Ptprz1 (protein tyrosine phosphatase, receptor type Z1) - Rat Genome Database

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Gene: Ptprz1 (protein tyrosine phosphatase, receptor type Z1) Rattus norvegicus
Analyze
Symbol: Ptprz1
Name: protein tyrosine phosphatase, receptor type Z1
RGD ID: 3455
Description: Enables fibroblast growth factor binding activity and protein tyrosine phosphatase activity. Involved in several processes, including nervous system development; positive regulation of cell migration; and regulation of dendrite development. Located in several cellular components, including lamellipodium; perineuronal net; and ruffle membrane. Is intrinsic component of plasma membrane. Is active in glutamatergic synapse. Is integral component of postsynaptic density membrane. Biomarker of amyotrophic lateral sclerosis; middle cerebral artery infarction; status epilepticus; temporal lobe epilepsy; and visual epilepsy. Orthologous to human PTPRZ1 (protein tyrosine phosphatase receptor type Z1); INTERACTS WITH (+)-pilocarpine; (+)-schisandrin B; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 3F8 chondroitin sulfate proteoglycan; 3H1 keratan sulfate proteoglycan; 6B4 proteoglycan; phosphacan; Protein tyrosine phosphatase receptor-type zeta polypeptide; protein tyrosine phosphatase, receptor-type, Z polypeptide 1; Protein tyrosine phosphatase, receptor-type, zeta polypeptide; PTP zeta; Ptpz; PTPzeta-A; PTPzeta-B; PTPzeta-S; R-PTP-zeta; receptor-type tyrosine-protein phosphatase zeta; RPTPbeta
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
mRatBN7.2451,397,316 - 51,595,220 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl451,397,601 - 51,595,218 (+)Ensembl
Rnor_6.0449,941,046 - 50,140,764 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl449,941,304 - 50,140,762 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0449,730,302 - 49,927,328 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4449,267,521 - 49,468,692 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1449,498,094 - 49,699,266 (+)NCBI
Celera446,598,237 - 46,787,500 (+)NCBICelera
Cytogenetic Map4q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(+)-schisandrin B  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-hydroxypropanoic acid  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-dichloroaniline  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acetaldehyde  (ISO)
acetamide  (EXP)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chrysene  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (EXP)
cobalt atom  (ISO)
cobalt dichloride  (ISO)
Cuprizon  (EXP)
cyclosporin A  (EXP)
cytarabine  (ISO)
dimethylarsinous acid  (ISO)
diuron  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fenvalerate  (EXP)
flutamide  (EXP)
furan  (EXP)
genistein  (ISO)
gentamycin  (EXP)
iron(III) nitrilotriacetate  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
manganese(II) chloride  (EXP)
methyl beta-cyclodextrin  (ISO)
methylmercury chloride  (ISO)
miconazole  (ISO)
nitrofen  (EXP)
oxaliplatin  (EXP)
paracetamol  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (EXP,ISO)
rac-lactic acid  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
sodium dodecyl sulfate  (ISO)
tacrolimus hydrate  (EXP)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
triclosan  (ISO)
Tungsten carbide  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
1. Carmichael ST, etal., Exp Neurol. 2005 Jun;193(2):291-311.
2. Davies JE, etal., Eur J Neurosci. 2004 Mar;19(5):1226-42.
3. Deepa SS, etal., J Biol Chem. 2006 Jun 30;281(26):17789-800. Epub 2006 Apr 27.
4. Engel M, etal., J Comp Neurol 1996 Feb 26;366(1):34-43.
5. Forostyak S, etal., Stem Cells. 2014 Aug 11. doi: 10.1002/stem.1812.
6. Fujikawa A, etal., J Biochem. 2007 Sep;142(3):343-50. Epub 2007 Jul 23.
7. Fujikawa A, etal., J Biol Chem. 2011 Oct 28;286(43):37137-46. doi: 10.1074/jbc.M111.270140. Epub 2011 Sep 2.
8. Fukada M, etal., FEBS Lett. 2006 Jul 24;580(17):4051-6. Epub 2006 Jun 27.
9. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. GOA data from the GO Consortium
11. Grumet M, etal., J Biol Chem 1994 Apr 22;269(16):12142-6.
12. Hayashi N, etal., Brain Res. 2005 Jul 19;1050(1-2):163-9.
13. Hayashi N, etal., Mol Cell Neurosci. 2005 Nov;30(3):364-77. Epub 2005 Sep 16.
14. Hayashi N, etal., Neuroscience. 2005;131(2):331-48.
15. Inatani M, etal., Invest Ophthalmol Vis Sci. 2001 Jul;42(8):1930-8.
16. Jones LL, etal., Exp Neurol. 2003 Aug;182(2):399-411.
17. Katoh-Semba R, etal., Neurosci Res. 1998 Aug;31(4):273-82.
18. Kawachi H, etal., Proc Natl Acad Sci U S A. 2001 Jun 5;98(12):6593-8. Epub 2001 May 29.
19. Kurazono S, etal., Brain Res. 2001 Apr 13;898(1):36-48.
20. Kurazono S, etal., Neurosci Lett. 2001 May 25;304(3):169-72.
21. Li J, etal., Brain Res Mol Brain Res. 1998 Sep 18;60(1):77-88.
22. Maeda N and Noda M, Development. 1996 Feb;122(2):647-58.
23. Maeda N and Noda M, J Cell Biol. 1998 Jul 13;142(1):203-16.
24. Maeda N, etal., J Biol Chem. 1996 Aug 30;271(35):21446-52.
25. Maeda N, etal., J Biol Chem. 1999 Apr 30;274(18):12474-9.
26. Matsui F, etal., J Neurosci Res. 2005 Sep 15;81(6):837-45.
27. Matsui F, etal., Neuroscience 2002;112(4):773-81.
28. Maurel P, etal., Proc Natl Acad Sci U S A 1994 Mar 29;91(7):2512-6.
29. Meyer-Puttlitz B, etal., J Comp Neurol 1996 Feb 26;366(1):44-54.
30. MGD data from the GO Consortium
31. Milev P, etal., J Biol Chem 1995 Oct 20;270(42):24650-3.
32. Milev P, etal., J Biol Chem. 1998 Aug 21;273(34):21439-42.
33. Milev P, etal., J Cell Biol 1994 Dec;127(6 Pt 1):1703-15.
34. Muramatsu H, etal., J Cell Sci. 2004 Oct 15;117(Pt 22):5405-15. doi: 10.1242/jcs.01423. Epub 2004 Oct 5.
35. Naffah-Mazzacoratti MG, etal., Brain Res Bull. 1999 Nov 1;50(4):229-39.
36. NCBI rat LocusLink and RefSeq merged data July 26, 2002
37. Nishiwaki T, etal., J Biochem. 1998 Mar;123(3):458-67.
38. Okamoto M, etal., Cell Tissue Res. 2001 Nov;306(2):217-29.
39. Okamoto M, etal., Exp Neurol. 2003 Nov;184(1):179-95.
40. OMIM Disease Annotation Pipeline
41. Qi M, etal., J Biol Chem. 2001 May 11;276(19):15868-75.
42. Ranjan M and Hudson LD, Mol Cell Neurosci. 1996 May;7(5):404-18.
43. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
44. RGD automated import pipeline for gene-chemical interactions
45. Robles Y, etal., Neurobiol Learn Mem. 2003 Jul;80(1):80-95.
46. Sango K, etal., Exp Neurol. 2003 Jul;182(1):1-11.
47. Tanaka M, etal., J Neurosci. 2003 Apr 1;23(7):2804-14.
48. Tanga N, etal., Glia. 2019 May;67(5):967-984. doi: 10.1002/glia.23583. Epub 2019 Jan 22.
49. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
50. Thomaidou D, etal., J Neurochem. 2001 Aug;78(4):767-78.
51. Vitellaro-Zuccarello L, etal., Neuroscience. 2008 Jan 24;151(2):452-66. Epub 2007 Nov 7.
52. Wilson MT and Snow DM, J Comp Neurol. 2000 Aug 28;424(3):532-46.
Additional References at PubMed
PMID:7579589   PMID:7628014   PMID:8889548   PMID:9118959   PMID:9182584   PMID:10234020   PMID:10706604   PMID:10769382   PMID:10793198   PMID:12573468   PMID:12700241   PMID:12840014  
PMID:16452087   PMID:16513268   PMID:17368428   PMID:18055543   PMID:18713734   PMID:19141078   PMID:19141530   PMID:19751804   PMID:21969550   PMID:24029230   PMID:25519047   PMID:26615567  
PMID:26857455   PMID:27374750   PMID:27445335   PMID:28717188  


Genomics

Comparative Map Data
Ptprz1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2451,397,316 - 51,595,220 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl451,397,601 - 51,595,218 (+)Ensembl
Rnor_6.0449,941,046 - 50,140,764 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl449,941,304 - 50,140,762 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0449,730,302 - 49,927,328 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4449,267,521 - 49,468,692 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1449,498,094 - 49,699,266 (+)NCBI
Celera446,598,237 - 46,787,500 (+)NCBICelera
Cytogenetic Map4q22NCBI
PTPRZ1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7121,873,089 - 122,062,036 (+)EnsemblGRCh38hg38GRCh38
GRCh387121,873,161 - 122,062,036 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh377121,513,215 - 121,702,090 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367121,300,395 - 121,489,326 (+)NCBINCBI36hg18NCBI36
Build 347121,107,357 - 121,296,039NCBI
Celera7116,322,385 - 116,511,311 (+)NCBI
Cytogenetic Map7q31.32NCBI
HuRef7115,876,018 - 116,065,533 (+)NCBIHuRef
CHM1_17121,446,481 - 121,635,390 (+)NCBICHM1_1
CRA_TCAGchr7v27120,907,807 - 121,096,757 (+)NCBI
Ptprz1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39622,875,302 - 23,052,915 (+)NCBIGRCm39mm39
GRCm39 Ensembl622,875,501 - 23,052,915 (+)Ensembl
GRCm38622,875,315 - 23,052,916 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl622,875,502 - 23,052,916 (+)EnsemblGRCm38mm10GRCm38
MGSCv37622,825,502 - 23,002,916 (+)NCBIGRCm37mm9NCBIm37
MGSCv36622,825,503 - 23,002,917 (+)NCBImm8
Celera622,923,288 - 23,100,277 (+)NCBICelera
Cytogenetic Map6A3.1NCBI
Ptprz1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554793,624,993 - 3,733,183 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554793,611,658 - 3,734,225 (+)NCBIChiLan1.0ChiLan1.0
PTPRZ1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17126,569,630 - 126,758,155 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7126,569,630 - 126,758,155 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07113,882,557 - 114,073,283 (+)NCBIMhudiblu_PPA_v0panPan3
PTPRZ1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11459,769,553 - 59,944,111 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1459,827,650 - 59,943,315 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1459,203,408 - 59,361,617 (+)NCBI
ROS_Cfam_1.01459,825,102 - 59,979,392 (+)NCBI
UMICH_Zoey_3.11459,916,795 - 60,071,051 (+)NCBI
UNSW_CanFamBas_1.01459,543,462 - 59,698,673 (+)NCBI
UU_Cfam_GSD_1.01459,919,950 - 60,076,006 (+)NCBI
Ptprz1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511848,835,842 - 49,007,255 (+)NCBI
SpeTri2.0NW_0049366053,195,893 - 3,368,102 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTPRZ1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1825,045,727 - 25,228,247 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11825,046,027 - 25,228,276 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21826,650,579 - 26,832,837 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PTPRZ1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12190,686,091 - 90,877,538 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2190,686,167 - 90,877,649 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604212,666,623 - 12,858,179 (-)NCBIVero_WHO_p1.0
Ptprz1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478313,911,525 - 14,105,403 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH144069  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2451,397,796 - 51,397,896 (+)MAPPERmRatBN7.2
Rnor_6.0449,941,500 - 49,941,599NCBIRnor6.0
Rnor_5.0449,730,748 - 49,730,847UniSTSRnor5.0
RGSC_v3.4449,267,717 - 49,267,816UniSTSRGSC3.4
Celera446,598,433 - 46,598,532UniSTS
Cytogenetic Map4q22UniSTS
BF386063  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2451,542,199 - 51,542,361 (+)MAPPERmRatBN7.2
Rnor_6.0450,087,617 - 50,087,778NCBIRnor6.0
Rnor_5.0449,874,248 - 49,874,409UniSTSRnor5.0
RGSC_v3.4449,415,743 - 49,415,904UniSTSRGSC3.4
Celera446,734,344 - 46,734,505UniSTS
RH 3.4 Map4300.0UniSTS
Cytogenetic Map4q22UniSTS
RH137971  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2451,546,075 - 51,546,250 (+)MAPPERmRatBN7.2
Rnor_6.0450,091,493 - 50,091,667NCBIRnor6.0
Rnor_5.0449,878,124 - 49,878,298UniSTSRnor5.0
RGSC_v3.4449,419,619 - 49,419,793UniSTSRGSC3.4
Celera446,738,220 - 46,738,394UniSTS
RH 3.4 Map4296.3UniSTS
Cytogenetic Map4q22UniSTS
AW521233  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2451,594,899 - 51,595,084 (+)MAPPERmRatBN7.2
Rnor_6.0450,140,444 - 50,140,628NCBIRnor6.0
Rnor_5.0449,927,008 - 49,927,192UniSTSRnor5.0
RGSC_v3.4449,468,377 - 49,468,561UniSTSRGSC3.4
Celera446,787,180 - 46,787,364UniSTS
RH 3.4 Map4299.7UniSTS
Cytogenetic Map4q22UniSTS
UniSTS:498441  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2451,594,309 - 51,594,380 (+)MAPPERmRatBN7.2
Rnor_6.0450,139,854 - 50,139,924NCBIRnor6.0
Rnor_5.0449,926,418 - 49,926,488UniSTSRnor5.0
RGSC_v3.4449,467,787 - 49,467,857UniSTSRGSC3.4
Celera446,786,590 - 46,786,660UniSTS
Cytogenetic Map4q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41793350862933508Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42133334362278020Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
11530004Niddm71Non-insulin dependent diabetes mellitus QTL 710.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)43258419952754138Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43443048482490359Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
61475Aia2Adjuvant induced arthritis QTL 25.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)43950527573892441Rat
1331807Rf31Renal function QTL 312.988urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)43952426474726312Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)439524264116179656Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44043338885433388Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44043341485433414Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44345797688457976Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
10450818Scl76Serum cholesterol level QTL 763.60.01blood VLDL cholesterol amount (VT:0005144)blood high density lipoprotein cholesterol level (CMO:0000052)44917811657114705Rat
10450821Scl77Serum cholesterol level QTL 774.10.01blood VLDL cholesterol amount (VT:0005144)blood high density lipoprotein cholesterol level (CMO:0000052)44917811657114705Rat
10450825Scl78Serum cholesterol level QTL 783.70.01blood VLDL cholesterol amount (VT:0005144)blood low density lipoprotein cholesterol level (CMO:0000053)44917811657114705Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:300
Count of miRNA genes:198
Interacting mature miRNAs:227
Transcripts:ENSRNOT00000008719
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 74
Low 2 6 32 16 8 16 3 3 23 33 11 3
Below cutoff 1 37 20 20 11 20 5 7 12 6 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008719   ⟹   ENSRNOP00000008719
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl451,397,601 - 51,595,218 (+)Ensembl
Rnor_6.0 Ensembl449,941,304 - 50,140,762 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000116498   ⟹   ENSRNOP00000097069
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl451,397,601 - 51,595,218 (+)Ensembl
RefSeq Acc Id: NM_001170685   ⟹   NP_001164156
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,397,601 - 51,545,567 (+)NCBI
Rnor_6.0449,941,304 - 50,090,984 (+)NCBI
Rnor_5.0449,730,302 - 49,927,328 (+)NCBI
Celera446,598,237 - 46,737,711 (+)NCBI
Sequence:
RefSeq Acc Id: NM_013080   ⟹   NP_037212
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,397,601 - 51,595,220 (+)NCBI
Rnor_6.0449,941,304 - 50,140,764 (+)NCBI
Rnor_5.0449,730,302 - 49,927,328 (+)NCBI
RGSC_v3.4449,267,521 - 49,468,692 (+)RGD
Celera446,598,237 - 46,787,500 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006236137   ⟹   XP_006236199
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,397,316 - 51,595,220 (+)NCBI
Rnor_6.0449,941,046 - 50,140,764 (+)NCBI
Rnor_5.0449,730,302 - 49,927,328 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006236138   ⟹   XP_006236200
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,397,321 - 51,595,220 (+)NCBI
Rnor_6.0449,941,049 - 50,140,764 (+)NCBI
Rnor_5.0449,730,302 - 49,927,328 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006236139   ⟹   XP_006236201
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2451,397,321 - 51,595,220 (+)NCBI
Rnor_6.0449,941,049 - 50,140,764 (+)NCBI
Rnor_5.0449,730,302 - 49,927,328 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_037212   ⟸   NM_013080
- Peptide Label: isoform 1 precursor
- UniProtKB: Q62656 (UniProtKB/Swiss-Prot),   F1LMY3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001164156   ⟸   NM_001170685
- Peptide Label: isoform 2 precursor
- UniProtKB: Q62656 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006236200   ⟸   XM_006236138
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006236201   ⟸   XM_006236139
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006236199   ⟸   XM_006236137
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000008719   ⟸   ENSRNOT00000008719
RefSeq Acc Id: ENSRNOP00000097069   ⟸   ENSRNOT00000116498
Protein Domains
Alpha-carbonic anhydrase   Fibronectin type-III   TYR_PHOSPHATASE_2   Tyrosine-protein phosphatase

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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
BBDP/Wor (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
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (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
BN/SsN (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
BN/SsN (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
BUF/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
BXH2/CubMcwi (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
BXH3/CubMcwi (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
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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
F344/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
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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)
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)
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
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
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)
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)
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
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 49861114 49861115 A T snv LE/Stm (KyushuU), SDLEF7/Barth (UDEL), SBN/Ygl (KNAW), MNS/Gib (KNAW), HTX/Kyo (KyushuU), LE/Stm (Illumina) (KNAW), MHS/Gib (KNAW), SBN/Ygl (MCW), LE/Stm (SOLiD) (KNAW)
4 49873073 49873074 C T snv WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), DA/BklArbNsi (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), SBH/Ygl (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), F344/Stm (KyushuU), F344/Jcl (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), SS/JrHsdMcwi (KNAW), SS/Jr (KNAW), MR/N (KNAW), WN/N (KNAW), SS/JrHsdMcwi (MCW), SBH/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW)
4 49874382 49874383 T C snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), WN/N (KNAW), MHS/Gib (KNAW), MR/N (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), DA/BklArbNsi (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), MNS/Gib (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), F344/Stm (KyushuU), F344/Jcl (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU)
4 49874858 49874859 G A snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), ZF (KyushuU), KFRS3B/Kyo (KyushuU), F344/Jcl (KyushuU), F344/Stm (KyushuU), RCS/Kyo (KyushuU), F344/NSlc (KyushuU), HTX/Kyo (KyushuU), LE/Stm (KyushuU), F344/DuCrlCrlj (KyushuU), NIG-III/Hok (KyushuU), BUF/MNa (KyushuU), Crl:SD (UDEL), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), WN/N (KNAW), MHS/Gib (KNAW), MR/N (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), DA/BklArbNsi (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), MNS/Gib (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL)
4 49875113 49875114 A G snv LE/Stm (SOLiD) (KNAW), SBN/Ygl (MCW), MHS/Gib (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (KyushuU), SDLEF7/Barth (UDEL), SBN/Ygl (KNAW), MNS/Gib (KNAW)
4 49889742 49889743 T C snv SDLEF7/Barth (UDEL), SBN/Ygl (KNAW), SBN/Ygl (MCW), MHS/Gib (KNAW), MNS/Gib (KNAW)


Assembly: mRatBN7.2
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 51541025 51541026 C T snv ACI/EurMcwi (2019), WN/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF4/Stm (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WKY/NCrl (2019), WKY/N (2020), ACI/N (2020)
4 51542334 51542335 T C snv ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WKY/NCrl (2019), WKY/N (2020), WN/N (2020)
4 51542810 51542811 G A snv ACI/EurMcwi (2019), WN/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WKY/NCrl (2019), WKY/N (2020), ACI/N (2020)


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 50074483 50074484 A T snv LEXF10A/StmMcwi (2020), LE/Stm (2019), LEXF3/Stm (2020), LEXF2B/Stm (2019), FXLE18/Stm (2020), SBN/Ygl (MCW), SBN/Ygl (RGD), MNS/Gib (RGD), MHS/Gib (RGD), LE/Stm (RGD), FXLE16/Stm (2020)
4 50086442 50086443 C T snv WN/N (MCW), BBDP/Wor (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), FHL/EurMcwi (RGD), WN/N (2020), LEW/NCrlBR (RGD), SBH/Ygl (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WAG/Rij (RGD), WKY/NCrl (RGD), WKY/NHsd (RGD), ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF4/Stm (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WKY/NCrl (2019), WKY/N (2020), WKY/N (MCW), MR/N (MCW), F344/NRrrc (MCW), ACI/N (MCW), SS/JrHsdMcwi (MCW), SBH/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), CDS, LEW/Crl (RGD)
4 50087751 50087752 T C snv CDS, ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), ACI/N (MCW), F344/NRrrc (MCW), MR/N (MCW), WKY/N (MCW), WN/N (MCW), ACI/EurMcwi (RGD), BBDP/Wor (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), FHL/EurMcwi (RGD), LE/Stm (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), MHS/Gib (RGD), MNS/Gib (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WAG/Rij (RGD), WKY/NCrl (RGD), WKY/NHsd (RGD), ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WKY/NCrl (2019), WKY/N (2020), WN/N (2020)
4 50088227 50088228 G A snv CDS, WN/N (2020), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), ACI/N (MCW), F344/NRrrc (MCW), MR/N (MCW), WKY/N (MCW), WN/N (MCW), ACI/EurMcwi (RGD), BBDP/Wor (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), FHL/EurMcwi (RGD), LE/Stm (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), MHS/Gib (RGD), MNS/Gib (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WAG/Rij (RGD), WKY/NCrl (RGD), ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WKY/NCrl (2019), WKY/N (2020), ACI/EurMcwi (MCW)
4 50088482 50088483 A G snv LEXF3/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), SBN/Ygl (MCW), LE/Stm (RGD), MHS/Gib (RGD), MNS/Gib (RGD), SBN/Ygl (RGD), FXLE16/Stm (2020), FXLE18/Stm (2020), LEXF2B/Stm (2019)
4 50103111 50103112 T C snv SBN/Ygl (MCW), SBN/Ygl (RGD), MNS/Gib (RGD), MHS/Gib (RGD)


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 49402608 49402609 A T snv MNS/Gib (ICL), MHS/Gib (ICL), LE/Stm (ICL), LE/Stm (KNAW), SBN/Ygl (ICL)
4 49414568 49414569 C T snv ACI/N (KNAW), F344/NRrrc (KNAW), MR/N (KNAW), WKY/N (KNAW), WN/N (KNAW), COP/CrCrl (MCW & UW), ACI/EurMcwi (ICL), BBDP/WorN (ICL), F344/NCrl (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), SBH/Ygl (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), WAG/Rij (ICL), WKY/NCrl (ICL), WKY/NHsd (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), DA/BklArbNsi (ICAHN), F344/NHsd (ICAHN), SS/JrHsdMcwi (MDC), FHH/EurMcwi (MDC), SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW)
4 49415877 49415878 T C snv ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SS/JrHsdMcwi (MCW), FHH/EurMcwi (MDC), SS/JrHsdMcwi (MDC), ACI/N (KNAW), F344/NRrrc (KNAW), LE/Stm (KNAW), MR/N (KNAW), WKY/N (KNAW), WN/N (KNAW), COP/CrCrl (MCW & UW), ACI/EurMcwi (ICL), BBDP/WorN (ICL), F344/NCrl (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), LE/Stm (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), MHS/Gib (ICL), MNS/Gib (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), WAG/Rij (ICL), WKY/NCrl (ICL), WKY/NHsd (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), DA/BklArbNsi (ICAHN), F344/NHsd (ICAHN)
4 49416353 49416354 G A snv ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), F344/NHsd (ICAHN), DA/BklArbNsi (ICAHN), LCR/2Mco (UMich), HCR/2Mco (UMich), LCR/1Mco (UMich), HCR/1Mco (UMich), WKY/NHsd (ICL), FHL/EurMcwi (MCW), SS/JrHsdMcwi (MCW), FHH/EurMcwi (MDC), SS/JrHsdMcwi (MDC), ACI/N (KNAW), F344/NRrrc (KNAW), LE/Stm (KNAW), MR/N (KNAW), WKY/N (KNAW), WN/N (KNAW), COP/CrCrl (MCW & UW), ACI/EurMcwi (ICL), BBDP/WorN (ICL), F344/NCrl (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), LE/Stm (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), MHS/Gib (ICL), MNS/Gib (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), WAG/Rij (ICL), WKY/NCrl (ICL)
4 49416608 49416609 A G snv MNS/Gib (ICL), MHS/Gib (ICL), LE/Stm (ICL), LE/Stm (KNAW), SBN/Ygl (ICL)
4 49431238 49431239 T C snv MHS/Gib (ICL), SBN/Ygl (ICL), MNS/Gib (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3455 AgrOrtholog
Ensembl Genes ENSRNOG00000006030 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008719 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000097069 ENTREZGENE
Ensembl Transcript ENSRNOT00000008719 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000116498 ENTREZGENE
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.10.200.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.90.190.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro alpha_CARP_receptor-type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CA_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CA_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold 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:25613 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 25613 ENTREZGENE
Pfam Carb_anhydrase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  fn3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Y_phosphatase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ptprz1 PhenoGen
PRINTS PRTYPHPHTASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ALPHA_CA_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3 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 Carb_anhydrase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTPc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTPc_motif UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49265 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF51069 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52799 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC218471
UniProt F1LMY3 ENTREZGENE, UniProtKB/TrEMBL
  PTPRZ_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q62621 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-13 Ptprz1  protein tyrosine phosphatase, receptor type Z1  Ptprz1  protein tyrosine phosphatase, receptor-type, Z polypeptide 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Ptprz1  protein tyrosine phosphatase, receptor-type, Z polypeptide 1    Protein tyrosine phosphatase, receptor-type, zeta polypeptide  Name updated 629478 APPROVED
2002-06-10 Ptprz1  Protein tyrosine phosphatase, receptor-type, zeta polypeptide      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction alternative splicing product phosphocan binds neural cell adhesion molecules, binding is mediated by phosphocan asparagine-linnked oligosaccharides 729925
gene_transcript phosphocan is a product of alternative splicing that contains the Ptprz1 extracellular domain 729925