Ptprg (protein tyrosine phosphatase, receptor type, G) - Rat Genome Database

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Gene: Ptprg (protein tyrosine phosphatase, receptor type, G) Rattus norvegicus
Analyze
Symbol: Ptprg
Name: protein tyrosine phosphatase, receptor type, G
RGD ID: 620774
Description: Predicted to enable identical protein binding activity and protein tyrosine phosphatase activity. Involved in brain development and negative regulation of neuron projection development. Located in extracellular space. Orthologous to human PTPRG (protein tyrosine phosphatase receptor type G); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 4-tert-Octylphenol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: protein tyrosine phosphatase gamma; Protein tyrosine phosphatase, gamma (provisional HGM11 symbol); Ptpg; receptor-like protein tyrosine phosphatase gamma; receptor-type tyrosine-protein phosphatase gamma; RPTP gamma; RPTP gamma A; RPTP gamma B; RPTP gamma C; RPTP gamma S
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
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21512,872,284 - 13,552,186 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1512,871,721 - 13,554,094 (-)Ensembl
Rnor_6.01512,926,056 - 13,633,839 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1512,926,167 - 13,228,607 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01516,953,275 - 17,647,626 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41514,449,352 - 15,130,760 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11514,449,351 - 14,966,931 (-)NCBI
Celera1512,868,965 - 13,547,381 (-)NCBICelera
Cytogenetic Map15p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-tert-Octylphenol  (EXP)
4-vinylcyclohexene dioxide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
7,12-dimethyltetraphene  (ISO)
acetamide  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bis(2-chloroethyl) sulfide  (EXP,ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
chrysene  (ISO)
cisplatin  (EXP,ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
Cuprizon  (EXP)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dibenz[a,h]anthracene  (ISO)
diethylstilbestrol  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fonofos  (ISO)
fulvestrant  (ISO)
genistein  (ISO)
irinotecan  (ISO)
isotretinoin  (ISO)
ivermectin  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (EXP,ISO)
melphalan  (ISO)
methapyrilene  (EXP)
methotrexate  (ISO)
methoxychlor  (ISO)
methylmercury chloride  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosomorpholine  (EXP)
nickel sulfate  (ISO)
p-tert-Amylphenol  (EXP)
paracetamol  (ISO)
parathion  (ISO)
phenobarbital  (ISO)
potassium chromate  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sodium fluoride  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
terbufos  (ISO)
Tesaglitazar  (EXP)
tetraphene  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:15978577   PMID:19167335   PMID:20014386   PMID:21724833   PMID:23376485   PMID:23533145   PMID:23716698  


Genomics

Comparative Map Data
Ptprg
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21512,872,284 - 13,552,186 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1512,871,721 - 13,554,094 (-)Ensembl
Rnor_6.01512,926,056 - 13,633,839 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1512,926,167 - 13,228,607 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01516,953,275 - 17,647,626 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41514,449,352 - 15,130,760 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11514,449,351 - 14,966,931 (-)NCBI
Celera1512,868,965 - 13,547,381 (-)NCBICelera
Cytogenetic Map15p16NCBI
PTPRG
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl361,561,569 - 62,297,609 (+)EnsemblGRCh38hg38GRCh38
GRCh38361,561,571 - 62,297,609 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37361,547,245 - 62,283,284 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36361,522,285 - 62,254,738 (+)NCBINCBI36hg18NCBI36
Build 34361,522,284 - 62,254,737NCBI
Celera361,560,149 - 62,297,663 (+)NCBI
Cytogenetic Map3p14.2NCBI
HuRef361,645,865 - 62,378,614 (+)NCBIHuRef
CHM1_1361,497,665 - 62,231,710 (+)NCBICHM1_1
Ptprg
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391410,227,722 - 10,916,341 (-)NCBIGRCm39mm39
GRCm381411,553,440 - 12,242,041 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1411,553,532 - 12,242,041 (+)EnsemblGRCm38mm10GRCm38
MGSCv371412,386,067 - 13,074,553 (+)NCBIGRCm37mm9NCBIm37
MGSCv361410,347,279 - 11,031,196 (+)NCBImm8
Celera147,168,551 - 7,867,137 (+)NCBICelera
Celera1415,457,844 - 15,462,854 (-)NCBICelera
Cytogenetic Map14A1NCBI
cM Map146.33NCBI
Ptprg
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555173,676,342 - 4,352,909 (-)NCBIChiLan1.0ChiLan1.0
PTPRG
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1362,876,655 - 63,608,175 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl362,877,232 - 63,604,275 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0361,487,734 - 62,221,149 (+)NCBIMhudiblu_PPA_v0panPan3
PTPRG
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12028,777,306 - 29,481,097 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2028,778,386 - 29,481,145 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2028,705,294 - 29,408,229 (-)NCBI
ROS_Cfam_1.02029,011,902 - 29,715,647 (-)NCBI
UMICH_Zoey_3.12028,497,557 - 29,200,144 (-)NCBI
UNSW_CanFamBas_1.02028,855,762 - 29,559,818 (-)NCBI
UU_Cfam_GSD_1.02028,955,575 - 29,659,297 (-)NCBI
Ptprg
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118165,734,435 - 165,784,177 (-)NCBI
SpeTri2.0NW_0049366374,126,058 - 4,248,190 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTPRG
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1343,548,770 - 43,869,270 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11343,132,786 - 43,869,843 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21347,543,401 - 47,873,302 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PTPRG
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12222,652,375 - 23,370,973 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2223,061,935 - 23,370,960 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041143,495,813 - 144,076,600 (-)NCBIVero_WHO_p1.0
Ptprg
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248228,378,048 - 8,942,342 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D15Rat136  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21512,929,603 - 12,929,785 (+)MAPPERmRatBN7.2
Rnor_6.01512,982,697 - 12,982,878NCBIRnor6.0
Rnor_5.01517,009,983 - 17,010,164UniSTSRnor5.0
RGSC_v3.41514,506,878 - 14,507,060RGDRGSC3.4
RGSC_v3.41514,506,879 - 14,507,060UniSTSRGSC3.4
RGSC_v3.11514,506,878 - 14,507,060RGD
Celera1512,925,256 - 12,925,437UniSTS
SHRSP x BN Map159.5698RGD
SHRSP x BN Map159.5698UniSTS
Cytogenetic Map15p16-p15UniSTS
D15Got18  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21513,434,438 - 13,434,565 (+)MAPPERmRatBN7.2
Rnor_6.01513,500,629 - 13,500,755NCBIRnor6.0
Rnor_5.01517,516,160 - 17,516,286UniSTSRnor5.0
RGSC_v3.41515,012,985 - 15,013,112RGDRGSC3.4
RGSC_v3.41515,012,986 - 15,013,112UniSTSRGSC3.4
RGSC_v3.11515,012,986 - 15,013,112RGD
Celera1513,429,108 - 13,429,234UniSTS
RH 3.4 Map15110.0UniSTS
RH 3.4 Map15110.0RGD
RH 2.0 Map1562.3RGD
Cytogenetic Map15p16-p15UniSTS
D15Kyo1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21513,520,624 - 13,520,771 (+)MAPPERmRatBN7.2
Rnor_6.01513,602,281 - 13,602,425NCBIRnor6.0
Rnor_5.01517,616,068 - 17,616,212UniSTSRnor5.0
RGSC_v3.41515,099,202 - 15,099,346UniSTSRGSC3.4
Celera1513,515,813 - 13,515,957UniSTS
Cytogenetic Map15p16-p15UniSTS
RH133004  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01517,198,751 - 17,199,159NCBIRnor5.0
RGSC_v3.41514,701,554 - 14,701,954UniSTSRGSC3.4
Celera1513,116,466 - 13,116,866UniSTS
Cytogenetic Map15p16-p15UniSTS
BE102252  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21513,548,177 - 13,548,351 (+)MAPPERmRatBN7.2
Rnor_6.01513,629,831 - 13,630,004NCBIRnor6.0
Rnor_5.01517,643,618 - 17,643,791UniSTSRnor5.0
RGSC_v3.41515,126,752 - 15,126,925UniSTSRGSC3.4
Celera1513,543,373 - 13,543,546UniSTS
RH 3.4 Map1596.6UniSTS
Cytogenetic Map15p16-p15UniSTS
BE116836  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21513,331,986 - 13,332,176 (+)MAPPERmRatBN7.2
Rnor_6.01513,398,010 - 13,398,199NCBIRnor6.0
Rnor_5.01517,413,541 - 17,413,730UniSTSRnor5.0
RGSC_v3.41514,910,301 - 14,910,490UniSTSRGSC3.4
Celera1513,326,770 - 13,326,959UniSTS
RH 3.4 Map15109.3UniSTS
Cytogenetic Map15p16-p15UniSTS
BF390487  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21513,387,062 - 13,387,232 (+)MAPPERmRatBN7.2
Rnor_6.01513,453,254 - 13,453,423NCBIRnor6.0
Rnor_5.01517,468,785 - 17,468,954UniSTSRnor5.0
RGSC_v3.41514,965,611 - 14,965,780UniSTSRGSC3.4
Celera1513,381,733 - 13,381,902UniSTS
RH 3.4 Map1596.9UniSTS
Cytogenetic Map15p16-p15UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15105825014481294Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)colorectal tumor number (CMO:0001794)15226636822711984Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15226636822711984Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:25
Count of miRNA genes:22
Interacting mature miRNAs:24
Transcripts:ENSRNOT00000042010
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 34 14 5 2 5 2 2 74 35 34 11 2
Low 2 9 43 36 17 36 6 9 7 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000042010   ⟹   ENSRNOP00000039045
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1512,871,721 - 13,554,094 (-)Ensembl
Rnor_6.0 Ensembl1512,926,167 - 13,228,607 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000088214   ⟹   ENSRNOP00000073305
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1512,871,721 - 13,164,493 (-)Ensembl
Rnor_6.0 Ensembl1512,926,167 - 13,228,607 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099333   ⟹   ENSRNOP00000095910
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1512,871,721 - 12,927,418 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101353   ⟹   ENSRNOP00000087710
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1512,871,721 - 13,554,094 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104654   ⟹   ENSRNOP00000094306
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1513,021,876 - 13,553,071 (-)Ensembl
RefSeq Acc Id: NM_134356   ⟹   NP_599183
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21512,872,284 - 13,552,186 (-)NCBI
Rnor_6.01512,926,056 - 13,633,839 (-)NCBI
Rnor_5.01516,953,275 - 17,647,626 (-)NCBI
RGSC_v3.41514,449,352 - 15,130,760 (-)RGD
Celera1512,868,965 - 13,547,381 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_599183 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB02231 (Get FASTA)   NCBI Sequence Viewer  
  AAN72429 (Get FASTA)   NCBI Sequence Viewer  
  AAN72430 (Get FASTA)   NCBI Sequence Viewer  
  AAN72431 (Get FASTA)   NCBI Sequence Viewer  
  AAN72432 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_599183   ⟸   NM_134356
- Sequence:
RefSeq Acc Id: ENSRNOP00000039045   ⟸   ENSRNOT00000042010
RefSeq Acc Id: ENSRNOP00000073305   ⟸   ENSRNOT00000088214
RefSeq Acc Id: ENSRNOP00000087710   ⟸   ENSRNOT00000101353
RefSeq Acc Id: ENSRNOP00000095910   ⟸   ENSRNOT00000099333
RefSeq Acc Id: ENSRNOP00000094306   ⟸   ENSRNOT00000104654
Protein Domains
Alpha-carbonic anhydrase   Fibronectin type-III   TYR_PHOSPHATASE_2   Tyrosine-protein phosphatase

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)
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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)
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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)
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)
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
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)
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
HXB20/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
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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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:620774 AgrOrtholog
Ensembl Genes ENSRNOG00000009419 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000039045 UniProtKB/TrEMBL
  ENSRNOP00000073305 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000042010 UniProtKB/TrEMBL
  ENSRNOT00000088214 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.10.200.10 UniProtKB/TrEMBL
  3.90.190.10 UniProtKB/TrEMBL
InterPro alpha_CARP_receptor-type UniProtKB/TrEMBL
  Carbonic_anhydrase_a UniProtKB/TrEMBL
  Carbonic_anhydrase_a_sf UniProtKB/TrEMBL
  Fibronectin_type3 UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Prot-tyrosine_phosphatase-like UniProtKB/TrEMBL
  Tyr/Dual-specificity_Pase UniProtKB/TrEMBL
  Tyr_Pase_AS UniProtKB/TrEMBL
  Tyr_Pase_cat UniProtKB/TrEMBL
  Tyr_Pase_rcpt/non-rcpt UniProtKB/TrEMBL
KEGG Report rno:171357 UniProtKB/TrEMBL
NCBI Gene 171357 ENTREZGENE
Pfam Carb_anhydrase UniProtKB/TrEMBL
  fn3 UniProtKB/TrEMBL
  Y_phosphatase UniProtKB/TrEMBL
PharmGKB PTPRG RGD
PhenoGen Ptprg PhenoGen
PRINTS PRTYPHPHTASE UniProtKB/TrEMBL
PROSITE ALPHA_CA_2 UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
  TYR_PHOSPHATASE_1 UniProtKB/TrEMBL
  TYR_PHOSPHATASE_2 UniProtKB/TrEMBL
  TYR_PHOSPHATASE_PTP UniProtKB/TrEMBL
SMART Carb_anhydrase UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
  PTPc UniProtKB/TrEMBL
  PTPc_motif UniProtKB/TrEMBL
Superfamily-SCOP Euk_COanhd UniProtKB/TrEMBL
  FN_III-like UniProtKB/TrEMBL
  SSF52799 UniProtKB/TrEMBL
UniProt A0A0G2K561_RAT UniProtKB/TrEMBL
  F1LP13_RAT UniProtKB/TrEMBL
  Q8CIN3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2003-04-09 Ptprg  protein tyrosine phosphatase, receptor type, G      Symbol and Name updated 629477 APPROVED
2003-03-06 Ptprg  protein tyrosine phosphatase, receptor type, G  Ptpg  Protein tyrosine phosphatase, gamma (provisional HGM11 symbol)  Data Merged 628472 PROVISIONAL
2002-08-07 Ptprg  protein tyrosine phosphatase, receptor type, G      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Ptpg  Protein tyrosine phosphatase, gamma (provisional HGM11 symbol)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in brain, kidney, lung, and heart 633859