Foxp1 (forkhead box P1) - Rat Genome Database

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Gene: Foxp1 (forkhead box P1) Rattus norvegicus
Analyze
Symbol: Foxp1
Name: forkhead box P1
RGD ID: 1308669
Description: Enables transcription cis-regulatory region binding activity. Involved in several processes, including cellular response to ionomycin; negative regulation of cell growth involved in cardiac muscle cell development; and positive regulation of hydrogen peroxide-induced cell death. Located in cytoplasm and nucleus. Biomarker of hepatocellular carcinoma; lung adenocarcinoma; and trichostrongyloidiasis. Human ortholog(s) of this gene implicated in several diseases, including Barrett's esophagus; congenital heart disease; esophagus adenocarcinoma; intellectual disability-severe speech delay-mild dysmorphism syndrome; and peritonitis. Orthologous to human FOXP1 (forkhead box P1); INTERACTS WITH 2,2',5,5'-tetrachlorobiphenyl; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: forkhead box protein P1; LOC297480; MGC116362
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
mRatBN7.24131,559,599 - 132,155,092 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4131,564,756 - 132,112,258 (-)Ensembl
Rnor_6.04131,362,178 - 131,963,466 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4131,366,744 - 131,694,755 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04195,854,029 - 196,362,864 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44133,773,373 - 134,007,018 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14134,017,481 - 134,251,846 (-)NCBI
Celera4120,424,629 - 120,655,076 (-)NCBICelera
Cytogenetic Map4q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(-)-demecolcine  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (ISO)
1,2-dichloroethane  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-hydroxynon-2-enal  (ISO)
4-vinylcyclohexene dioxide  (ISO)
acrolein  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (EXP,ISO)
alpha-pinene  (ISO)
amphetamine  (EXP)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
Benzo[k]fluoranthene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
carbon nanotube  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
cocaine  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (EXP,ISO)
D-glucose  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (ISO)
disodium selenite  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
gentamycin  (EXP)
glucose  (ISO)
hydralazine  (ISO)
indometacin  (ISO)
ionomycin  (EXP)
leflunomide  (ISO)
menadione  (ISO)
methapyrilene  (EXP)
methoxychlor  (ISO)
methylmercury chloride  (ISO)
morphine  (ISO)
nicotine  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
PCB138  (EXP,ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
rifampicin  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sirolimus  (ISO)
sodium arsenate  (ISO)
Stanolone benzoate  (EXP)
succimer  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
triclosan  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)
wortmannin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cardiac muscle cell differentiation  (ISO)
cellular response to DNA damage stimulus  (ISO)
cellular response to ionomycin  (IDA)
cellular response to tumor necrosis factor  (IEP)
circulatory system development  (ISO)
endothelial cell activation  (ISO)
forebrain development  (IEP)
heart development  (ISO)
immunoglobulin V(D)J recombination  (ISO)
in utero embryonic development  (ISO)
innate vocalization behavior  (ISO)
lung development  (ISO)
lung secretory cell differentiation  (ISO)
macrophage activation  (ISO)
monocyte activation  (ISO)
motor neuron axon guidance  (ISO)
negative regulation of androgen receptor signaling pathway  (ISO)
negative regulation of B cell apoptotic process  (ISO)
negative regulation of cell growth involved in cardiac muscle cell development  (IMP)
negative regulation of gene expression  (ISO)
negative regulation of lung goblet cell differentiation  (ISO)
negative regulation of transcription by RNA polymerase II  (IBA,IMP,ISO)
negative regulation of transcription, DNA-templated  (ISO,ISS)
osteoclast development  (ISO)
osteoclast differentiation  (ISO)
positive regulation of B cell receptor signaling pathway  (ISO)
positive regulation of endothelial cell migration  (ISO)
positive regulation of epithelial cell proliferation  (ISO)
positive regulation of hydrogen peroxide-induced cell death  (IMP)
positive regulation of immunoglobulin production  (ISO)
positive regulation of interleukin-21 production  (ISO)
positive regulation of mesenchymal cell proliferation  (ISO)
positive regulation of smooth muscle cell proliferation  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of transcription, DNA-templated  (ISO)
pre-B cell differentiation  (ISO)
regulation of action potential  (ISO)
regulation of cardiac muscle cell proliferation  (ISO)
regulation of chemokine (C-X-C motif) ligand 2 production  (ISO)
regulation of defense response to bacterium  (ISO)
regulation of endothelial tube morphogenesis  (ISO)
regulation of gene expression  (ISO)
regulation of inflammatory response  (ISO)
regulation of interleukin-1 beta production  (ISO)
regulation of interleukin-12 production  (ISO)
regulation of lung goblet cell differentiation  (ISO)
regulation of macrophage colony-stimulating factor production  (ISO)
regulation of monocyte differentiation  (ISO)
regulation of transcription by RNA polymerase II  (IBA)
regulation of tumor necrosis factor production  (ISO)
response to lipopolysaccharide  (ISO)
response to testosterone  (IEP)
sarcomere organization  (ISO)
skeletal muscle tissue development  (ISO)
smooth muscle tissue development  (ISO)
striatum development  (IEP)
T follicular helper cell differentiation  (ISO)
ventral spinal cord development  (ISO)

Cellular Component
cytoplasm  (IDA)
nucleoplasm  (ISO)
nucleus  (IBA,IDA,ISO,ISS)

References

References - curated
1. Ahmed HH, etal., Toxicol Mech Methods. 2014 Sep 4:1-10.
2. Arai A, etal., Brain Res. 2012 Aug 27;1470:89-97. doi: 10.1016/j.brainres.2012.06.009. Epub 2012 Jul 1.
3. Athanasiadou S, etal., PLoS One. 2011;6(6):e20771. doi: 10.1371/journal.pone.0020771. Epub 2011 Jun 16.
4. Bai S and Kerppola TK, Mol Cell Biol. 2011 Jul;31(14):3068-80. doi: 10.1128/MCB.00925-10. Epub 2011 May 23.
5. Becker J, etal., Cancer Med. 2015 Nov;4(11):1700-4. doi: 10.1002/cam4.500. Epub 2015 Aug 15.
6. Bowers JM, etal., Endocrinology. 2014 Dec;155(12):4881-94. doi: 10.1210/en.2014-1486. Epub 2014 Sep 23.
7. Chang SW, etal., Hum Mutat. 2013 Sep;34(9):1226-30. doi: 10.1002/humu.22366. Epub 2013 Jul 11.
8. Desplats PA, etal., J Neurochem. 2006 Feb;96(3):743-57. Epub 2006 Jan 9.
9. Gambetta K, etal., Am J Physiol Heart Circ Physiol. 2008 May;294(5):H2268-75. doi: 10.1152/ajpheart.91494.2007. Epub 2008 Mar 14.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Hannenhalli S, etal., Circulation. 2006 Sep 19;114(12):1269-76. Epub 2006 Sep 4.
12. Ingason A, etal., Transl Psychiatry. 2015 Oct 13;5:e656. doi: 10.1038/tp.2015.151.
13. MGD data from the GO Consortium
14. OMIM Disease Annotation Pipeline
15. Palles C, etal., Gastroenterology. 2015 Feb;148(2):367-78. doi: 10.1053/j.gastro.2014.10.041. Epub 2014 Nov 5.
16. RGD automated data pipeline
17. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. RGD automated import pipeline for gene-chemical interactions
19. Shi C, etal., Blood. 2008 Dec 1;112(12):4699-711. doi: 10.1182/blood-2008-01-137018. Epub 2008 Sep 17.
20. Shimizu K, etal., Cancer Lett. 2006 May 18;236(2):186-90. Epub 2005 Jul 14.
21. Tajiri N, etal., CNS Neurosci Ther. 2016 Apr;22(4):306-15. doi: 10.1111/cns.12501. Epub 2016 Feb 4.
22. Takahashi K, etal., J Neurosci Res. 2003 Jul 1;73(1):61-72.
23. Takahashi K, etal., J Neurosci Res. 2008 Nov 1;86(14):3106-16. doi: 10.1002/jnr.21770.
24. Yang Y, etal., Circ Res. 2015 Oct 23;117(10):891-904. doi: 10.1161/CIRCRESAHA.115.306624. Epub 2015 Sep 2.
Additional References at PubMed
PMID:11358962   PMID:12477932   PMID:14701752   PMID:15286807   PMID:15342473   PMID:16819554   PMID:17428829   PMID:18347093   PMID:18640093   PMID:19797899   PMID:20457810   PMID:20711475  
PMID:20713518   PMID:20950788   PMID:22675208   PMID:23610558   PMID:24023716   PMID:24859450   PMID:25027557   PMID:25267198   PMID:25609649   PMID:26494785   PMID:26647308   PMID:28218735  
PMID:28408745   PMID:30111844   PMID:30170733   PMID:30302539  


Genomics

Comparative Map Data
Foxp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24131,559,599 - 132,155,092 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4131,564,756 - 132,112,258 (-)Ensembl
Rnor_6.04131,362,178 - 131,963,466 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4131,366,744 - 131,694,755 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04195,854,029 - 196,362,864 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44133,773,373 - 134,007,018 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14134,017,481 - 134,251,846 (-)NCBI
Celera4120,424,629 - 120,655,076 (-)NCBICelera
Cytogenetic Map4q34NCBI
FOXP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl370,954,708 - 71,583,989 (-)EnsemblGRCh38hg38GRCh38
GRCh38370,954,708 - 71,583,978 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37371,003,859 - 71,633,129 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36371,087,426 - 71,715,830 (-)NCBINCBI36hg18NCBI36
Build 34371,087,426 - 71,715,830NCBI
Celera370,931,660 - 71,563,756 (-)NCBI
Cytogenetic Map3p13NCBI
HuRef371,002,782 - 71,635,428 (-)NCBIHuRef
CHM1_1370,955,452 - 71,584,748 (-)NCBICHM1_1
Foxp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39698,902,303 - 99,510,587 (-)NCBIGRCm39mm39
GRCm39 Ensembl698,902,299 - 99,499,682 (-)Ensembl
GRCm38698,925,342 - 99,522,746 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl698,925,338 - 99,522,721 (-)EnsemblGRCm38mm10GRCm38
MGSCv37698,880,084 - 99,113,012 (-)NCBIGRCm37mm9NCBIm37
MGSCv36698,895,553 - 99,128,481 (-)NCBImm8
Celera6100,793,018 - 101,026,348 (-)NCBICelera
Cytogenetic Map6D3NCBI
Foxp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495542116,595,445 - 17,075,923 (+)NCBIChiLan1.0ChiLan1.0
FOXP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1372,255,364 - 72,878,625 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl372,258,456 - 72,498,173 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0370,893,933 - 71,523,892 (-)NCBIMhudiblu_PPA_v0panPan3
FOXP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12020,438,631 - 21,020,516 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2020,788,433 - 21,016,397 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2020,414,104 - 20,995,815 (+)NCBI
ROS_Cfam_1.02020,472,109 - 21,055,068 (+)NCBI
UMICH_Zoey_3.12020,158,227 - 20,741,182 (+)NCBI
UNSW_CanFamBas_1.02020,506,753 - 21,089,395 (+)NCBI
UU_Cfam_GSD_1.02020,573,511 - 21,158,112 (+)NCBI
Foxp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049422,631,781 - 3,146,462 (-)NCBI
SpeTri2.0NW_0049366032,631,781 - 3,146,104 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FOXP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1352,347,849 - 52,974,261 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11352,346,844 - 52,974,358 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21357,861,735 - 58,095,301 (-)NCBISscrofa10.2Sscrofa10.2susScr3
FOXP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12231,907,941 - 32,538,294 (-)NCBI
Vero_WHO_p1.0NW_023666041134,241,728 - 134,871,978 (+)NCBI
Foxp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247735,543,529 - 6,076,522 (-)NCBI

Position Markers
D4Mit18  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24131,730,729 - 131,730,924 (+)MAPPERmRatBN7.2
Rnor_6.04131,532,260 - 131,532,452NCBIRnor6.0
Rnor_5.04196,023,935 - 196,024,127UniSTSRnor5.0
RGSC_v3.44133,939,399 - 133,939,591UniSTSRGSC3.4
RGSC_v3.44133,939,398 - 133,939,591RGDRGSC3.4
RGSC_v3.14134,184,239 - 134,184,432RGD
Celera4120,589,296 - 120,589,480UniSTS
Cytogenetic Map4q34UniSTS
D4Wox17  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24131,730,755 - 131,730,914 (+)MAPPERmRatBN7.2
Rnor_6.04131,532,286 - 131,532,442NCBIRnor6.0
Rnor_5.04196,023,961 - 196,024,117UniSTSRnor5.0
RGSC_v3.44133,939,425 - 133,939,581UniSTSRGSC3.4
RGSC_v3.44133,939,424 - 133,939,581RGDRGSC3.4
Celera4120,589,322 - 120,589,470UniSTS
Cytogenetic Map4q34UniSTS
D4Arb16  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24131,730,738 - 131,730,991 (+)MAPPERmRatBN7.2
Rnor_6.04131,532,269 - 131,532,519NCBIRnor6.0
Rnor_5.04196,023,944 - 196,024,194UniSTSRnor5.0
RGSC_v3.44133,939,407 - 133,939,659RGDRGSC3.4
RGSC_v3.44133,939,408 - 133,939,658UniSTSRGSC3.4
Celera4120,589,305 - 120,589,547UniSTS
RH 3.4 Map4801.3RGD
RH 3.4 Map4801.3UniSTS
RH 2.0 Map4863.3RGD
SHRSP x BN Map458.74RGD
FHH x ACI Map475.85RGD
Cytogenetic Map4q34UniSTS
RH138314  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24131,596,485 - 131,596,608 (+)MAPPERmRatBN7.2
Rnor_6.04131,397,864 - 131,397,986NCBIRnor6.0
Rnor_5.04195,889,692 - 195,889,814UniSTSRnor5.0
RGSC_v3.44133,804,406 - 133,804,528UniSTSRGSC3.4
Celera4120,455,616 - 120,455,738UniSTS
RH 3.4 Map4801.2UniSTS
Cytogenetic Map4q34UniSTS
RH140136  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24131,775,302 - 131,775,486 (+)MAPPERmRatBN7.2
Rnor_6.04131,576,852 - 131,577,035NCBIRnor6.0
Rnor_5.04196,068,479 - 196,068,662UniSTSRnor5.0
RGSC_v3.44133,985,566 - 133,985,749UniSTSRGSC3.4
Celera4120,633,629 - 120,633,812UniSTS
RH 3.4 Map4801.4UniSTS
Cytogenetic Map4q34UniSTS
RH142550  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24131,766,560 - 131,766,814 (+)MAPPERmRatBN7.2
Rnor_6.04131,567,986 - 131,568,239NCBIRnor6.0
Rnor_5.04196,059,613 - 196,059,866UniSTSRnor5.0
RGSC_v3.44133,976,160 - 133,976,413UniSTSRGSC3.4
Celera4120,624,916 - 120,625,169UniSTS
Cytogenetic Map4q34UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293840Kiddil9Kidney dilation QTL 92.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)4120926564148090731Rat
61434Cia3Collagen induced arthritis QTL 34.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4103194656148194656Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)482798864152731274Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
70201Gcr1Gastric cancer resistance QTL 12.7stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)4120260281147278687Rat
1578655Bmd11Bone mineral density QTL 1111femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)490850165135850165Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
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
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
61476Aia3Adjuvant induced arthritis QTL 33.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)486730991131730991Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106649412151649412Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
631646Stl4Serum triglyceride level QTL 46.50.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)473169846132642728Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
631689Scl4Serum cholesterol level QTL 41.90.008blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)495174120140174120Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
1582232Gluco25Glucose level QTL 253.60.0023blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)485253748148090731Rat
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
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
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
1300116Hrtrt5Heart rate QTL 53.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)4116179486151161268Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
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
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109827074154827074Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)470362013132642728Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4106805662151805662Rat
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
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
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109827074154827074Rat
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
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
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

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:79
Count of miRNA genes:67
Interacting mature miRNAs:75
Transcripts:ENSRNOT00000013271
Prediction methods:Microtar, 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 28 23 7 19 7 1 1 70 25 39 11 1
Low 15 34 34 34 7 10 4 10 2 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001034131 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236955 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763148 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763149 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763150 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763152 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763153 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592559 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592560 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592561 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592562 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592563 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592564 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107378 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107379 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107380 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107381 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107382 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107383 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107384 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107385 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107386 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107387 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107388 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107389 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC100267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230225 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233115 (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: ENSRNOT00000013271   ⟹   ENSRNOP00000013271
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4131,564,756 - 132,112,258 (-)Ensembl
Rnor_6.0 Ensembl4131,366,744 - 131,694,755 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100443   ⟹   ENSRNOP00000095477
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4131,564,756 - 132,112,258 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103186   ⟹   ENSRNOP00000082807
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4131,564,756 - 131,663,897 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108862   ⟹   ENSRNOP00000088588
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4131,564,756 - 132,112,258 (-)Ensembl
RefSeq Acc Id: NM_001034131   ⟹   NP_001029303
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,565,491 - 131,796,755 (-)NCBI
Rnor_6.04131,366,878 - 131,598,304 (-)NCBI
Rnor_5.04195,854,029 - 196,362,864 (-)NCBI
RGSC_v3.44133,773,373 - 134,007,018 (-)RGD
Celera4120,424,629 - 120,655,076 (-)RGD
Sequence:
RefSeq Acc Id: XM_006236954   ⟹   XP_006237016
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 131,663,228 (-)NCBI
Rnor_6.04131,362,178 - 131,464,564 (-)NCBI
Rnor_5.04195,854,029 - 196,362,864 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006236955   ⟹   XP_006237017
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 131,664,286 (-)NCBI
Rnor_6.04131,362,178 - 131,465,599 (-)NCBI
Rnor_5.04195,854,029 - 196,362,864 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006236956   ⟹   XP_006237018
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 131,663,205 (-)NCBI
Rnor_6.04131,362,178 - 131,464,523 (-)NCBI
Rnor_5.04195,854,029 - 196,362,864 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763149   ⟹   XP_008761371
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 132,155,092 (-)NCBI
Rnor_6.04131,362,178 - 131,963,465 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592560   ⟹   XP_017448049
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 132,155,092 (-)NCBI
Rnor_6.04131,362,178 - 131,963,466 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592561   ⟹   XP_017448050
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 132,155,092 (-)NCBI
Rnor_6.04131,362,178 - 131,963,466 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592562   ⟹   XP_017448051
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 131,730,438 (-)NCBI
Rnor_6.04131,362,178 - 131,532,029 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039107377   ⟹   XP_038963305
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 132,155,092 (-)NCBI
RefSeq Acc Id: XM_039107378   ⟹   XP_038963306
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 132,155,092 (-)NCBI
RefSeq Acc Id: XM_039107379   ⟹   XP_038963307
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 132,154,388 (-)NCBI
RefSeq Acc Id: XM_039107380   ⟹   XP_038963308
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 132,113,580 (-)NCBI
RefSeq Acc Id: XM_039107381   ⟹   XP_038963309
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 131,899,397 (-)NCBI
RefSeq Acc Id: XM_039107382   ⟹   XP_038963310
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 131,808,272 (-)NCBI
RefSeq Acc Id: XM_039107383   ⟹   XP_038963311
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 132,155,092 (-)NCBI
RefSeq Acc Id: XM_039107384   ⟹   XP_038963312
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 132,155,092 (-)NCBI
RefSeq Acc Id: XM_039107385   ⟹   XP_038963313
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 132,155,092 (-)NCBI
RefSeq Acc Id: XM_039107386   ⟹   XP_038963314
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 132,155,092 (-)NCBI
RefSeq Acc Id: XM_039107387   ⟹   XP_038963315
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 131,782,489 (-)NCBI
RefSeq Acc Id: XM_039107388   ⟹   XP_038963316
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 131,782,488 (-)NCBI
RefSeq Acc Id: XM_039107389   ⟹   XP_038963317
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24131,559,599 - 132,155,092 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001029303   ⟸   NM_001034131
- UniProtKB: Q498D1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006237017   ⟸   XM_006236955
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_006237018   ⟸   XM_006236956
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_006237016   ⟸   XM_006236954
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_008761371   ⟸   XM_008763149
- Peptide Label: isoform X6
- UniProtKB: Q498D1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017448049   ⟸   XM_017592560
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017448050   ⟸   XM_017592561
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_017448051   ⟸   XM_017592562
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: ENSRNOP00000013271   ⟸   ENSRNOT00000013271
RefSeq Acc Id: XP_038963317   ⟸   XM_039107389
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038963314   ⟸   XM_039107386
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038963312   ⟸   XM_039107384
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038963311   ⟸   XM_039107383
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038963313   ⟸   XM_039107385
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038963305   ⟸   XM_039107377
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963306   ⟸   XM_039107378
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963307   ⟸   XM_039107379
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963308   ⟸   XM_039107380
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963309   ⟸   XM_039107381
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963310   ⟸   XM_039107382
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963315   ⟸   XM_039107387
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038963316   ⟸   XM_039107388
- Peptide Label: isoform X9
RefSeq Acc Id: ENSRNOP00000095477   ⟸   ENSRNOT00000100443
RefSeq Acc Id: ENSRNOP00000088588   ⟸   ENSRNOT00000108862
RefSeq Acc Id: ENSRNOP00000082807   ⟸   ENSRNOT00000103186

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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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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)
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)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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)
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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)
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)
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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)
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)
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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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308669 AgrOrtholog
Ensembl Genes ENSRNOG00000009184 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000013271 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000013271 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7383433 IMAGE-MGC_LOAD
InterPro Fork_head_dom UniProtKB/Swiss-Prot
  FOXP-CC UniProtKB/Swiss-Prot
  TF_fork_head_CS_2 UniProtKB/Swiss-Prot
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot
  WH_DNA-bd_sf UniProtKB/Swiss-Prot
KEGG Report rno:297480 UniProtKB/Swiss-Prot
MGC_CLONE MGC:116362 IMAGE-MGC_LOAD
NCBI Gene 297480 ENTREZGENE
Pfam Forkhead UniProtKB/Swiss-Prot
  FOXP-CC UniProtKB/Swiss-Prot
PhenoGen Foxp1 PhenoGen
PRINTS FORKHEAD UniProtKB/Swiss-Prot
PROSITE FORK_HEAD_2 UniProtKB/Swiss-Prot
  FORK_HEAD_3 UniProtKB/Swiss-Prot
  ZINC_FINGER_C2H2_1 UniProtKB/Swiss-Prot
SMART SM00339 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46785 UniProtKB/Swiss-Prot
UniProt FOXP1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Foxp1  forkhead box P1  Foxp1_predicted  forkhead box P1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Foxp1_predicted  forkhead box P1 (predicted)      Symbol and Name status set to approved 70820 APPROVED