SHR/NCrlPrin (KNAW), SBN/Ygl (KNAW), SBH/Ygl (KNAW), GK/Ox (KNAW), SBH/Ygl (MCW), SBN/Ygl (MCW), WN/N (KNAW), MHS/Gib (KNAW)
20 15160556 15160557 G A snv BBDP/WorN (KNAW), LEW/Crl (KNAW), BUF/N (KNAW), LEW/NCrl (KNAW), MNS/Gib (KNAW), WKY/NCrl (KNAW), MR/N (KNAW)
20 15174499 15174500 G C snv LEW/NCrl (KNAW), LEW/Crl (KNAW), MNS/Gib (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), GK/Ox (KNAW), BBDP/WorN (KNAW), DOB/Oda (KyushuU)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 12195247 12195248 G A snv WKY/N (2020), LEXF4/Stm (2020), LEXF2B/Stm (2019), LEW/Crl (2019), GK/FarMcwi (2019), FXLE16/Stm (2020), ACI/N (2020), ACI/EurMcwi (2019), LEXF10A/StmMcwi (2020), MR/N (2020), WKY/NCrl (2019), LE/Stm (2019)
20 12216572 12216573 G A snv WKY/NCrl (2019), GK/FarMcwi (2019), WKY/N (2020)
20 12218116 12218117 C T snv BUF/N (2020), WN/N (2020)
20 12232375 12232376 G A snv HXB4/IpcvMcwi (2020), HXB31/IpcvMcwi (2019), HXB2/IpcvMcwi (2019), GK/FarMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), BXH2/CubMcwi (2020), WKY/N (2020), WN/N (2020), WKY/NCrl (2019)
20 12244150 12244151 G A snv LEW/Crl (2019), MR/N (2020), BUF/N (2020)
20 12247223 12247224 C T snv BUF/N (2020)
20 12258093 12258094 G C snv WKY/NCrl (2019), MR/N (2020), LEW/Crl (2019), GK/FarMcwi (2019), WKY/N (2020)
20 12265675 12265676 G A snv BUF/N (2020)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 12947121 12947122 G A snv CDS, ACI/EurMcwi (MCW), WKY/N (2020), WKY/NCrl (2019), MR/N (2020), LEXF10A/StmMcwi (2020), COP/CrCrl (MCW & UW), ACI/N (MCW), WKY/N (MCW), ACI/EurMcwi (RGD), BBDP/Wor (RGD), GK/Ox (RGD), LE/Stm (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), MNS/Gib (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), ACI/EurMcwi (2019), ACI/N (2020), FXLE16/Stm (2020), GK/FarMcwi (2019), LEW/Crl (2019), LEXF2B/Stm (2019), LEXF4/Stm (2020), LE/Stm (2019)
20 12969981 12969982 C T snv BUF/N (2020), WN/N (MCW), MR/N (MCW), Buf/N (MCW), WN/N (2020)
20 12991669 12991670 G A snv CDR, SBH/Ygl (MCW), SBN/Ygl (MCW), WN/N (MCW), MHS/Gib (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), WKY/NHsd (RGD), BXH2/CubMcwi (2020), GK/FarMcwi (2019), HXB2/IpcvMcwi (2019), HXB31/IpcvMcwi (2019), HXB4/IpcvMcwi (2020), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), WKY/NCrl (2019), WKY/N (2020), WN/N (2020)
20 13003444 13003445 G A snv MR/N (2020), LEW/Crl (2019), BUF/N (2020), WKY/NCrl (RGD), CDS, LEW/NCrlBR (RGD), LEW/Crl (RGD), BBDP/Wor (RGD), MR/N (MCW), MNS/Gib (RGD)
20 13006517 13006518 C T snv MR/N (MCW), BUF/N (2020), Buf/N (MCW)
20 13017387 13017388 G C snv WKY/NCrl (2019), GK/FarMcwi (2019), WKY/NHsd (RGD), WKY/Gcrc (RGD), WKY/NCrl (RGD), MNS/Gib (RGD), LEW/NCrlBR (RGD), LEW/Crl (RGD), GK/Ox (RGD), BBDP/Wor (RGD), WKY/N (MCW), CDS, WKY/N (2020), LEW/Crl (2019), MR/N (2020)
20 13025077 13025078 G A snv BUF/N (2020), MR/N (MCW), Buf/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595865 AgrOrtholog
Ensembl Genes ENSRNOG00000001276 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000039329 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000095505 ENTREZGENE
Ensembl Transcript ENSRNOT00000048218 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000097925 ENTREZGENE
InterPro AKAP9/Pericentrin UniProtKB/TrEMBL
  PACT_domain UniProtKB/TrEMBL
NCBI Gene 309692 ENTREZGENE
PANTHER PTHR44981 UniProtKB/TrEMBL
Pfam PACT_coil_coil UniProtKB/TrEMBL
PhenoGen Pcnt PhenoGen
UniProt D3ZMY8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-09-17 Pcnt  pericentrin  LOC309692  similar to pericentrin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC309692  similar to pericentrin      Symbol and Name status set to provisional 70820 PROVISIONAL