Ptk2b (protein tyrosine kinase 2 beta) - Rat Genome Database

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Gene: Ptk2b (protein tyrosine kinase 2 beta) Rattus norvegicus
Analyze
Symbol: Ptk2b
Name: protein tyrosine kinase 2 beta
RGD ID: 628758
Description: Enables 3-phosphoinositide-dependent protein kinase binding activity; calmodulin-dependent protein kinase activity; and ubiquitin protein ligase binding activity. Involved in several processes, including negative regulation of apoptotic process; positive regulation of cell communication; and positive regulation of cellular biosynthetic process. Located in several cellular components, including dendrite; focal adhesion; and postsynaptic density. Part of NMDA selective glutamate receptor complex. Is active in glutamatergic synapse and postsynapse. Used to study brain ischemia; diabetic angiopathy; and nephritis. Biomarker of anti-basement membrane glomerulonephritis; hypertension; and status epilepticus. Human ortholog(s) of this gene implicated in breast cancer and hypertension. Orthologous to human PTK2B (protein tyrosine kinase 2 beta); PARTICIPATES IN Jak-Stat signaling pathway; Rho/Rac/Cdc42 mediated signaling pathway; the extracellular signal-regulated Raf/Mek/Erk signaling pathway; INTERACTS WITH (+)-pilocarpine; 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CADTK; CAK beta; CAK-beta; CAKB; CAKbeta; calcium-dependent tyrosine kinase; calcium-regulated non-receptor proline-rich tyrosine kinase; cell adhesion kinase beta; FADK 2; focal adhesion kinase 2; MGC124628; proline-rich tyrosine kinase 2; protein-tyrosine kinase 2-beta; PTK2 protein tyrosine kinase 2 beta; PTK2B protein tyrosine kinase 2 beta; Pyk2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Ptk2bem1Mcwi  
Genetic Models: SS-Ptk2bem1Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21540,360,722 - 40,481,235 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1540,360,723 - 40,481,282 (-)Ensembl
Rnor_6.01542,827,306 - 42,947,796 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1542,827,310 - 42,947,656 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01548,646,476 - 48,766,708 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41545,589,222 - 45,717,866 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11545,604,992 - 45,733,824 (-)NCBI
Celera1540,034,001 - 40,153,993 (-)NCBICelera
Cytogenetic Map15p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(S)-colchicine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
1-octadec-9-enoylglycero-3-phosphate  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,6-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
7,9-dihydro-1H-purine-2,6,8(3H)-trione  (ISO)
7-ketocholesterol  (ISO)
[2,8-bis(trifluoromethyl)quinolin-4-yl]-(2-piperidyl)methanol  (EXP)
acetamide  (EXP)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
AICA ribonucleotide  (EXP)
alachlor  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
apigenin  (ISO)
apocynin  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
azoxystrobin  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
buta-1,3-diene  (ISO)
butan-1-ol  (EXP)
butanal  (ISO)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
captan  (ISO)
carbachol  (EXP)
carbon nanotube  (ISO)
chlordecone  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cocaine  (EXP)
Cuprizon  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibenziodolium  (EXP)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
dimethylarsinic acid  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP,ISO)
ethanol  (ISO)
ethylene glycol bis(2-aminoethyl)tetraacetic acid  (EXP)
fenpyroximate  (ISO)
fenvalerate  (EXP)
flavonoids  (EXP)
fluoxetine  (EXP)
folic acid  (ISO)
folpet  (ISO)
furan  (EXP,ISO)
glyphosate  (EXP)
hydralazine  (ISO)
hydrogen peroxide  (EXP)
ionomycin  (EXP)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lithium atom  (EXP)
lithium hydride  (EXP)
Malonoben  (ISO)
mancozeb  (ISO)
maneb  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
mefloquine  (EXP)
methapyrilene  (ISO)
methimazole  (EXP)
mono(2-ethylhexyl) phthalate  (ISO)
N-acetyl-L-cysteine  (EXP)
N-Nitrosopyrrolidine  (ISO)
naphthalene  (ISO)
paracetamol  (EXP,ISO)
paraoxon  (ISO)
PCB138  (ISO)
phorbol 13-acetate 12-myristate  (EXP)
picoxystrobin  (ISO)
pirinixic acid  (ISO)
ponatinib  (ISO)
potassium chloride  (EXP)
pregnenolone 16alpha-carbonitrile  (ISO)
propiconazole  (ISO)
prostaglandin F2alpha  (EXP)
quercitrin  (ISO)
rotenone  (ISO)
silicon dioxide  (EXP,ISO)
sodium arsenite  (EXP,ISO)
Soman  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
titanium dioxide  (ISO)
trichloroethene  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
actin filament organization  (IMP)
activation of GTPase activity  (IMP)
activation of Janus kinase activity  (IMP,ISO)
adaptive immune response  (IEA)
angiogenesis  (IBA,IMP)
blood vessel endothelial cell migration  (IMP)
bone resorption  (ISO,ISS)
cell adhesion  (IMP)
cell differentiation  (IBA,IEP)
cell surface receptor signaling pathway  (ISO,ISS)
cellular defense response  (IMP)
cellular response to fluid shear stress  (ISO)
cellular response to retinoic acid  (ISO)
chemokine-mediated signaling pathway  (ISO,ISS)
endothelin receptor signaling pathway  (ISO,ISS)
epidermal growth factor receptor signaling pathway  (IBA,IMP)
focal adhesion assembly  (IMP)
glial cell proliferation  (IEP)
innate immune response  (IBA)
integrin-mediated signaling pathway  (ISO,ISS)
ionotropic glutamate receptor signaling pathway  (IMP)
long-term synaptic depression  (IMP)
long-term synaptic potentiation  (IMP)
MAPK cascade  (IMP)
marginal zone B cell differentiation  (ISO,ISS)
negative regulation of apoptotic process  (ISO,ISS)
negative regulation of bone mineralization  (ISO,ISS)
negative regulation of cell population proliferation  (ISO,ISS)
negative regulation of muscle cell apoptotic process  (IMP)
negative regulation of myeloid cell differentiation  (ISO)
negative regulation of neuron apoptotic process  (IMP)
negative regulation of ossification  (IMP)
negative regulation of potassium ion transport  (ISO)
neuron projection development  (IMP)
oocyte maturation  (IMP)
peptidyl-tyrosine autophosphorylation  (IDA,IMP,ISO)
peptidyl-tyrosine phosphorylation  (IDA,IMP,ISO)
positive regulation of actin filament polymerization  (ISO,ISS)
positive regulation of angiogenesis  (ISO)
positive regulation of B cell chemotaxis  (ISO,ISS)
positive regulation of cell growth  (IMP)
positive regulation of cell migration  (IMP,ISO)
positive regulation of cell population proliferation  (IEP,ISO)
positive regulation of cell-matrix adhesion  (ISO,ISS)
positive regulation of cellular protein metabolic process  (IMP)
positive regulation of cytosolic calcium ion concentration  (IMP)
positive regulation of DNA biosynthetic process  (IMP)
positive regulation of endothelial cell migration  (ISO)
positive regulation of ERK1 and ERK2 cascade  (ISO,ISS)
positive regulation of excitatory postsynaptic potential  (IMP)
positive regulation of JNK cascade  (ISO,ISS)
positive regulation of JUN kinase activity  (IMP)
positive regulation of neuron projection development  (ISO)
positive regulation of nitric oxide biosynthetic process  (IMP)
positive regulation of nitric-oxide synthase activity  (IMP,ISO)
positive regulation of peptidyl-tyrosine phosphorylation  (ISO)
positive regulation of phosphatidylinositol 3-kinase activity  (ISO,ISS)
positive regulation of protein kinase activity  (ISO,ISS)
positive regulation of reactive oxygen species metabolic process  (IMP)
positive regulation of synaptic transmission, glutamatergic  (IMP)
positive regulation of translation  (IMP)
positive regulation of ubiquitin-dependent protein catabolic process  (ISO,ISS)
protein phosphorylation  (ISO)
regulation of actin cytoskeleton reorganization  (ISO,ISS)
regulation of calcium-mediated signaling  (ISO)
regulation of cell adhesion  (IBA,ISO,ISS)
regulation of cell shape  (ISO,ISS)
regulation of cGMP-mediated signaling  (ISO)
regulation of establishment of cell polarity  (ISO,ISS)
regulation of inositol trisphosphate biosynthetic process  (ISO,ISS)
regulation of macrophage chemotaxis  (ISO,ISS)
regulation of nitric oxide biosynthetic process  (ISO)
regulation of NMDA receptor activity  (IMP)
regulation of release of sequestered calcium ion into cytosol  (ISO,ISS)
regulation of ubiquitin-dependent protein catabolic process  (ISO)
response to calcium ion  (IEP)
response to cAMP  (IEP)
response to cocaine  (IEP)
response to ethanol  (IEP)
response to glucose  (IEP)
response to hormone  (IEP)
response to hydrogen peroxide  (IPI)
response to hypoxia  (IEP)
response to immobilization stress  (IEP)
response to lithium ion  (IEP)
response to mechanical stimulus  (IEP)
response to organonitrogen compound  (IEP)
response to osmotic stress  (IEP)
response to reactive oxygen species  (IEP)
response to xenobiotic stimulus  (IEP)
signal complex assembly  (IEA)
sprouting angiogenesis  (ISO,ISS)
stress fiber assembly  (IMP)
transmembrane receptor protein tyrosine kinase signaling pathway  (IBA)
tumor necrosis factor-mediated signaling pathway  (ISO)
vascular endothelial growth factor receptor signaling pathway  (ISO)

References

References - curated
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Additional References at PubMed
PMID:7544443   PMID:7673154   PMID:8670418   PMID:8910543   PMID:8939945   PMID:9545257   PMID:9750131   PMID:10518561   PMID:10881171   PMID:11274221   PMID:12477932   PMID:12576483  
PMID:12651850   PMID:12746290   PMID:12900387   PMID:12950452   PMID:12960403   PMID:14739300   PMID:15050747   PMID:15172101   PMID:15322113   PMID:15705590   PMID:15911746   PMID:15967096  
PMID:16199135   PMID:16236484   PMID:17644565   PMID:17684059   PMID:17698736   PMID:17910947   PMID:18667434   PMID:18765415   PMID:18981321   PMID:19086031   PMID:19484266   PMID:19759375  
PMID:19880522   PMID:20180987   PMID:20688918   PMID:21245381   PMID:21640103   PMID:21852560   PMID:22802128   PMID:24718602   PMID:24841674   PMID:24981431   PMID:25349423   PMID:25708150  
PMID:25713079   PMID:28019664   PMID:28916471   PMID:30053369   PMID:31213568   PMID:32391653   PMID:32453021  


Genomics

Comparative Map Data
Ptk2b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21540,360,722 - 40,481,235 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1540,360,723 - 40,481,282 (-)Ensembl
Rnor_6.01542,827,306 - 42,947,796 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1542,827,310 - 42,947,656 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01548,646,476 - 48,766,708 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41545,589,222 - 45,717,866 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11545,604,992 - 45,733,824 (-)NCBI
Celera1540,034,001 - 40,153,993 (-)NCBICelera
Cytogenetic Map15p12NCBI
PTK2B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl827,311,482 - 27,459,391 (+)EnsemblGRCh38hg38GRCh38
GRCh38827,311,478 - 27,459,391 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37827,168,995 - 27,316,908 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36827,224,916 - 27,372,820 (+)NCBINCBI36hg18NCBI36
Build 34827,238,970 - 27,372,820NCBI
Celera826,131,907 - 26,277,021 (+)NCBI
Cytogenetic Map8p21.2NCBI
HuRef825,714,123 - 25,861,970 (+)NCBIHuRef
CHM1_1827,370,923 - 27,518,777 (+)NCBICHM1_1
Ptk2b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391466,390,706 - 66,518,549 (-)NCBIGRCm39mm39
GRCm39 Ensembl1466,390,706 - 66,518,501 (-)Ensembl
GRCm381466,153,257 - 66,281,100 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1466,153,257 - 66,281,052 (-)EnsemblGRCm38mm10GRCm38
MGSCv371466,772,094 - 66,899,889 (-)NCBIGRCm37mm9NCBIm37
MGSCv361465,107,372 - 65,235,162 (-)NCBImm8
Celera1463,901,704 - 64,032,818 (-)NCBICelera
Cytogenetic Map14D1NCBI
cM Map1434.36NCBI
Ptk2b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540349,855,541 - 49,973,225 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540349,856,056 - 49,970,800 (+)NCBIChiLan1.0ChiLan1.0
PTK2B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1823,783,624 - 23,932,472 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl823,869,825 - 23,932,474 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0826,580,855 - 26,729,378 (+)NCBIMhudiblu_PPA_v0panPan3
PTK2B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12530,137,546 - 30,264,221 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2530,138,209 - 30,264,133 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2530,723,893 - 30,850,311 (-)NCBI
ROS_Cfam_1.02530,327,673 - 30,454,390 (-)NCBI
ROS_Cfam_1.0 Ensembl2530,327,667 - 30,454,389 (-)Ensembl
UMICH_Zoey_3.12530,257,967 - 30,384,306 (-)NCBI
UNSW_CanFamBas_1.02530,138,848 - 30,265,191 (-)NCBI
UU_Cfam_GSD_1.02530,305,247 - 30,431,983 (-)NCBI
Ptk2b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049438,260,472 - 8,369,219 (-)NCBI
SpeTri2.0NW_004936675216,970 - 325,670 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTK2B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1411,064,492 - 11,194,194 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11411,063,662 - 11,194,196 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21412,244,257 - 12,375,188 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PTK2B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1825,437,680 - 25,571,594 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl825,437,564 - 25,571,782 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605216,572,610 - 16,706,737 (-)NCBIVero_WHO_p1.0
Ptk2b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475822,065,448 - 22,182,604 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
BE120275  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21540,476,452 - 40,476,626 (+)MAPPERmRatBN7.2
Rnor_6.01542,943,009 - 42,943,182NCBIRnor6.0
Rnor_5.01548,651,092 - 48,651,265UniSTSRnor5.0
RGSC_v3.41545,713,220 - 45,713,393UniSTSRGSC3.4
Celera1540,149,347 - 40,149,520UniSTS
RH 3.4 Map15311.61UniSTS
Cytogenetic Map15p12UniSTS
BE120442  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21540,411,680 - 40,411,830 (+)MAPPERmRatBN7.2
Rnor_6.01542,878,251 - 42,878,400NCBIRnor6.0
Rnor_5.01548,715,589 - 48,715,738UniSTSRnor5.0
RGSC_v3.41545,640,451 - 45,640,600UniSTSRGSC3.4
Celera1540,084,831 - 40,084,980UniSTS
RH 3.4 Map15309.6UniSTS
Cytogenetic Map15p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154028990149308583Rat


Genetic Models
This gene Ptk2b is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1070
Count of miRNA genes:261
Interacting mature miRNAs:312
Transcripts:ENSRNOT00000030007, ENSRNOT00000030036
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 3 30 22 19 22 25 10 9 10
Low 43 27 19 19 8 11 33 25 32 1 8
Below cutoff 16

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_017318 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252143 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252144 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252145 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770773 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770774 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093607 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC112574 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF063890 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC101921 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474023 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D45854 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214346 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000270 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U69109 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000030007   ⟹   ENSRNOP00000031615
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1540,360,723 - 40,481,282 (-)Ensembl
Rnor_6.0 Ensembl1542,827,310 - 42,947,656 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000030036   ⟹   ENSRNOP00000036813
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1540,360,723 - 40,481,282 (-)Ensembl
Rnor_6.0 Ensembl1542,827,846 - 42,898,150 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105571   ⟹   ENSRNOP00000078730
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1540,360,723 - 40,481,282 (-)Ensembl
RefSeq Acc Id: NM_017318   ⟹   NP_059014
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21540,360,732 - 40,481,104 (-)NCBI
Rnor_6.01542,827,310 - 42,947,656 (-)NCBI
Rnor_5.01548,646,476 - 48,766,708 (+)NCBI
RGSC_v3.41545,589,222 - 45,717,866 (-)RGD
Celera1540,034,001 - 40,153,993 (-)RGD
Sequence:
RefSeq Acc Id: XM_006252145   ⟹   XP_006252207
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21540,360,722 - 40,481,235 (-)NCBI
Rnor_6.01542,827,306 - 42,947,796 (-)NCBI
Rnor_5.01548,646,476 - 48,766,708 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008770773   ⟹   XP_008768995
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21540,360,722 - 40,429,442 (-)NCBI
Rnor_6.01542,827,306 - 42,897,560 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770774   ⟹   XP_008768996
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21540,360,722 - 40,423,256 (-)NCBI
Rnor_6.01542,827,306 - 42,894,599 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039093607   ⟹   XP_038949535
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21540,360,722 - 40,481,235 (-)NCBI
RefSeq Acc Id: XM_039093608   ⟹   XP_038949536
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21540,360,722 - 40,414,740 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_059014   ⟸   NM_017318
- UniProtKB: P70600 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006252207   ⟸   XM_006252145
- Peptide Label: isoform X2
- UniProtKB: P70600 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008768995   ⟸   XM_008770773
- Peptide Label: isoform X1
- UniProtKB: P70600 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008768996   ⟸   XM_008770774
- Peptide Label: isoform X1
- UniProtKB: P70600 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000036813   ⟸   ENSRNOT00000030036
RefSeq Acc Id: ENSRNOP00000031615   ⟸   ENSRNOT00000030007
RefSeq Acc Id: XP_038949535   ⟸   XM_039093607
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038949536   ⟸   XM_039093608
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000078730   ⟸   ENSRNOT00000105571
Protein Domains
FERM   Protein kinase

Transcriptome

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

Promoters
RGD ID:13699756
Promoter ID:EPDNEW_R10279
Type:initiation region
Name:Ptk2b_1
Description:protein tyrosine kinase 2 beta
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01542,947,710 - 42,947,770EPDNEW

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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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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)
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)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
15 42842619 42842620 G A snv MNS/Gib (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628758 AgrOrtholog
Ensembl Genes ENSRNOG00000027839 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000031615 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000036813 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000030007 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000030036 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.80.10 UniProtKB/Swiss-Prot
  2.30.29.30 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7937929 IMAGE-MGC_LOAD
InterPro Band_41_domain UniProtKB/Swiss-Prot
  FADK_N UniProtKB/Swiss-Prot
  FAK1/PYK2_FERM_C UniProtKB/Swiss-Prot
  FERM/acyl-CoA-bd_prot_sf UniProtKB/Swiss-Prot
  FERM_2 UniProtKB/Swiss-Prot
  FERM_central UniProtKB/Swiss-Prot
  FERM_domain UniProtKB/Swiss-Prot
  Focal_adhe_kin_target_dom_sf UniProtKB/Swiss-Prot
  Focal_adhesion_kin_target_dom UniProtKB/Swiss-Prot
  Kinase-like_dom_sf UniProtKB/Swiss-Prot
  PH-like_dom_sf UniProtKB/Swiss-Prot
  Prot_kinase_dom UniProtKB/Swiss-Prot
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot
  PTK2B UniProtKB/Swiss-Prot
  Ser-Thr/Tyr_kinase_cat_dom UniProtKB/Swiss-Prot
  Tyr_kinase_AS UniProtKB/Swiss-Prot
  Tyr_kinase_cat_dom UniProtKB/Swiss-Prot
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot
KEGG Report rno:50646 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124628 IMAGE-MGC_LOAD
NCBI Gene 50646 ENTREZGENE
PANTHER PTHR24418:SF94 UniProtKB/Swiss-Prot
Pfam FERM_M UniProtKB/Swiss-Prot
  FERM_N_2 UniProtKB/Swiss-Prot
  Focal_AT UniProtKB/Swiss-Prot
  Pkinase_Tyr UniProtKB/Swiss-Prot
PhenoGen Ptk2b PhenoGen
PRINTS TYRKINASE UniProtKB/Swiss-Prot
PROSITE FERM_3 UniProtKB/Swiss-Prot
  PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot
  PROTEIN_KINASE_TYR UniProtKB/Swiss-Prot
SMART B41 UniProtKB/Swiss-Prot
  TyrKc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47031 UniProtKB/Swiss-Prot
  SSF54236 UniProtKB/Swiss-Prot
  SSF56112 UniProtKB/Swiss-Prot
  SSF68993 UniProtKB/Swiss-Prot
UniProt FAK2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O88489 UniProtKB/Swiss-Prot
  Q3T1H4 UniProtKB/Swiss-Prot
  Q63201 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-20 Ptk2b  protein tyrosine kinase 2 beta  Ptk2b  PTK2B protein tyrosine kinase 2 beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-11-20 Ptk2b  PTK2B protein tyrosine kinase 2 beta  Ptk2b  PTK2 protein tyrosine kinase 2 beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-15 Ptk2b  PTK2 protein tyrosine kinase 2 beta  Ptk2b  protein tyrosine kinase 2 beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Ptk2b  protein tyrosine kinase 2 beta      Symbol and Name status set to approved 1299863 APPROVED
2003-02-27 Ptk2b  protein tyrosine kinase 2 beta      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression selectively expressed in the lung and pulmonary vascular endothelial cells 70597
gene_physical_interaction forms a complex with Src tyrosine kinase in response to thrombin stimulation 729770
gene_process involved in cell motility, cell spreading, migration and morphogenesis processes 70597
gene_process involved in angiogenesis 70597
gene_process kinase activity may be involved in the expression of FAK and Cas proteins 70597
gene_process regulator of pulmonary angiogenesis 70597