Magi1 (membrane associated guanylate kinase, WW and PDZ domain containing 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Magi1 (membrane associated guanylate kinase, WW and PDZ domain containing 1) Rattus norvegicus
Analyze
Symbol: Magi1
Name: membrane associated guanylate kinase, WW and PDZ domain containing 1
RGD ID: 1586025
Description: Predicted to enable alpha-actinin binding activity. Predicted to be involved in positive regulation of cell-cell adhesion and signal transduction. Predicted to be located in several cellular components, including adherens junction; nuclear lumen; and plasma membrane. Predicted to be active in cell-cell junction and cytoplasm. Orthologous to human MAGI1 (membrane associated guanylate kinase, WW and PDZ domain containing 1); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: BAI1-associated protein 1; Baiap1; BAP-1; LOC500261; MAGI-1; membrane associated guanylate kinase 1 b NT-short isoform; membrane-associated guanylate kinase inverted 1; membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
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
mRatBN7.24126,205,667 - 126,811,354 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4126,206,816 - 126,811,691 (-)Ensembl
Rnor_6.04125,684,816 - 126,300,013 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4125,687,307 - 125,958,112 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04190,203,221 - 190,812,582 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44127,975,386 - 128,597,119 (-)NCBIRGSC3.4rn4RGSC3.4
Celera4115,124,711 - 115,720,952 (-)NCBICelera
Cytogenetic Map4q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
7,12-dimethyltetraphene  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt dichloride  (EXP)
coumestrol  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
Deguelin  (ISO)
diclofenac  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
ethanol  (ISO)
folic acid  (ISO)
gemcitabine  (ISO)
genistein  (EXP)
hemin  (ISO)
hydroquinone  (ISO)
irinotecan  (EXP)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
methamphetamine  (ISO)
methapyrilene  (EXP)
methylmercury chloride  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-Nitrosopyrrolidine  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
O-methyleugenol  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
PCB138  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
picoxystrobin  (ISO)
potassium chromate  (ISO)
propiconazole  (ISO)
rotenone  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sulindac sulfide  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zinc sulfate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
adherens junction  (IEA,ISO,ISS)
bicellular tight junction  (IEA)
cell junction  (ISO)
cell periphery  (ISO)
cell projection  (ISO)
cell-cell junction  (IBA,ISO)
cytoplasm  (IBA,IEA,ISO)
membrane  (IEA,ISO)
nucleolus  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (ISO)
plasma membrane  (ISO)

Molecular Function

References

Additional References at PubMed
PMID:9395497   PMID:15458844   PMID:15908431   PMID:16464232   PMID:18303016   PMID:20298433   PMID:21426345   PMID:22166940   PMID:22605569   PMID:29476059   PMID:30860870  


Genomics

Comparative Map Data
Magi1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24126,205,667 - 126,811,354 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4126,206,816 - 126,811,691 (-)Ensembl
Rnor_6.04125,684,816 - 126,300,013 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4125,687,307 - 125,958,112 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04190,203,221 - 190,812,582 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44127,975,386 - 128,597,119 (-)NCBIRGSC3.4rn4RGSC3.4
Celera4115,124,711 - 115,720,952 (-)NCBICelera
Cytogenetic Map4q34NCBI
MAGI1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl365,353,525 - 66,038,834 (-)EnsemblGRCh38hg38GRCh38
GRCh38365,353,526 - 66,038,918 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37365,339,201 - 66,024,593 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36365,314,946 - 65,999,549 (-)NCBINCBI36hg18NCBI36
Build 34365,321,089 - 65,999,265NCBI
Celera365,356,153 - 66,040,780 (-)NCBI
Cytogenetic Map3p14.1NCBI
HuRef365,437,034 - 66,121,819 (-)NCBIHuRef
CHM1_1365,289,925 - 65,975,909 (-)NCBICHM1_1
Magi1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39693,652,434 - 94,260,901 (-)NCBIGRCm39mm39
GRCm39 Ensembl693,652,436 - 94,260,898 (-)Ensembl
GRCm38693,675,453 - 94,283,929 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl693,675,455 - 94,283,917 (-)EnsemblGRCm38mm10GRCm38
MGSCv37693,625,449 - 94,233,898 (-)NCBIGRCm37mm9NCBIm37
MGSCv36693,643,498 - 94,249,367 (-)NCBImm8
Celera695,559,133 - 96,179,163 (-)NCBICelera
Cytogenetic Map6D1NCBI
Magi1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495551755,091 - 655,638 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495551754,699 - 654,398 (+)NCBIChiLan1.0ChiLan1.0
MAGI1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1366,632,730 - 67,303,854 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl366,635,580 - 66,757,358 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0365,257,763 - 65,932,527 (-)NCBIMhudiblu_PPA_v0panPan3
MAGI1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12025,314,597 - 25,952,256 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2025,314,923 - 25,949,921 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2025,239,937 - 25,879,104 (+)NCBI
ROS_Cfam_1.02025,354,604 - 25,993,500 (+)NCBI
UMICH_Zoey_3.12025,051,678 - 25,685,908 (+)NCBI
UNSW_CanFamBas_1.02025,399,375 - 26,040,537 (+)NCBI
UU_Cfam_GSD_1.02025,459,448 - 26,096,907 (+)NCBI
LOC101962705
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118162,642,831 - 162,765,123 (+)NCBI
SpeTri2.0NW_004936637985,706 - 1,154,670 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MAGI1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1346,896,518 - 47,567,518 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11346,896,515 - 47,568,140 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21351,684,581 - 52,291,085 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MAGI1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12226,383,310 - 27,057,081 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2226,384,511 - 26,645,528 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041139,752,144 - 140,429,908 (+)NCBIVero_WHO_p1.0
Magi1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462488846,089 - 686,823 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D4Mgh18  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24126,395,976 - 126,396,065 (+)MAPPERmRatBN7.2
mRatBN7.21862,057,116 - 62,057,171 (+)MAPPERmRatBN7.2
Rnor_6.04125,884,464 - 125,884,552NCBIRnor6.0
Rnor_5.04190,397,443 - 190,397,531UniSTSRnor5.0
RGSC_v3.44128,179,957 - 128,180,046RGDRGSC3.4
RGSC_v3.44128,179,958 - 128,180,046UniSTSRGSC3.4
RGSC_v3.14128,424,798 - 128,424,887RGD
Celera4115,307,251 - 115,307,339UniSTS
RH 3.4 Map4757.7UniSTS
RH 3.4 Map4757.7RGD
RH 2.0 Map4847.3RGD
Cytogenetic Map4q34UniSTS
D4Rat105  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24126,278,101 - 126,278,340 (+)MAPPERmRatBN7.2
Rnor_6.04125,765,814 - 125,766,052NCBIRnor6.0
Rnor_5.04190,278,357 - 190,278,595UniSTSRnor5.0
RGSC_v3.44128,053,666 - 128,053,905RGDRGSC3.4
RGSC_v3.44128,053,667 - 128,053,905UniSTSRGSC3.4
RGSC_v3.14128,298,477 - 128,298,965RGD
Celera4115,189,805 - 115,190,043UniSTS
SHRSP x BN Map455.49RGD
SHRSP x BN Map455.49UniSTS
Cytogenetic Map4q34UniSTS
D6Mit178  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24126,752,841 - 126,752,943 (+)MAPPERmRatBN7.2
Rnor_6.04126,242,010 - 126,242,111NCBIRnor6.0
Rnor_5.04190,754,793 - 190,754,894UniSTSRnor5.0
RGSC_v3.44128,538,682 - 128,538,783UniSTSRGSC3.4
Celera4115,663,315 - 115,663,416UniSTS
Cytogenetic Map4q34UniSTS
BB468191  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24126,445,402 - 126,445,503 (+)MAPPERmRatBN7.2
Rnor_6.04125,934,228 - 125,934,328NCBIRnor6.0
Rnor_5.04190,447,002 - 190,447,102UniSTSRnor5.0
RGSC_v3.44128,230,550 - 128,230,650UniSTSRGSC3.4
Celera4115,356,501 - 115,356,601UniSTS
Cytogenetic Map4q34UniSTS
RH128955  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.04190,527,965 - 190,528,140NCBIRnor5.0
Rnor_5.01056,349,164 - 56,349,340NCBIRnor5.0
RGSC_v3.41056,840,530 - 56,840,705UniSTSRGSC3.4
RGSC_v3.44128,311,608 - 128,311,782UniSTSRGSC3.4
Celera1053,871,176 - 53,871,351UniSTS
Celera4115,437,302 - 115,437,476UniSTS
RH 3.4 Map4757.8UniSTS
Cytogenetic Map10q24UniSTS
Cytogenetic Map4q34UniSTS
RH132066  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24126,313,294 - 126,313,508 (+)MAPPERmRatBN7.2
Rnor_6.04125,801,128 - 125,801,341NCBIRnor6.0
Rnor_5.04190,313,931 - 190,314,144UniSTSRnor5.0
RGSC_v3.44128,095,368 - 128,095,581UniSTSRGSC3.4
Celera4115,224,960 - 115,225,173UniSTS
RH 3.4 Map4757.6UniSTS
Cytogenetic Map4q34UniSTS
BI278044  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24126,584,909 - 126,585,082 (+)MAPPERmRatBN7.2
Rnor_6.04126,073,752 - 126,073,924NCBIRnor6.0
Rnor_5.04190,586,535 - 190,586,707UniSTSRnor5.0
RGSC_v3.44128,370,280 - 128,370,452UniSTSRGSC3.4
Celera4115,495,876 - 115,496,048UniSTS
RH 3.4 Map4760.0UniSTS
Cytogenetic Map4q34UniSTS
BF395930  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24126,327,764 - 126,327,897 (+)MAPPERmRatBN7.2
Rnor_6.04125,815,328 - 125,815,460NCBIRnor6.0
Rnor_5.04190,328,131 - 190,328,263UniSTSRnor5.0
RGSC_v3.44128,111,284 - 128,111,416UniSTSRGSC3.4
Celera4115,239,227 - 115,239,359UniSTS
RH 3.4 Map4757.6UniSTS
Cytogenetic Map4q34UniSTS
BE112829  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24126,758,147 - 126,758,347 (+)MAPPERmRatBN7.2
Rnor_6.04126,247,123 - 126,247,322NCBIRnor6.0
Rnor_5.04190,759,906 - 190,760,105UniSTSRnor5.0
RGSC_v3.44128,543,987 - 128,544,186UniSTSRGSC3.4
Celera4115,668,356 - 115,668,555UniSTS
RH 3.4 Map4761.3UniSTS
Cytogenetic Map4q34UniSTS
AU048387  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24126,458,110 - 126,458,377 (+)MAPPERmRatBN7.2
Rnor_6.04125,946,874 - 125,947,140NCBIRnor6.0
Rnor_5.04190,459,731 - 190,459,997UniSTSRnor5.0
RGSC_v3.44128,243,320 - 128,243,586UniSTSRGSC3.4
Celera4115,369,232 - 115,369,498UniSTS
Cytogenetic Map4q34UniSTS
BG380331  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24126,728,933 - 126,729,164 (+)MAPPERmRatBN7.2
Rnor_6.04126,217,770 - 126,218,000NCBIRnor6.0
Rnor_5.04190,730,553 - 190,730,783UniSTSRnor5.0
RGSC_v3.44128,514,774 - 128,515,004UniSTSRGSC3.4
Celera4115,639,451 - 115,639,681UniSTS
RH 3.4 Map4763.1UniSTS
Cytogenetic Map4q34UniSTS
AW252028  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.04190,210,234 - 190,211,492NCBIRnor5.0
RGSC_v3.44127,978,154 - 127,979,411UniSTSRGSC3.4
Celera4115,127,480 - 115,128,737UniSTS
RH 3.4 Map4749.3UniSTS
Cytogenetic Map4q34UniSTS
AU048577  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24126,444,892 - 126,445,000 (+)MAPPERmRatBN7.2
Rnor_6.04125,933,718 - 125,933,825NCBIRnor6.0
Rnor_5.04190,446,492 - 190,446,599UniSTSRnor5.0
RGSC_v3.44128,230,040 - 128,230,147UniSTSRGSC3.4
Celera4115,355,991 - 115,356,098UniSTS
Cytogenetic Map4q34UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
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
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)462277855128289560Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)470362013132642728Rat
631646Stl4Serum triglyceride level QTL 46.50.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)473169846132642728Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)482798864152731274Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
634334Xhs3X-ray hypersensitivity QTL 310intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)484728680129854654Rat
1582232Gluco25Glucose level QTL 253.60.0023blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)485253748148090731Rat
12798523Anxrr56Anxiety related response QTL 562.830.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)485253748150276390Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
61476Aia3Adjuvant induced arthritis QTL 33.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)486730991131730991Rat
1578662Bss15Bone structure and strength QTL 1519.6femur width (VT:1000666)femoral neck width (CMO:0001695)487327165132327165Rat
1578670Bss14Bone structure and strength QTL 1416.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)487327165132327165Rat
1578655Bmd11Bone mineral density QTL 1111femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)490850165135850165Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
631689Scl4Serum cholesterol level QTL 41.90.008blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)495174120140174120Rat
61434Cia3Collagen induced arthritis QTL 34.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4103194656148194656Rat
2302049Pia32Pristane induced arthritis QTL 325.10.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)4105789505150789505Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106649412151649412Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4106805662151805662Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109827074154827074Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109827074154827074Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4114627026159627026Rat
1300116Hrtrt5Heart rate QTL 53.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)4116179486151161268Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
12798527Anxrr58Anxiety related response QTL 584.110.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4119463257147278687Rat
70201Gcr1Gastric cancer resistance QTL 12.7stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)4120260281147278687Rat
2293840Kiddil9Kidney dilation QTL 92.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)4120926564148090731Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:62
Count of miRNA genes:30
Interacting mature miRNAs:31
Transcripts:ENSRNOT00000037848, ENSRNOT00000071315
Prediction methods: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 30 20 12 2 12 74 29 37 11
Low 3 13 37 29 17 29 8 11 6 4 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001030045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236927 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236928 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236929 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763133 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592832 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108173 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108174 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108175 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108176 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108178 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108179 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108181 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108182 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108183 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108184 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108186 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108187 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108188 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108189 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108191 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108192 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108193 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108194 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108195 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AY598951 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY598952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212459 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000148 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000037848   ⟹   ENSRNOP00000033083
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4126,207,991 - 126,811,691 (-)Ensembl
Rnor_6.0 Ensembl4125,690,234 - 125,808,281 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000071315   ⟹   ENSRNOP00000065881
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4126,211,598 - 126,469,278 (-)Ensembl
Rnor_6.0 Ensembl4125,690,237 - 125,958,112 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000083271   ⟹   ENSRNOP00000071015
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4126,208,103 - 126,342,711 (-)Ensembl
Rnor_6.0 Ensembl4125,687,307 - 125,929,002 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096892   ⟹   ENSRNOP00000090018
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4126,206,816 - 126,811,691 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108766   ⟹   ENSRNOP00000077345
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4126,206,816 - 126,811,691 (-)Ensembl
RefSeq Acc Id: NM_001030045   ⟹   NP_001025216
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,213,009 - 126,810,759 (-)NCBI
Rnor_6.04125,690,234 - 126,299,410 (-)NCBI
Rnor_5.04190,203,221 - 190,812,582 (-)NCBI
RGSC_v3.44127,975,386 - 128,597,119 (-)RGD
Celera4115,124,711 - 115,720,952 (-)RGD
Sequence:
RefSeq Acc Id: XM_006236927   ⟹   XP_006236989
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,350 (-)NCBI
Rnor_6.04125,684,816 - 126,300,013 (-)NCBI
Rnor_5.04190,203,221 - 190,812,582 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006236928   ⟹   XP_006236990
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,349 (-)NCBI
Rnor_6.04125,684,816 - 126,300,013 (-)NCBI
Rnor_5.04190,203,221 - 190,812,582 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006236929   ⟹   XP_006236991
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,350 (-)NCBI
Rnor_6.04125,684,816 - 126,300,013 (-)NCBI
Rnor_5.04190,203,221 - 190,812,582 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763133   ⟹   XP_008761355
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,350 (-)NCBI
Rnor_6.04125,684,816 - 126,300,013 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592832   ⟹   XP_017448321
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,350 (-)NCBI
Rnor_6.04125,684,816 - 126,300,013 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039108173   ⟹   XP_038964101
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,350 (-)NCBI
RefSeq Acc Id: XM_039108174   ⟹   XP_038964102
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,350 (-)NCBI
RefSeq Acc Id: XM_039108175   ⟹   XP_038964103
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,351 (-)NCBI
RefSeq Acc Id: XM_039108176   ⟹   XP_038964104
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,351 (-)NCBI
RefSeq Acc Id: XM_039108177   ⟹   XP_038964105
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,350 (-)NCBI
RefSeq Acc Id: XM_039108178   ⟹   XP_038964106
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,350 (-)NCBI
RefSeq Acc Id: XM_039108179   ⟹   XP_038964107
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,349 (-)NCBI
RefSeq Acc Id: XM_039108181   ⟹   XP_038964109
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,350 (-)NCBI
RefSeq Acc Id: XM_039108182   ⟹   XP_038964110
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,353 (-)NCBI
RefSeq Acc Id: XM_039108183   ⟹   XP_038964111
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,352 (-)NCBI
RefSeq Acc Id: XM_039108184   ⟹   XP_038964112
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,352 (-)NCBI
RefSeq Acc Id: XM_039108185   ⟹   XP_038964113
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,439,515 (-)NCBI
RefSeq Acc Id: XM_039108186   ⟹   XP_038964114
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,211,115 - 126,811,353 (-)NCBI
RefSeq Acc Id: XM_039108187   ⟹   XP_038964115
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,211,115 - 126,811,352 (-)NCBI
RefSeq Acc Id: XM_039108188   ⟹   XP_038964116
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,440,399 (-)NCBI
RefSeq Acc Id: XM_039108189   ⟹   XP_038964117
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,211,115 - 126,811,352 (-)NCBI
RefSeq Acc Id: XM_039108191   ⟹   XP_038964119
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,440,042 (-)NCBI
RefSeq Acc Id: XM_039108192   ⟹   XP_038964120
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,208,735 - 126,811,354 (-)NCBI
RefSeq Acc Id: XM_039108193   ⟹   XP_038964121
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,205,667 - 126,811,350 (-)NCBI
RefSeq Acc Id: XM_039108194   ⟹   XP_038964122
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,208,735 - 126,811,352 (-)NCBI
RefSeq Acc Id: XM_039108195   ⟹   XP_038964123
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24126,208,735 - 126,811,352 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001025216 (Get FASTA)   NCBI Sequence Viewer  
  XP_006236989 (Get FASTA)   NCBI Sequence Viewer  
  XP_006236990 (Get FASTA)   NCBI Sequence Viewer  
  XP_006236991 (Get FASTA)   NCBI Sequence Viewer  
  XP_008761355 (Get FASTA)   NCBI Sequence Viewer  
  XP_017448321 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964101 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964102 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964103 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964104 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964105 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964106 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964107 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964109 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964110 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964111 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964112 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964113 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964114 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964115 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964116 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964117 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964119 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964120 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964121 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964122 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964123 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT99088 (Get FASTA)   NCBI Sequence Viewer  
  AAT99089 (Get FASTA)   NCBI Sequence Viewer  
  Q4L1J4 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001025216   ⟸   NM_001030045
- UniProtKB: Q4L1J4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006236991   ⟸   XM_006236929
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_006236990   ⟸   XM_006236928
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_006236989   ⟸   XM_006236927
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008761355   ⟸   XM_008763133
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_017448321   ⟸   XM_017592832
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: ENSRNOP00000065881   ⟸   ENSRNOT00000071315
RefSeq Acc Id: ENSRNOP00000071015   ⟸   ENSRNOT00000083271
RefSeq Acc Id: ENSRNOP00000033083   ⟸   ENSRNOT00000037848
RefSeq Acc Id: XP_038964110   ⟸   XM_039108182
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038964112   ⟸   XM_039108184
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038964111   ⟸   XM_039108183
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038964104   ⟸   XM_039108176
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038964103   ⟸   XM_039108175
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038964121   ⟸   XM_039108193
- Peptide Label: isoform X22
RefSeq Acc Id: XP_038964105   ⟸   XM_039108177
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038964106   ⟸   XM_039108178
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038964109   ⟸   XM_039108181
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038964102   ⟸   XM_039108174
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038964101   ⟸   XM_039108173
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038964107   ⟸   XM_039108179
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038964116   ⟸   XM_039108188
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038964119   ⟸   XM_039108191
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038964113   ⟸   XM_039108185
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038964120   ⟸   XM_039108192
- Peptide Label: isoform X21
RefSeq Acc Id: XP_038964123   ⟸   XM_039108195
- Peptide Label: isoform X24
RefSeq Acc Id: XP_038964122   ⟸   XM_039108194
- Peptide Label: isoform X23
RefSeq Acc Id: XP_038964114   ⟸   XM_039108186
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038964117   ⟸   XM_039108189
- Peptide Label: isoform X20
RefSeq Acc Id: XP_038964115   ⟸   XM_039108187
- Peptide Label: isoform X19
RefSeq Acc Id: ENSRNOP00000090018   ⟸   ENSRNOT00000096892
RefSeq Acc Id: ENSRNOP00000077345   ⟸   ENSRNOT00000108766
Protein Domains
Guanylate kinase-like   PDZ   WW

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)
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
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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
PVG/Seac (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
SBH/Ygl (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: 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)
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: 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)
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/OlalpcvMcwi (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
SHRSP/A3NCrl (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
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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
SS/JrHsdMcwi (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)
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)
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/RijCrl (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: 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)
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
WKY/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
WKY/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
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)
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
WN/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
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 126208972 126208973 C T snv HXB10/IpcvMcwi (2019)
4 126320749 126320750 C G snv LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), SS/JrHsdMcwi (2019), LH/MavRrrcAek (2020), SR/JrHsd (2020)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 125688120 125688121 C T snv HXB10/IpcvMcwi (2019)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1586025 AgrOrtholog
Ensembl Genes ENSRNOG00000022060 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000033083 UniProtKB/TrEMBL
  ENSRNOP00000065881 UniProtKB/TrEMBL
  ENSRNOP00000071015 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037848 UniProtKB/TrEMBL
  ENSRNOT00000071315 UniProtKB/TrEMBL
  ENSRNOT00000083271 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro GK/Ca_channel_bsu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Guanylate_kin-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Guanylate_kinase_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MAGI1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WW_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WW_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:500261 UniProtKB/Swiss-Prot
NCBI Gene 500261 ENTREZGENE
PANTHER PTHR10316:SF12 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Guanylate_kin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00397 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Magi1 PhenoGen
PROSITE GUANYLATE_KINASE_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GUANYLATE_KINASE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WW_DOMAIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WW_DOMAIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART GuKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00456 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50156 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF51045 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JZE4_RAT UniProtKB/TrEMBL
  F1M7H7_RAT UniProtKB/TrEMBL
  M0R8T1_RAT UniProtKB/TrEMBL
  MAGI1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q4L1J5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Magi1  membrane associated guanylate kinase, WW and PDZ domain containing 1  LOC500261  membrane associated guanylate kinase 1 b NT-short isoform  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC500261  membrane associated guanylate kinase 1 b NT-short isoform      Symbol and Name status set to provisional 70820 PROVISIONAL