Ptprs (protein tyrosine phosphatase, receptor type, S) - Rat Genome Database

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Gene: Ptprs (protein tyrosine phosphatase, receptor type, S) Rattus norvegicus
Analyze
Symbol: Ptprs
Name: protein tyrosine phosphatase, receptor type, S
RGD ID: 3452
Description: Enables protein tyrosine phosphatase activity. Involved in regulation of postsynaptic density assembly; regulation of presynapse assembly; and synaptic membrane adhesion. Located in glutamatergic synapse. Is integral component of postsynaptic density membrane and integral component of synaptic vesicle membrane. Is integral component of presynaptic membrane. Orthologous to human PTPRS (protein tyrosine phosphatase receptor type S); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-diaminodiphenylmethane; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LAR-PTP2; Larptp2; leukocyte common antigen-related protein-tyrosine phosphatase 2; leukocyte common antigen-related proten-tyrosine phosphatase 2; MGC124537; protein tyrosine phosphatase, receptor type, D; Ptprd; Ptpsigma; Ptpsigma.; R-PTP-S; R-PTP-sigma; receptor-type tyrosine-protein phosphatase S; receptor-type tyrosine-protein phosphatase sigma; Rptpd
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
mRatBN7.291,245,408 - 1,307,015 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl91,245,410 - 1,306,947 (-)Ensembl
Rnor_6.0910,585,360 - 10,646,205 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,603,813 - 10,645,939 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,578,004 - 9,637,940 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,203,284 - 7,264,120 (+)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-butoxyethanol  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP)
carbon nanotube  (ISO)
chlordecone  (ISO)
chloroprene  (EXP)
choline  (ISO)
clobetasol  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
dibutyl phthalate  (EXP,ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
folic acid  (ISO)
glutathione  (EXP)
glyphosate  (ISO)
indole-3-methanol  (EXP)
L-methionine  (ISO)
methamphetamine  (ISO)
methapyrilene  (EXP)
miconazole  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP)
paraquat  (EXP)
PCB138  (ISO)
phenylmercury acetate  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
propanal  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sodium fluoride  (ISO)
tamoxifen  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

Additional References at PubMed
PMID:7529177   PMID:8229209   PMID:8524829   PMID:12110683   PMID:12477932   PMID:15750591   PMID:15842738   PMID:19780196   PMID:22406547   PMID:23345436   PMID:23376485   PMID:23533145  
PMID:23718120   PMID:24385580   PMID:25470046   PMID:25624497   PMID:26231120   PMID:26464223   PMID:28752900   PMID:33662380  


Genomics

Comparative Map Data
Ptprs
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.291,245,408 - 1,307,015 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl91,245,410 - 1,306,947 (-)Ensembl
Rnor_6.0910,585,360 - 10,646,205 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,603,813 - 10,645,939 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,578,004 - 9,637,940 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,203,284 - 7,264,120 (+)NCBICelera
Cytogenetic Map9q12NCBI
PTPRS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl195,158,495 - 5,340,803 (-)EnsemblGRCh38hg38GRCh38
GRCh38195,205,503 - 5,340,812 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37195,205,519 - 5,340,823 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36195,156,519 - 5,291,814 (-)NCBINCBI36hg18NCBI36
Build 34195,157,380 - 5,237,399NCBI
Celera195,143,031 - 5,278,326 (-)NCBI
Cytogenetic Map19p13.3NCBI
HuRef194,967,302 - 5,101,977 (-)NCBIHuRef
CHM1_1195,205,046 - 5,340,693 (-)NCBICHM1_1
Ptprs
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391756,719,426 - 56,783,526 (-)NCBIGRCm39mm39
GRCm39 Ensembl1756,719,426 - 56,783,483 (-)Ensembl
GRCm381756,412,426 - 56,476,561 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1756,412,426 - 56,476,483 (-)EnsemblGRCm38mm10GRCm38
MGSCv371756,551,849 - 56,615,903 (-)NCBIGRCm37mm9NCBIm37
MGSCv361756,046,141 - 56,110,077 (-)NCBImm8
Celera1760,758,165 - 60,822,309 (-)NCBICelera
Cytogenetic Map17DNCBI
cM Map1729.32NCBI
Ptprs
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554953,943,170 - 3,990,927 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554953,943,075 - 3,991,361 (+)NCBIChiLan1.0ChiLan1.0
PTPRS
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1195,167,338 - 5,254,343 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl195,168,599 - 5,247,778 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0194,227,038 - 4,361,958 (-)NCBIMhudiblu_PPA_v0panPan3
PTPRS
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12054,575,853 - 54,672,141 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2054,575,895 - 54,672,068 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2054,301,762 - 54,397,754 (+)NCBI
ROS_Cfam_1.02055,231,459 - 55,327,738 (+)NCBI
UMICH_Zoey_3.12054,293,104 - 54,389,219 (+)NCBI
UNSW_CanFamBas_1.02054,773,757 - 54,869,877 (+)NCBI
UU_Cfam_GSD_1.02054,971,421 - 55,067,624 (+)NCBI
Ptprs
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118214,761,700 - 214,813,370 (+)NCBI
SpeTri2.0NW_0049365883,021,418 - 3,073,080 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTPRS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl273,574,854 - 73,680,685 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1273,607,815 - 73,680,685 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2274,545,303 - 74,550,135 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PTPRS
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.164,880,942 - 5,019,654 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl64,882,223 - 4,964,919 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660813,106,747 - 3,243,187 (+)NCBIVero_WHO_p1.0
Ptprs
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248284,688,555 - 4,764,805 (+)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1091
Count of miRNA genes:257
Interacting mature miRNAs:312
Transcripts:ENSRNOT00000073991, ENSRNOT00000074469
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 42 45 29 18 29 4 7 74 22 41 11 4
Low 3 1 12 12 1 12 4 4 13 4
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_019140 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083054 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083056 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083057 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083058 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083059 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083060 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083061 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083064 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083066 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083068 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC105753 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474092 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000204 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L12329 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L19180 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L19181 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L19933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U03273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000073991   ⟹   ENSRNOP00000065227
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,246,039 - 1,306,947 (-)Ensembl
Rnor_6.0 Ensembl910,603,813 - 10,645,939 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000074469   ⟹   ENSRNOP00000066443
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,245,998 - 1,285,600 (-)Ensembl
Rnor_6.0 Ensembl910,603,813 - 10,645,939 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079999   ⟹   ENSRNOP00000071910
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,246,039 - 1,306,947 (-)Ensembl
Rnor_6.0 Ensembl910,603,813 - 10,645,939 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099559   ⟹   ENSRNOP00000084660
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,245,998 - 1,285,600 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103214   ⟹   ENSRNOP00000084874
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,245,410 - 1,292,680 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104893   ⟹   ENSRNOP00000084417
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,245,410 - 1,292,680 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111910   ⟹   ENSRNOP00000093127
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,245,410 - 1,285,600 (-)Ensembl
RefSeq Acc Id: NM_019140   ⟹   NP_062013
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,246,039 - 1,306,945 (-)NCBI
Rnor_6.0910,585,360 - 10,646,205 (+)NCBI
Rnor_5.099,578,004 - 9,637,940 (+)NCBI
Celera97,203,284 - 7,264,120 (+)RGD
Sequence:
RefSeq Acc Id: XM_039083051   ⟹   XP_038938979
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,307,015 (-)NCBI
RefSeq Acc Id: XM_039083052   ⟹   XP_038938980
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,292,675 (-)NCBI
RefSeq Acc Id: XM_039083053   ⟹   XP_038938981
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,292,098 (-)NCBI
RefSeq Acc Id: XM_039083054   ⟹   XP_038938982
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,307,015 (-)NCBI
RefSeq Acc Id: XM_039083055   ⟹   XP_038938983
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,307,015 (-)NCBI
RefSeq Acc Id: XM_039083056   ⟹   XP_038938984
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,307,015 (-)NCBI
RefSeq Acc Id: XM_039083057   ⟹   XP_038938985
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,307,015 (-)NCBI
RefSeq Acc Id: XM_039083058   ⟹   XP_038938986
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,307,015 (-)NCBI
RefSeq Acc Id: XM_039083059   ⟹   XP_038938987
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,409 - 1,292,680 (-)NCBI
RefSeq Acc Id: XM_039083060   ⟹   XP_038938988
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,307,015 (-)NCBI
RefSeq Acc Id: XM_039083061   ⟹   XP_038938989
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,273,165 (-)NCBI
RefSeq Acc Id: XM_039083062   ⟹   XP_038938990
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,307,015 (-)NCBI
RefSeq Acc Id: XM_039083063   ⟹   XP_038938991
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,307,015 (-)NCBI
RefSeq Acc Id: XM_039083064   ⟹   XP_038938992
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,307,015 (-)NCBI
RefSeq Acc Id: XM_039083065   ⟹   XP_038938993
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,307,015 (-)NCBI
RefSeq Acc Id: XM_039083066   ⟹   XP_038938994
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,246,037 - 1,306,945 (-)NCBI
RefSeq Acc Id: XM_039083067   ⟹   XP_038938995
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,307,015 (-)NCBI
RefSeq Acc Id: XM_039083068   ⟹   XP_038938996
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,245,408 - 1,267,584 (-)NCBI
Protein Sequences
Protein RefSeqs NP_062013 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938979 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938980 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938981 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938982 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938983 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938984 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938985 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938986 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938987 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938988 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938989 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938990 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938991 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938992 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938993 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938994 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938995 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938996 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA42309 (Get FASTA)   NCBI Sequence Viewer  
  AAA50568 (Get FASTA)   NCBI Sequence Viewer  
  AAA75407 (Get FASTA)   NCBI Sequence Viewer  
  AAC37657 (Get FASTA)   NCBI Sequence Viewer  
  AAC52124 (Get FASTA)   NCBI Sequence Viewer  
  AAI05754 (Get FASTA)   NCBI Sequence Viewer  
  EDL83634 (Get FASTA)   NCBI Sequence Viewer  
  EDL83635 (Get FASTA)   NCBI Sequence Viewer  
  EDL83636 (Get FASTA)   NCBI Sequence Viewer  
  EDL83637 (Get FASTA)   NCBI Sequence Viewer  
  EDL83638 (Get FASTA)   NCBI Sequence Viewer  
  EDL83639 (Get FASTA)   NCBI Sequence Viewer  
  EDL83640 (Get FASTA)   NCBI Sequence Viewer  
  EDL83641 (Get FASTA)   NCBI Sequence Viewer  
  Q64605 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_062013   ⟸   NM_019140
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000071910   ⟸   ENSRNOT00000079999
RefSeq Acc Id: ENSRNOP00000065227   ⟸   ENSRNOT00000073991
RefSeq Acc Id: ENSRNOP00000066443   ⟸   ENSRNOT00000074469
RefSeq Acc Id: XP_038938995   ⟸   XM_039083067
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038938986   ⟸   XM_039083058
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038938992   ⟸   XM_039083064
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038938984   ⟸   XM_039083056
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038938993   ⟸   XM_039083065
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038938982   ⟸   XM_039083054
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038938991   ⟸   XM_039083063
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038938990   ⟸   XM_039083062
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038938988   ⟸   XM_039083060
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038938985   ⟸   XM_039083057
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038938983   ⟸   XM_039083055
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038938979   ⟸   XM_039083051
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038938980   ⟸   XM_039083052
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038938981   ⟸   XM_039083053
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038938989   ⟸   XM_039083061
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038938996   ⟸   XM_039083068
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038938987   ⟸   XM_039083059
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038938994   ⟸   XM_039083066
- Peptide Label: isoform X14
RefSeq Acc Id: ENSRNOP00000084874   ⟸   ENSRNOT00000103214
RefSeq Acc Id: ENSRNOP00000084417   ⟸   ENSRNOT00000104893
RefSeq Acc Id: ENSRNOP00000084660   ⟸   ENSRNOT00000099559
RefSeq Acc Id: ENSRNOP00000093127   ⟸   ENSRNOT00000111910
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)
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)
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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)
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)
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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)
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)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3452 AgrOrtholog
Ensembl Genes ENSRNOG00000047247 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000065227 UniProtKB/TrEMBL
  ENSRNOP00000066443 UniProtKB/TrEMBL
  ENSRNOP00000071910 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000073991 UniProtKB/TrEMBL
  ENSRNOT00000074469 UniProtKB/TrEMBL
  ENSRNOT00000079999 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.90.190.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5599711 IMAGE-MGC_LOAD
InterPro FN3_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot-tyrosine_phosphatase-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTPase_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_Pase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_Pase_cat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYR_PHOSPHATASE_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25529 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124537 IMAGE-MGC_LOAD
NCBI Gene 25529 ENTREZGENE
Pfam fn3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Y_phosphatase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ptprs PhenoGen
PRINTS PRTYPHPHTASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYR_PHOSPHATASE_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYR_PHOSPHATASE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYR_PHOSPHATASE_PTP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGc2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTPc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTPc_motif UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49265 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52799 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC228239
UniProt A0A0G2K1N1_RAT UniProtKB/TrEMBL
  M0R711_RAT UniProtKB/TrEMBL
  M0RA99_RAT UniProtKB/TrEMBL
  PTPRS_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q07808 UniProtKB/Swiss-Prot
  Q3KRE9 UniProtKB/Swiss-Prot
  Q64621 UniProtKB/Swiss-Prot
  Q64675 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-04-29 Ptprs  protein tyrosine phosphatase, receptor type, S  Ptprd  protein tyrosine phosphatase, receptor type, D  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Ptprd  protein tyrosine phosphatase, receptor type, D      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_product member of a family of protein tyrosine phosphatases related to human leukocyte common antigen-related PTPase 69951