Gpc6 (glypican 6) - Rat Genome Database

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Gene: Gpc6 (glypican 6) Rattus norvegicus
Analyze
Symbol: Gpc6
Name: glypican 6
RGD ID: 1593308
Description: Involved in regulation of neurotransmitter receptor localization to postsynaptic specialization membrane. Located in glutamatergic synapse. Human ortholog(s) of this gene implicated in omodysplasia 1. Orthologous to human GPC6 (glypican 6); PARTICIPATES IN Hedgehog signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; atrazine.
Type: protein-coding
RefSeq Status: MODEL
Also known as: glypican-6; LOC306163; LOC691984; similar to Glypican-6 precursor; similar to Gpc6 protein
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
mRatBN7.21594,030,218 - 95,027,883 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1594,029,884 - 95,024,006 (+)Ensembl
Rnor_6.015102,164,091 - 103,174,721 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl15102,164,751 - 103,170,847 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015105,607,785 - 106,611,654 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415101,763,223 - 102,656,127 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1592,888,323 - 93,881,886 (+)NCBICelera
Cytogenetic Map15q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:16452087   PMID:21630459   PMID:21871017  


Genomics

Comparative Map Data
Gpc6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21594,030,218 - 95,027,883 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1594,029,884 - 95,024,006 (+)Ensembl
Rnor_6.015102,164,091 - 103,174,721 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl15102,164,751 - 103,170,847 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015105,607,785 - 106,611,654 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415101,763,223 - 102,656,127 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1592,888,323 - 93,881,886 (+)NCBICelera
Cytogenetic Map15q24NCBI
GPC6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1393,226,807 - 94,408,020 (+)EnsemblGRCh38hg38GRCh38
GRCh381393,226,807 - 94,408,020 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371393,879,060 - 95,060,274 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361392,677,096 - 93,853,948 (+)NCBINCBI36hg18NCBI36
Build 341392,677,095 - 93,853,948NCBI
Celera1374,727,460 - 75,908,516 (+)NCBI
Cytogenetic Map13q31.3-q32.1NCBI
HuRef1374,476,112 - 75,657,237 (+)NCBIHuRef
CHM1_11393,848,682 - 95,029,827 (+)NCBICHM1_1
Gpc6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914117,162,332 - 118,216,941 (+)NCBIGRCm39mm39
GRCm39 Ensembl14117,162,727 - 118,213,956 (+)Ensembl
GRCm3814116,924,920 - 117,979,529 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14116,925,315 - 117,976,544 (+)EnsemblGRCm38mm10GRCm38
MGSCv3714117,324,537 - 118,378,751 (+)NCBIGRCm37mm9NCBIm37
MGSCv3614115,808,387 - 116,859,339 (+)NCBImm8
Celera14115,484,341 - 116,531,683 (+)NCBICelera
Cytogenetic Map14E4NCBI
Gpc6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540415,433,962 - 16,504,351 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540415,429,811 - 16,504,973 (-)NCBIChiLan1.0ChiLan1.0
GPC6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11393,556,152 - 94,744,052 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1393,874,849 - 94,739,894 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01374,408,999 - 75,588,065 (+)NCBIMhudiblu_PPA_v0panPan3
GPC6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12244,154,690 - 45,237,398 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2244,154,944 - 45,233,549 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2244,008,265 - 45,024,162 (+)NCBI
ROS_Cfam_1.02244,583,937 - 45,667,974 (+)NCBI
UMICH_Zoey_3.12244,239,373 - 45,321,705 (+)NCBI
UNSW_CanFamBas_1.02244,280,456 - 45,362,460 (+)NCBI
UU_Cfam_GSD_1.02244,290,207 - 45,372,251 (+)NCBI
Gpc6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945179,774,517 - 180,818,680 (+)NCBI
SpeTri2.0NW_00493647215,136,656 - 16,177,597 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GPC6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1162,438,652 - 63,560,903 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11162,436,143 - 63,560,908 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
GPC6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1372,075,622 - 73,242,678 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604628,496,652 - 29,624,562 (+)NCBIVero_WHO_p1.0
Gpc6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462487997,125 - 1,196,747 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D15Mgh5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21595,018,120 - 95,018,228 (+)MAPPERmRatBN7.2
Rnor_6.015103,164,962 - 103,165,069NCBIRnor6.0
Rnor_5.015106,602,088 - 106,602,195UniSTSRnor5.0
RGSC_v3.415102,741,230 - 102,741,337UniSTSRGSC3.4
RGSC_v3.415102,741,229 - 102,741,337RGDRGSC3.4
RGSC_v3.115102,757,010 - 102,757,117RGD
Celera1593,872,048 - 93,872,155UniSTS
RH 3.4 Map15649.6UniSTS
RH 3.4 Map15649.6RGD
SHRSP x BN Map1560.7698UniSTS
SHRSP x BN Map1560.7698RGD
Cytogenetic Map15q24UniSTS
D15Rat24  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21594,441,768 - 94,441,898 (+)MAPPERmRatBN7.2
Rnor_6.015102,573,998 - 102,574,127NCBIRnor6.0
Rnor_5.015106,016,785 - 106,016,914UniSTSRnor5.0
RGSC_v3.415102,173,544 - 102,173,673UniSTSRGSC3.4
RGSC_v3.415102,173,543 - 102,173,673RGDRGSC3.4
RGSC_v3.115102,189,324 - 102,189,453RGD
Celera1593,299,727 - 93,299,856UniSTS
RH 3.4 Map16729.0RGD
RH 3.4 Map16729.0UniSTS
RH 2.0 Map16845.9RGD
SHRSP x BN Map1559.7198RGD
Cytogenetic Map15q24UniSTS
D15Rat51  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21594,389,730 - 94,389,966 (+)MAPPERmRatBN7.2
Rnor_6.015102,522,908 - 102,523,143NCBIRnor6.0
Rnor_5.015105,965,695 - 105,965,930UniSTSRnor5.0
RGSC_v3.415102,122,540 - 102,122,775UniSTSRGSC3.4
RGSC_v3.415102,122,539 - 102,122,775RGDRGSC3.4
RGSC_v3.115102,138,320 - 102,138,555RGD
Celera1593,248,478 - 93,248,713UniSTS
RH 3.4 Map15642.8RGD
RH 3.4 Map15642.8UniSTS
RH 2.0 Map15539.1RGD
SHRSP x BN Map1560.7698RGD
Cytogenetic Map15q24UniSTS
D15Rat104  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21594,163,880 - 94,164,117 (+)MAPPERmRatBN7.2
Rnor_6.015102,298,523 - 102,298,759NCBIRnor6.0
Rnor_5.015105,741,310 - 105,741,546UniSTSRnor5.0
RGSC_v3.415101,897,012 - 101,897,248UniSTSRGSC3.4
RGSC_v3.415101,896,772 - 101,897,301RGDRGSC3.4
RGSC_v3.115101,912,792 - 101,913,028RGD
Celera1593,022,852 - 93,023,092UniSTS
RH 3.4 Map15638.1RGD
RH 3.4 Map15638.1UniSTS
RH 2.0 Map15534.9RGD
SHRSP x BN Map1559.6798RGD
Cytogenetic Map15q24UniSTS
D15Got90  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21594,318,513 - 94,318,757 (+)MAPPERmRatBN7.2
Rnor_6.015102,452,123 - 102,452,366NCBIRnor6.0
Rnor_5.015105,894,910 - 105,895,153UniSTSRnor5.0
RGSC_v3.415102,051,784 - 102,052,028RGDRGSC3.4
RGSC_v3.415102,051,785 - 102,052,028UniSTSRGSC3.4
RGSC_v3.115102,067,565 - 102,067,808RGD
Celera1593,177,269 - 93,177,506UniSTS
RH 3.4 Map15642.7UniSTS
RH 3.4 Map15642.7RGD
RH 2.0 Map15546.0RGD
Cytogenetic Map15q24UniSTS
D10Chm22  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21594,463,361 - 94,463,582 (+)MAPPERmRatBN7.2
Rnor_6.015102,595,592 - 102,595,812NCBIRnor6.0
Rnor_5.015106,038,379 - 106,038,599UniSTSRnor5.0
RGSC_v3.415102,195,138 - 102,195,358UniSTSRGSC3.4
Celera1593,321,110 - 93,321,330UniSTS
Cytogenetic Map15q24UniSTS
RH128206  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21595,027,420 - 95,027,625 (+)MAPPERmRatBN7.2
Rnor_6.015103,174,259 - 103,174,463NCBIRnor6.0
Rnor_5.015106,611,192 - 106,611,396UniSTSRnor5.0
RGSC_v3.415102,750,816 - 102,751,020UniSTSRGSC3.4
Celera1593,881,424 - 93,881,628UniSTS
RH 3.4 Map15646.7UniSTS
Cytogenetic Map15q24UniSTS
RH133768  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21598,040,273 - 98,040,459 (+)MAPPERmRatBN7.2
Rnor_6.015106,292,526 - 106,292,711NCBIRnor6.0
Rnor_5.015109,688,425 - 109,688,610UniSTSRnor5.0
RGSC_v3.415106,021,203 - 106,021,388UniSTSRGSC3.4
Celera1596,848,677 - 96,848,862UniSTS
Celera1593,556,470 - 93,556,654UniSTS
RH 3.4 Map15644.7UniSTS
Cytogenetic Map15q24UniSTS
RH144677  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21594,347,429 - 94,347,603 (+)MAPPERmRatBN7.2
Rnor_6.015102,480,606 - 102,480,779NCBIRnor6.0
Rnor_5.015105,923,393 - 105,923,566UniSTSRnor5.0
RGSC_v3.415102,080,259 - 102,080,432UniSTSRGSC3.4
Celera1593,206,173 - 93,206,346UniSTS
RH 3.4 Map15644.1UniSTS
Cytogenetic Map15q24UniSTS
BF399195  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21594,823,825 - 94,824,007 (+)MAPPERmRatBN7.2
Rnor_6.015102,971,315 - 102,971,496NCBIRnor6.0
Rnor_5.015106,410,902 - 106,411,083UniSTSRnor5.0
RGSC_v3.415102,561,547 - 102,561,728UniSTSRGSC3.4
Celera1593,681,172 - 93,681,353UniSTS
RH 3.4 Map15646.7UniSTS
Cytogenetic Map15q24UniSTS
RH135097  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21595,024,353 - 95,024,572 (+)MAPPERmRatBN7.2
Rnor_6.015103,171,192 - 103,171,410NCBIRnor6.0
Rnor_5.015106,608,125 - 106,608,343UniSTSRnor5.0
RGSC_v3.415102,747,749 - 102,747,967UniSTSRGSC3.4
Celera1593,878,357 - 93,878,575UniSTS
RH 3.4 Map15646.2UniSTS
Cytogenetic Map15q24UniSTS
RH141325  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21595,024,109 - 95,024,297 (+)MAPPERmRatBN7.2
Rnor_6.015103,170,948 - 103,171,135NCBIRnor6.0
Rnor_5.015106,607,881 - 106,608,068UniSTSRnor5.0
RGSC_v3.415102,747,505 - 102,747,692UniSTSRGSC3.4
Celera1593,878,113 - 93,878,300UniSTS
RH 3.4 Map15647.8UniSTS
Cytogenetic Map15q24UniSTS
BE118647  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21594,349,733 - 94,349,900 (+)MAPPERmRatBN7.2
Rnor_6.015102,482,910 - 102,483,076NCBIRnor6.0
Rnor_5.015105,925,697 - 105,925,863UniSTSRnor5.0
RGSC_v3.415102,082,563 - 102,082,729UniSTSRGSC3.4
Celera1593,208,477 - 93,208,643UniSTS
RH 3.4 Map15642.8UniSTS
Cytogenetic Map15q24UniSTS
GPC6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21594,030,942 - 94,031,057 (+)MAPPERmRatBN7.2
Rnor_6.015102,165,079 - 102,165,193NCBIRnor6.0
Rnor_5.015105,608,848 - 105,608,962UniSTSRnor5.0
RGSC_v3.415101,763,235 - 101,763,349UniSTSRGSC3.4
Celera1592,889,311 - 92,889,425UniSTS
Cytogenetic Map15q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat
1576315Schws6Schwannoma susceptibility QTL 60.0069nervous system integrity trait (VT:0010566)post-insult time of death (CMO:0002005)155380615298806152Rat
631516Gluco31Glucose level QTL 317blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)155559608995018120Rat
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1558156477101769107Rat
731177Uae26Urinary albumin excretion QTL 262.40.025urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1567588667101769107Rat
2300326Plaw1Placental weight QTL 1150.005placenta mass (VT:0004257)placenta wet weight (CMO:0002088)1568327165100062518Rat
1331724Bp223Blood pressure QTL 2233.53715arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)157369051895018228Rat
1641889Colcr6Colorectal carcinoma resistance QTL 62.90.0126intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)157369051899794247Rat
70182BpQTLcluster12Blood pressure QTL cluster 123.53arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)157369065795018120Rat
2317055Aia10Adjuvant induced arthritis QTL 103.41joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1575788062101769107Rat
1549844Bss7Bone structure and strength QTL 76.4femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1575788062101769107Rat
70155Gcs1Gastric cancer susceptibility QTL13.8stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)1576306099101769107Rat
1300118Bp190Blood pressure QTL 1902.94arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)158226252098288169Rat
1300120Kidm7Kidney mass QTL 73.55kidney mass (VT:0002707)left kidney wet weight to body weight ratio (CMO:0001954)158226252098288169Rat
1581519Cm59Cardiac mass QTL 592.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)158885347095840528Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:129
Count of miRNA genes:87
Interacting mature miRNAs:90
Transcripts:ENSRNOT00000072531, ENSRNOT00000074982
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 28 8 6 6 23 24 28
Low 3 15 42 28 19 28 8 10 51 11 8 11 8
Below cutoff 7 7 7 1 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000076400   ⟹   ENSRNOP00000068304
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1594,029,884 - 95,024,006 (+)Ensembl
Rnor_6.0 Ensembl15102,164,751 - 103,170,847 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000119031   ⟹   ENSRNOP00000086451
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1594,029,884 - 95,024,006 (+)Ensembl
RefSeq Acc Id: XM_001077762   ⟹   XP_001077762
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21594,030,219 - 95,027,883 (+)NCBI
Rnor_6.015102,164,093 - 103,174,721 (+)NCBI
Rnor_5.015105,607,785 - 106,611,654 (+)NCBI
RGSC_v3.415101,763,223 - 102,656,127 (+)RGD
Sequence:
RefSeq Acc Id: XM_003751533   ⟹   XP_003751581
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21594,030,218 - 95,027,883 (+)NCBI
Rnor_6.015102,164,091 - 103,174,721 (+)NCBI
Rnor_5.015105,607,785 - 106,611,654 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_001077762 (Get FASTA)   NCBI Sequence Viewer  
  XP_003751581 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM02516 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_001077762   ⟸   XM_001077762
- Peptide Label: isoform X2
- UniProtKB: A0A096MJY1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_003751581   ⟸   XM_003751533
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000068304   ⟸   ENSRNOT00000076400
RefSeq Acc Id: ENSRNOP00000086451   ⟸   ENSRNOT00000119031

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)
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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
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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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)
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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/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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1593308 AgrOrtholog
Ensembl Genes ENSRNOG00000046660 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000068304 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000076400 UniProtKB/TrEMBL
InterPro Glypican UniProtKB/TrEMBL
  Glypican-6 UniProtKB/TrEMBL
  Glypican_CS UniProtKB/TrEMBL
KEGG Report rno:691984 UniProtKB/TrEMBL
NCBI Gene 691984 ENTREZGENE
PANTHER PTHR10822 UniProtKB/TrEMBL
  PTHR10822:SF31 UniProtKB/TrEMBL
Pfam Glypican UniProtKB/TrEMBL
PhenoGen Gpc6 PhenoGen
PROSITE GLYPICAN UniProtKB/TrEMBL
UniProt A0A096MJY1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-10-22 Gpc6  glypican 6  LOC691984  similar to Glypican-6 precursor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC691984  similar to Glypican-6 precursor  RGD1563063_predicted  similar to Gpc6 protein (predicted)  Data Merged 1643240 APPROVED
2006-11-20 LOC691984  similar to Glypican-6 precursor      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-07 RGD1563063_predicted  similar to Gpc6 protein (predicted)  LOC306163  similar to Gpc6 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC306163  similar to Gpc6 protein      Symbol and Name status set to provisional 70820 PROVISIONAL