Ptprd (protein tyrosine phosphatase, receptor type, D) - Rat Genome Database

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Gene: Ptprd (protein tyrosine phosphatase, receptor type, D) Rattus norvegicus
Analyze
Symbol: Ptprd
Name: protein tyrosine phosphatase, receptor type, D
RGD ID: 1561090
Description: Predicted to enable cell adhesion molecule binding activity; protein tyrosine phosphatase activity; and signaling receptor binding activity. Involved in regulation of postsynaptic density assembly and synaptic membrane adhesion. Is active in glutamatergic synapse. Orthologous to human PTPRD (protein tyrosine phosphatase receptor type D); INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC103692382; LOC313278; receptor-type tyrosine-protein phosphatase delta; RGD1561090; similar to protein tyrosine phosphatase, receptor type, D; uncharacterized LOC103692382
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
mRatBN7.2590,046,993 - 90,698,977 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl590,048,966 - 92,369,396 (-)Ensembl
Rnor_6.0592,862,229 - 93,514,071 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl592,862,267 - 93,244,202 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0596,907,323 - 97,286,547 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4594,069,724 - 94,286,657 (+)NCBIRGSC3.4rn4RGSC3.4
Celera588,728,402 - 89,389,021 (-)NCBICelera
Cytogenetic Map5q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
4-hydroxyphenyl retinamide  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
aristolochic acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (EXP)
bisphenol A  (EXP)
butanal  (ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
casticin  (ISO)
chloroprene  (EXP)
choline  (ISO)
cisplatin  (EXP)
clofibrate  (ISO)
clofibric acid  (EXP)
cumene  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diazinon  (EXP)
dibutyl phthalate  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
furan  (EXP)
geldanamycin  (ISO)
Heliotrine  (ISO)
irinotecan  (ISO)
isoprenaline  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
manganese(II) chloride  (EXP)
methapyrilene  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
nefazodone  (EXP)
nickel atom  (ISO)
nimesulide  (EXP)
O-methyleugenol  (ISO)
oxaliplatin  (EXP)
paracetamol  (ISO)
paraquat  (EXP)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
phenobarbital  (EXP,ISO)
pirinixic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
propiconazole  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
senecionine  (ISO)
Senkirkine  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
streptozocin  (EXP)
temozolomide  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP,ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
topotecan  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
valdecoxib  (EXP)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
vorinostat  (ISO)
zinc atom  (EXP)
zinc sulfate  (EXP)
zinc(0)  (EXP)

References

Additional References at PubMed
PMID:10856223   PMID:21926414   PMID:21940441   PMID:22357843   PMID:23345436   PMID:23533145   PMID:24843164   PMID:25908590   PMID:25989451  


Genomics

Comparative Map Data
Ptprd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2590,046,993 - 90,698,977 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl590,048,966 - 92,369,396 (-)Ensembl
Rnor_6.0592,862,229 - 93,514,071 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl592,862,267 - 93,244,202 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0596,907,323 - 97,286,547 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4594,069,724 - 94,286,657 (+)NCBIRGSC3.4rn4RGSC3.4
Celera588,728,402 - 89,389,021 (-)NCBICelera
Cytogenetic Map5q31NCBI
PTPRD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl98,314,246 - 10,613,002 (-)EnsemblGRCh38hg38GRCh38
GRCh3898,314,246 - 10,613,002 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3798,314,246 - 10,613,002 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3698,304,246 - 10,602,509 (-)NCBINCBI36hg18NCBI36
Build 3498,307,267 - 9,008,737NCBI
Celera98,248,560 - 10,545,456 (-)NCBI
Cytogenetic Map9p24.1-p23NCBI
HuRef98,274,893 - 10,576,645 (-)NCBIHuRef
CHM1_198,314,050 - 10,612,534 (-)NCBICHM1_1
Ptprd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39475,859,474 - 78,132,282 (-)NCBIGRCm39mm39
GRCm39 Ensembl475,859,475 - 78,130,198 (-)Ensembl
GRCm38475,941,237 - 78,211,742 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl475,941,238 - 78,211,961 (-)EnsemblGRCm38mm10GRCm38
MGSCv37475,587,143 - 76,240,203 (-)NCBIGRCm37mm9NCBIm37
MGSCv36475,416,037 - 76,065,530 (-)NCBImm8
Celera474,401,961 - 75,072,056 (-)NCBICelera
Cytogenetic Map4C3NCBI
cM Map436.94NCBI
Ptprd
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543412,031,420 - 12,428,774 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543412,033,825 - 14,132,636 (-)NCBIChiLan1.0ChiLan1.0
PTPRD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.198,284,946 - 10,587,642 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl98,288,569 - 8,831,227 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v098,113,171 - 10,420,732 (-)NCBIMhudiblu_PPA_v0panPan3
PTPRD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11129,100,913 - 31,278,495 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1129,104,448 - 29,501,600 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1127,899,386 - 28,554,986 (-)NCBI
ROS_Cfam_1.01129,983,665 - 32,164,492 (-)NCBI
UMICH_Zoey_3.11128,699,584 - 30,884,051 (-)NCBI
UNSW_CanFamBas_1.01128,519,644 - 30,692,371 (-)NCBI
UU_Cfam_GSD_1.01129,185,571 - 31,348,978 (-)NCBI
Ptprd
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947144,112,128 - 146,247,876 (-)NCBI
SpeTri2.0NW_0049365392,564,815 - 3,369,975 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTPRD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1213,482,964 - 214,009,895 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11211,832,409 - 214,013,013 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PTPRD
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11270,160,253 - 71,237,292 (+)NCBI
ChlSab1.1 Ensembl1270,693,214 - 71,239,437 (+)Ensembl
Vero_WHO_p1.0NW_02366603857,226,835 - 59,559,270 (+)NCBI
Ptprd
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473612,874,884 - 13,558,030 (-)NCBI

Position Markers
D5Rat107  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2590,405,302 - 90,405,423 (+)MAPPERmRatBN7.2
Rnor_6.0593,227,981 - 93,228,101NCBIRnor6.0
Rnor_5.0597,270,362 - 97,270,482UniSTSRnor5.0
RGSC_v3.4594,470,752 - 94,470,873RGDRGSC3.4
RGSC_v3.4594,470,753 - 94,470,873UniSTSRGSC3.4
RGSC_v3.1594,475,866 - 94,475,986RGD
Celera589,089,638 - 89,089,758UniSTS
RH 3.4 Map5701.0RGD
RH 3.4 Map5701.0UniSTS
RH 2.0 Map5565.6RGD
SHRSP x BN Map551.3999RGD
Cytogenetic Map5q31UniSTS
BE097842  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2590,263,544 - 90,263,763 (+)MAPPERmRatBN7.2
Rnor_6.0593,081,022 - 93,081,240NCBIRnor6.0
Rnor_5.0597,123,917 - 97,124,135UniSTSRnor5.0
RGSC_v3.4594,328,091 - 94,328,309UniSTSRGSC3.4
Celera588,947,981 - 88,948,199UniSTS
RH 3.4 Map5696.9UniSTS
Cytogenetic Map5q31UniSTS
AI703917  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2590,240,196 - 90,240,412 (+)MAPPERmRatBN7.2
Rnor_6.0593,058,206 - 93,058,421NCBIRnor6.0
Rnor_5.0597,100,865 - 97,101,080UniSTSRnor5.0
RGSC_v3.4594,080,181 - 94,080,396UniSTSRGSC3.4
Celera588,924,532 - 88,924,747UniSTS
RH 3.4 Map5696.9UniSTS
Cytogenetic Map5q31UniSTS
RH142256  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2590,048,601 - 90,048,779 (+)MAPPERmRatBN7.2
Rnor_6.0592,863,838 - 92,864,015NCBIRnor6.0
Rnor_5.0596,908,932 - 96,909,109UniSTSRnor5.0
RGSC_v3.4594,284,871 - 94,285,048UniSTSRGSC3.4
Celera588,730,011 - 88,730,190UniSTS
RH 3.4 Map5692.1UniSTS
Cytogenetic Map5q31UniSTS
BF410120  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2590,166,521 - 90,166,760 (+)MAPPERmRatBN7.2
Rnor_6.0592,982,495 - 92,982,733NCBIRnor6.0
Rnor_5.0597,026,961 - 97,027,199UniSTSRnor5.0
RGSC_v3.4594,165,897 - 94,166,135UniSTSRGSC3.4
Celera588,847,833 - 88,848,071UniSTS
RH 3.4 Map1909.29UniSTS
Cytogenetic Map5q31UniSTS
RH135104  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2590,050,283 - 90,050,472 (+)MAPPERmRatBN7.2
Rnor_6.0592,865,520 - 92,865,708NCBIRnor6.0
Rnor_5.0596,910,614 - 96,910,802UniSTSRnor5.0
RGSC_v3.4594,283,178 - 94,283,366UniSTSRGSC3.4
Celera588,731,695 - 88,731,883UniSTS
RH 3.4 Map5692.1UniSTS
Cytogenetic Map5q31UniSTS
RH138901  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2590,049,295 - 90,049,484 (+)MAPPERmRatBN7.2
Rnor_6.0592,864,532 - 92,864,720NCBIRnor6.0
Rnor_5.0596,909,626 - 96,909,814UniSTSRnor5.0
RGSC_v3.4594,284,166 - 94,284,354UniSTSRGSC3.4
Celera588,730,707 - 88,730,895UniSTS
RH 3.4 Map5692.1UniSTS
Cytogenetic Map5q31UniSTS
PTPRD  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2590,060,612 - 90,061,733 (+)MAPPERmRatBN7.2
Rnor_6.0592,875,847 - 92,876,967NCBIRnor6.0
Rnor_5.0596,920,941 - 96,922,061UniSTSRnor5.0
RGSC_v3.4594,271,919 - 94,273,039UniSTSRGSC3.4
Celera588,742,018 - 88,743,142UniSTS
Cytogenetic Map5q31UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54786906290099692Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)54946360094463600Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)54946360094463600Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55098389595983895Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)55349671998496719Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)555715622100715622Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)55979352890450144Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)56029343498603051Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
2290005Mcs24Mammary carcinoma susceptibility QTL 24mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)564719390109719390Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)566174080124160948Rat
2312671Scl64Serum cholesterol level QTL 640.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)568984307104251008Rat
61380Edpm5Estrogen-dependent pituitary mass QTL 54.50.92pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)568984307104251008Rat
1357396Bw44Body weight QTL 444.19body mass (VT:0001259)body weight (CMO:0000012)568984307104251008Rat
1357402Bw46Body weight QTL 464.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
2302381Bw84Body weight QTL 844.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1298070Scl18Serum cholesterol level QTL 183.7blood LDL cholesterol amount (VT:0000181)calculated plasma low density lipoprotein cholesterol level (CMO:0001245)579584860124584860Rat
1598846Bp293Blood pressure QTL 2933.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)579584860124584860Rat
1598859Cm66Cardiac mass QTL 662heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)579584860124584860Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1331782Rf36Renal function QTL 363.296kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)58384059897059958Rat
1298086Bp156Blood pressure QTL 156arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)584132602129132602Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)587468046132468046Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)587765973132765973Rat
1358889Bp261Blood pressure QTL 2612.86arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)590067849128034027Rat
1358909Kidm25Kidney mass QTL 251.87kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)590067849128034027Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)590450144135450144Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:514
Count of miRNA genes:115
Interacting mature miRNAs:123
Transcripts:ENSRNOT00000008897, ENSRNOT00000025426, ENSRNOT00000066046, ENSRNOT00000071089, ENSRNOT00000074491, ENSRNOT00000075474
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 2 35 34 25 2 25 2 2 74 35 34 11 2
Low 1 8 23 16 17 16 6 8 7 6
Below cutoff 1

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_001067936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003754043 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225346 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225347 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225348 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225349 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225352 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225353 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225354 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225357 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225358 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225359 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225370 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225372 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225375 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225376 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225378 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225379 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225380 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763819 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763820 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763821 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763823 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763824 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763825 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763826 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763827 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763828 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763829 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763830 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763831 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593938 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593939 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593940 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593941 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593942 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593943 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593944 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593945 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593946 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593950 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593951 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593953 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593955 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602893 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602894 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602895 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602896 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111412 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111413 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111414 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111417 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111418 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111419 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111420 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111421 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111422 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111424 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111426 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111427 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111428 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111429 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111430 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111431 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111432 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111433 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111434 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111435 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111437 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111438 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111439 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111441 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111442 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111443 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111444 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111445 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111446 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111449 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111450 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111451 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111452 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111453 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111454 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111455 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111456 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111457 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111458 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111459 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111460 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111461 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111462 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111463 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473978 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U57502 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000075474   ⟹   ENSRNOP00000066744
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl590,048,966 - 90,341,310 (-)Ensembl
Rnor_6.0 Ensembl592,862,267 - 93,244,202 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000094348   ⟹   ENSRNOP00000089430
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl590,048,966 - 92,369,396 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110800   ⟹   ENSRNOP00000085531
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl590,048,966 - 90,550,297 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113220   ⟹   ENSRNOP00000086806
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl590,048,966 - 90,550,297 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115119   ⟹   ENSRNOP00000080613
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl590,048,966 - 90,893,576 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000119354   ⟹   ENSRNOP00000091521
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl590,048,966 - 90,527,316 (-)Ensembl
RefSeq Acc Id: XM_017593939   ⟹   XP_017449428
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
Rnor_6.0592,862,229 - 93,514,071 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593957   ⟹   XP_017449446
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,046,993 - 90,421,239 (-)NCBI
Rnor_6.0592,862,229 - 93,346,812 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039111412   ⟹   XP_038967340
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,046,993 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111413   ⟹   XP_038967341
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,549,674 (-)NCBI
RefSeq Acc Id: XM_039111414   ⟹   XP_038967342
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,437,928 (-)NCBI
RefSeq Acc Id: XM_039111416   ⟹   XP_038967344
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111417   ⟹   XP_038967345
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111418   ⟹   XP_038967346
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111419   ⟹   XP_038967347
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111420   ⟹   XP_038967348
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111421   ⟹   XP_038967349
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111422   ⟹   XP_038967350
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111423   ⟹   XP_038967351
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111424   ⟹   XP_038967352
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111426   ⟹   XP_038967354
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111427   ⟹   XP_038967355
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111428   ⟹   XP_038967356
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111429   ⟹   XP_038967357
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111430   ⟹   XP_038967358
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111431   ⟹   XP_038967359
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111432   ⟹   XP_038967360
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111433   ⟹   XP_038967361
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111434   ⟹   XP_038967362
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111435   ⟹   XP_038967363
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111437   ⟹   XP_038967365
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111438   ⟹   XP_038967366
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111439   ⟹   XP_038967367
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111440   ⟹   XP_038967368
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111441   ⟹   XP_038967369
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111442   ⟹   XP_038967370
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111443   ⟹   XP_038967371
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111444   ⟹   XP_038967372
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111445   ⟹   XP_038967373
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111446   ⟹   XP_038967374
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111448   ⟹   XP_038967376
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111449   ⟹   XP_038967377
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111450   ⟹   XP_038967378
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111451   ⟹   XP_038967379
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111452   ⟹   XP_038967380
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111453   ⟹   XP_038967381
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111454   ⟹   XP_038967382
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111455   ⟹   XP_038967383
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111456   ⟹   XP_038967384
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111457   ⟹   XP_038967385
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111458   ⟹   XP_038967386
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111459   ⟹   XP_038967387
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111460   ⟹   XP_038967388
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111461   ⟹   XP_038967389
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111462   ⟹   XP_038967390
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,049,220 - 90,698,977 (-)NCBI
RefSeq Acc Id: XM_039111463   ⟹   XP_038967391
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2590,046,993 - 90,421,239 (-)NCBI
Protein Sequences
Protein RefSeqs XP_017449428 (Get FASTA)   NCBI Sequence Viewer  
  XP_017449446 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967340 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967341 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967342 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967344 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967345 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967346 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967347 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967348 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967349 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967350 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967351 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967352 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967354 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967355 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967356 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967357 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967358 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967359 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967360 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967361 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967362 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967363 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967365 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967366 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967367 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967368 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967369 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967370 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967371 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967372 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967373 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967374 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967376 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967377 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967378 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967379 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967380 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967381 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967382 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967383 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967384 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967385 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967386 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967387 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967388 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967389 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967390 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967391 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB02007 (Get FASTA)   NCBI Sequence Viewer  
  EDM10485 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_017449428   ⟸   XM_017593939
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017449446   ⟸   XM_017593957
- Peptide Label: isoform X48
- Sequence:
RefSeq Acc Id: ENSRNOP00000066744   ⟸   ENSRNOT00000075474
RefSeq Acc Id: XP_038967340   ⟸   XM_039111412
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038967391   ⟸   XM_039111463
- Peptide Label: isoform X47
RefSeq Acc Id: XP_038967390   ⟸   XM_039111462
- Peptide Label: isoform X46
RefSeq Acc Id: XP_038967389   ⟸   XM_039111461
- Peptide Label: isoform X45
RefSeq Acc Id: XP_038967373   ⟸   XM_039111445
- Peptide Label: isoform X30
RefSeq Acc Id: XP_038967372   ⟸   XM_039111444
- Peptide Label: isoform X29
RefSeq Acc Id: XP_038967368   ⟸   XM_039111440
- Peptide Label: isoform X25
RefSeq Acc Id: XP_038967366   ⟸   XM_039111438
- Peptide Label: isoform X23
RefSeq Acc Id: XP_038967359   ⟸   XM_039111431
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038967387   ⟸   XM_039111459
- Peptide Label: isoform X43
RefSeq Acc Id: XP_038967371   ⟸   XM_039111443
- Peptide Label: isoform X28
RefSeq Acc Id: XP_038967381   ⟸   XM_039111453
- Peptide Label: isoform X37
RefSeq Acc Id: XP_038967384   ⟸   XM_039111456
- Peptide Label: isoform X40
RefSeq Acc Id: XP_038967370   ⟸   XM_039111442
- Peptide Label: isoform X27
RefSeq Acc Id: XP_038967380   ⟸   XM_039111452
- Peptide Label: isoform X36
RefSeq Acc Id: XP_038967388   ⟸   XM_039111460
- Peptide Label: isoform X44
RefSeq Acc Id: XP_038967386   ⟸   XM_039111458
- Peptide Label: isoform X42
RefSeq Acc Id: XP_038967377   ⟸   XM_039111449
- Peptide Label: isoform X33
RefSeq Acc Id: XP_038967385   ⟸   XM_039111457
- Peptide Label: isoform X41
RefSeq Acc Id: XP_038967352   ⟸   XM_039111424
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038967383   ⟸   XM_039111455
- Peptide Label: isoform X39
RefSeq Acc Id: XP_038967379   ⟸   XM_039111451
- Peptide Label: isoform X35
RefSeq Acc Id: XP_038967378   ⟸   XM_039111450
- Peptide Label: isoform X34
RefSeq Acc Id: XP_038967365   ⟸   XM_039111437
- Peptide Label: isoform X22
RefSeq Acc Id: XP_038967361   ⟸   XM_039111433
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038967344   ⟸   XM_039111416
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038967357   ⟸   XM_039111429
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038967355   ⟸   XM_039111427
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038967347   ⟸   XM_039111419
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038967356   ⟸   XM_039111428
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038967351   ⟸   XM_039111423
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038967349   ⟸   XM_039111421
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038967382   ⟸   XM_039111454
- Peptide Label: isoform X38
RefSeq Acc Id: XP_038967376   ⟸   XM_039111448
- Peptide Label: isoform X32
RefSeq Acc Id: XP_038967374   ⟸   XM_039111446
- Peptide Label: isoform X31
RefSeq Acc Id: XP_038967369   ⟸   XM_039111441
- Peptide Label: isoform X26
RefSeq Acc Id: XP_038967367   ⟸   XM_039111439
- Peptide Label: isoform X24
RefSeq Acc Id: XP_038967354   ⟸   XM_039111426
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038967348   ⟸   XM_039111420
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038967363   ⟸   XM_039111435
- Peptide Label: isoform X21
RefSeq Acc Id: XP_038967345   ⟸   XM_039111417
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038967346   ⟸   XM_039111418
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038967362   ⟸   XM_039111434
- Peptide Label: isoform X20
RefSeq Acc Id: XP_038967350   ⟸   XM_039111422
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038967360   ⟸   XM_039111432
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038967358   ⟸   XM_039111430
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038967341   ⟸   XM_039111413
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038967342   ⟸   XM_039111414
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000089430   ⟸   ENSRNOT00000094348
RefSeq Acc Id: ENSRNOP00000080613   ⟸   ENSRNOT00000115119
RefSeq Acc Id: ENSRNOP00000085531   ⟸   ENSRNOT00000110800
RefSeq Acc Id: ENSRNOP00000091521   ⟸   ENSRNOT00000119354
RefSeq Acc Id: ENSRNOP00000086806   ⟸   ENSRNOT00000113220
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)
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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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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)
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)
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
LEXF11/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
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561090 AgrOrtholog
Ensembl Genes ENSRNOG00000005711 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000066744 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000075474 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.90.190.10 UniProtKB/TrEMBL
InterPro Fibronectin_type3 UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_I-set UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/TrEMBL
  Prot-tyrosine_phosphatase-like UniProtKB/TrEMBL
  Tyr/Dual-sp_Pase UniProtKB/TrEMBL
  Tyr_Pase_AS UniProtKB/TrEMBL
  Tyr_Pase_cat UniProtKB/TrEMBL
  Tyr_Pase_rcpt/non-rcpt UniProtKB/TrEMBL
NCBI Gene 313278 ENTREZGENE
Pfam fn3 UniProtKB/TrEMBL
  I-set UniProtKB/TrEMBL
  Y_phosphatase UniProtKB/TrEMBL
PhenoGen Ptprd PhenoGen
PRINTS PRTYPHPHTASE UniProtKB/TrEMBL
PROSITE FN3 UniProtKB/TrEMBL
  IG_LIKE UniProtKB/TrEMBL
  TYR_PHOSPHATASE_1 UniProtKB/TrEMBL
  TYR_PHOSPHATASE_2 UniProtKB/TrEMBL
  TYR_PHOSPHATASE_PTP UniProtKB/TrEMBL
SMART FN3 UniProtKB/TrEMBL
  IGc2 UniProtKB/TrEMBL
  PTPc UniProtKB/TrEMBL
  PTPc_motif UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP FN_III-like UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
  SSF52799 UniProtKB/TrEMBL
UniProt M0RB22_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Ptprd  protein tyrosine phosphatase, receptor type, D  LOC103692382  uncharacterized LOC103692382  Data Merged 737654 PROVISIONAL
2014-08-25 LOC103692382  uncharacterized LOC103692382      Symbol and Name status set to provisional 70820 PROVISIONAL
2009-04-29 Ptprd  protein tyrosine phosphatase, receptor type, D  RGD1561090  similar to protein tyrosine phosphatase, receptor type, D   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1561090  similar to protein tyrosine phosphatase, receptor type, D   RGD1561090_predicted  similar to protein tyrosine phosphatase, receptor type, D (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1561090_predicted  similar to protein tyrosine phosphatase, receptor type, D (predicted)  LOC313278  similar to protein tyrosine phosphatase, receptor type, D  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC313278  similar to protein tyrosine phosphatase, receptor type, D      Symbol and Name status set to provisional 70820 PROVISIONAL