Ptprt (protein tyrosine phosphatase, receptor type, T) - Rat Genome Database

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Gene: Ptprt (protein tyrosine phosphatase, receptor type, T) Rattus norvegicus
Analyze
Symbol: Ptprt
Name: protein tyrosine phosphatase, receptor type, T
RGD ID: 1309653
Description: Predicted to enable several functions, including STAT family protein binding activity; alpha-catenin binding activity; and beta-catenin binding activity. Involved in regulation of synapse organization. Located in glutamatergic synapse. Is integral component of postsynaptic density membrane. Orthologous to human PTPRT (protein tyrosine phosphatase receptor type T); INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC362263; LOC680887; LOC680897; receptor-type tyrosine-protein phosphatase T; similar to protein tyrosine phosphatase, receptor type, T
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
mRatBN7.23150,189,343 - 151,287,977 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl3150,194,859 - 151,288,124 (-)Ensembl
Rnor_6.03157,537,192 - 158,328,984 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3157,544,583 - 158,328,881 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03163,757,891 - 164,563,677 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43152,380,772 - 153,172,076 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13152,154,289 - 153,093,067 (-)NCBI
Celera3148,867,063 - 149,656,746 (-)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

Additional References at PubMed
PMID:16973135   PMID:17360477   PMID:18644975   PMID:22767509   PMID:23962429   PMID:24846175  


Genomics

Comparative Map Data
Ptprt
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23150,189,343 - 151,287,977 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl3150,194,859 - 151,288,124 (-)Ensembl
Rnor_6.03157,537,192 - 158,328,984 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3157,544,583 - 158,328,881 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03163,757,891 - 164,563,677 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43152,380,772 - 153,172,076 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13152,154,289 - 153,093,067 (-)NCBI
Celera3148,867,063 - 149,656,746 (-)NCBICelera
Cytogenetic Map3q42NCBI
PTPRT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2042,072,752 - 43,189,970 (-)EnsemblGRCh38hg38GRCh38
GRCh382042,029,959 - 43,189,906 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372040,701,396 - 41,818,546 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362040,134,806 - 41,251,971 (-)NCBINCBI36hg18NCBI36
Build 342040,134,806 - 41,251,971NCBI
Celera2037,412,018 - 38,527,269 (-)NCBI
Cytogenetic Map20q12-q13.11NCBI
HuRef2037,438,892 - 38,251,263 (-)NCBIHuRef
CHM1_12040,605,787 - 41,722,632 (-)NCBICHM1_1
Ptprt
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392161,363,908 - 162,503,106 (-)NCBIGRCm39mm39
GRCm39 Ensembl2161,363,910 - 162,503,067 (-)Ensembl
GRCm382161,521,988 - 162,661,147 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2161,521,990 - 162,661,147 (-)EnsemblGRCm38mm10GRCm38
MGSCv372161,353,359 - 162,486,883 (-)NCBIGRCm37mm9NCBIm37
MGSCv362161,219,064 - 162,352,588 (-)NCBImm8
Celera2167,464,067 - 168,594,641 (-)NCBICelera
Cytogenetic Map2H2NCBI
cM Map281.91NCBI
Ptprt
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544514,185,732 - 14,952,980 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544514,185,751 - 14,961,000 (+)NCBIChiLan1.0ChiLan1.0
PTPRT
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12039,494,674 - 40,317,701 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2039,502,794 - 40,317,701 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02038,399,267 - 39,526,776 (-)NCBIMhudiblu_PPA_v0panPan3
PTPRT
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12429,992,957 - 30,764,469 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2430,000,637 - 30,820,835 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2429,632,448 - 30,668,607 (-)NCBI
ROS_Cfam_1.02430,697,308 - 31,823,739 (-)NCBI
UMICH_Zoey_3.12429,966,056 - 30,996,470 (-)NCBI
UNSW_CanFamBas_1.02430,064,525 - 31,108,057 (-)NCBI
UU_Cfam_GSD_1.02430,613,756 - 31,646,408 (-)NCBI
Ptprt
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640178,978,646 - 179,802,109 (-)NCBI
SpeTri2.0NW_0049365303,555,070 - 4,327,558 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTPRT
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1744,714,620 - 45,880,822 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11744,717,539 - 45,880,822 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21749,805,722 - 49,866,203 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PTPRT
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1220,613,352 - 21,720,417 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605069,391,453 - 70,534,508 (+)NCBIVero_WHO_p1.0
Ptprt
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479011,368,745 - 12,144,895 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D3Rat236  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23150,610,883 - 150,611,091 (+)MAPPERmRatBN7.2
Rnor_6.03157,953,288 - 157,953,495NCBIRnor6.0
Rnor_5.03164,174,074 - 164,174,281UniSTSRnor5.0
RGSC_v3.43152,802,829 - 152,803,037RGDRGSC3.4
RGSC_v3.43152,802,830 - 152,803,037UniSTSRGSC3.4
RGSC_v3.13152,708,865 - 152,709,073RGD
Celera3149,280,665 - 149,280,872UniSTS
FHH x ACI Map392.4599RGD
FHH x ACI Map392.4599UniSTS
Cytogenetic Map3q42UniSTS
D3Got133  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23150,686,852 - 150,687,133 (+)MAPPERmRatBN7.2
Rnor_6.03158,029,703 - 158,029,983NCBIRnor6.0
Rnor_5.03164,250,283 - 164,250,563UniSTSRnor5.0
RGSC_v3.43152,878,781 - 152,879,062RGDRGSC3.4
RGSC_v3.43152,878,782 - 152,879,062UniSTSRGSC3.4
RGSC_v3.13152,784,817 - 152,785,098RGD
Celera3149,355,961 - 149,356,241UniSTS
RH 2.0 Map3958.3RGD
Cytogenetic Map3q42UniSTS
D3Got138  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23150,979,153 - 150,979,373 (+)MAPPERmRatBN7.2
Rnor_6.03158,319,283 - 158,319,500NCBIRnor6.0
Rnor_5.03164,539,828 - 164,540,045UniSTSRnor5.0
RGSC_v3.43153,162,265 - 153,162,483RGDRGSC3.4
RGSC_v3.43153,162,266 - 153,162,483UniSTSRGSC3.4
RGSC_v3.13153,068,302 - 153,068,519RGD
Celera3149,647,512 - 149,647,729UniSTS
RH 3.4 Map31390.3RGD
RH 3.4 Map31390.3UniSTS
Cytogenetic Map3q42UniSTS
BF394173  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23150,768,118 - 150,768,277 (+)MAPPERmRatBN7.2
Rnor_6.03158,111,335 - 158,111,493NCBIRnor6.0
Rnor_5.03164,331,844 - 164,332,002UniSTSRnor5.0
RGSC_v3.43152,960,002 - 152,960,160UniSTSRGSC3.4
Celera3149,437,185 - 149,437,343UniSTS
RH 3.4 Map31390.4UniSTS
Cytogenetic Map3q42UniSTS
AU048282  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23150,790,129 - 150,790,269 (+)MAPPERmRatBN7.2
Rnor_6.03158,133,295 - 158,133,434NCBIRnor6.0
Rnor_5.03164,353,999 - 164,354,138UniSTSRnor5.0
RGSC_v3.43152,982,294 - 152,982,433UniSTSRGSC3.4
Celera3149,458,747 - 149,458,886UniSTS
Cytogenetic Map3q42UniSTS
AU049385  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23150,820,313 - 150,820,446 (+)MAPPERmRatBN7.2
Rnor_6.03158,163,867 - 158,163,999NCBIRnor6.0
Rnor_5.03164,384,412 - 164,384,544UniSTSRnor5.0
RGSC_v3.43153,043,438 - 153,043,570UniSTSRGSC3.4
Celera3149,488,901 - 149,489,033UniSTS
Cytogenetic Map3q42UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141339013162184794Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141339236155617360Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3145925360166177555Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3145925360166177555Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3145925360166177555Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3145925360166177555Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3145925360166177555Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3145925360166177555Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3145925360166177555Rat
1300113Bp176Blood pressure QTL 1763.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3145956084157309487Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)3145956084161299569Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3149040888168026850Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:688
Count of miRNA genes:281
Interacting mature miRNAs:349
Transcripts:ENSRNOT00000044466
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 56
Low 5 15 8 14 8 1 1 18 16 26 5 1
Below cutoff 3 38 19 10 5 10 7 10 14 15 5 7

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001108603 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591934 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591935 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591937 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591938 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105523 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105524 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105525 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105526 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105527 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105528 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105529 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105530 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105532 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105533 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105534 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105535 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105536 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105537 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105538 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105539 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105540 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH474005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000120 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000044466   ⟹   ENSRNOP00000041324
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3150,194,859 - 151,288,124 (-)Ensembl
Rnor_6.0 Ensembl3157,544,583 - 158,328,881 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102150   ⟹   ENSRNOP00000091531
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3150,194,859 - 151,288,124 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102159   ⟹   ENSRNOP00000083869
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3150,194,859 - 151,288,124 (-)Ensembl
RefSeq Acc Id: NM_001108603   ⟹   NP_001102073
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,194,859 - 150,988,663 (-)NCBI
Rnor_6.03157,542,706 - 158,328,984 (-)NCBI
Rnor_5.03163,757,891 - 164,563,677 (-)NCBI
RGSC_v3.43152,380,772 - 153,172,076 (-)RGD
Celera3148,867,063 - 149,656,746 (-)RGD
Sequence:
RefSeq Acc Id: XM_039105523   ⟹   XP_038961451
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105524   ⟹   XP_038961452
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105525   ⟹   XP_038961453
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105526   ⟹   XP_038961454
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105527   ⟹   XP_038961455
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105528   ⟹   XP_038961456
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105529   ⟹   XP_038961457
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105530   ⟹   XP_038961458
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105532   ⟹   XP_038961460
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105533   ⟹   XP_038961461
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105534   ⟹   XP_038961462
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105535   ⟹   XP_038961463
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105536   ⟹   XP_038961464
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105537   ⟹   XP_038961465
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105538   ⟹   XP_038961466
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105539   ⟹   XP_038961467
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
RefSeq Acc Id: XM_039105540   ⟹   XP_038961468
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23150,189,343 - 151,287,977 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001102073   ⟸   NM_001108603
- UniProtKB: F1LXJ9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000041324   ⟸   ENSRNOT00000044466
RefSeq Acc Id: XP_038961468   ⟸   XM_039105540
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038961464   ⟸   XM_039105536
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038961461   ⟸   XM_039105533
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038961467   ⟸   XM_039105539
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038961466   ⟸   XM_039105538
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038961458   ⟸   XM_039105530
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038961465   ⟸   XM_039105537
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038961456   ⟸   XM_039105528
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038961455   ⟸   XM_039105527
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038961452   ⟸   XM_039105524
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038961463   ⟸   XM_039105535
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038961454   ⟸   XM_039105526
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038961453   ⟸   XM_039105525
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038961462   ⟸   XM_039105534
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038961457   ⟸   XM_039105529
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038961460   ⟸   XM_039105532
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038961451   ⟸   XM_039105523
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000091531   ⟸   ENSRNOT00000102150
RefSeq Acc Id: ENSRNOP00000083869   ⟸   ENSRNOT00000102159
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)
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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
ACI/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)
ACI/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
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)
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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)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 163889536 163889537 C T snv SDLEF7/Barth (UDEL)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 157668569 157668570 C T snv CDS
3 158206767 158206768 A G snv MR/N (MCW), M520/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309653 AgrOrtholog
Ensembl Genes ENSRNOG00000032656 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000041324 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044466 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.90.190.10 UniProtKB/TrEMBL
InterPro ConA-like_dom UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  FN_III UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  MAM_dom UniProtKB/TrEMBL
  Prot-tyrosine_phosphatase-like UniProtKB/TrEMBL
  PTPRJ_TM 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:362263 UniProtKB/TrEMBL
NCBI Gene 362263 ENTREZGENE
Pfam fn3 UniProtKB/TrEMBL
  MAM UniProtKB/TrEMBL
  PTP_tm UniProtKB/TrEMBL
  Y_phosphatase UniProtKB/TrEMBL
PhenoGen Ptprt PhenoGen
PRINTS MAMDOMAIN UniProtKB/TrEMBL
  PRTYPHPHTASE UniProtKB/TrEMBL
PROSITE FN3 UniProtKB/TrEMBL
  IG_LIKE UniProtKB/TrEMBL
  MAM_1 UniProtKB/TrEMBL
  MAM_2 UniProtKB/TrEMBL
  TYR_PHOSPHATASE_1 UniProtKB/TrEMBL
  TYR_PHOSPHATASE_2 UniProtKB/TrEMBL
  TYR_PHOSPHATASE_PTP UniProtKB/TrEMBL
SMART FN3 UniProtKB/TrEMBL
  MAM UniProtKB/TrEMBL
  PTPc UniProtKB/TrEMBL
  PTPc_motif UniProtKB/TrEMBL
Superfamily-SCOP ConA_like_lec_gl UniProtKB/TrEMBL
  FN_III-like UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
  SSF52799 UniProtKB/TrEMBL
UniProt F1LXJ9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Ptprt  protein tyrosine phosphatase, receptor type, T  LOC680887  similar to protein tyrosine phosphatase, receptor type, T  Data Merged 737654 PROVISIONAL
2015-07-29 Ptprt  protein tyrosine phosphatase, receptor type, T  LOC680897  similar to protein tyrosine phosphatase, receptor type, T  Data Merged 737654 PROVISIONAL
2008-04-30 Ptprt  protein tyrosine phosphatase, receptor type, T   Ptprt_predicted  protein tyrosine phosphatase, receptor type, T (predicted)  'predicted' is removed 2292626 APPROVED
2006-11-19 LOC680887  similar to protein tyrosine phosphatase, receptor type, T      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC680897  similar to protein tyrosine phosphatase, receptor type, T      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-12 Ptprt_predicted  protein tyrosine phosphatase, receptor type, T (predicted)      Symbol and Name status set to approved 70820 APPROVED