Lef1 (lymphoid enhancer binding factor 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Lef1 (lymphoid enhancer binding factor 1) Rattus norvegicus
Analyze
Symbol: Lef1
Name: lymphoid enhancer binding factor 1
RGD ID: 620241
Description: Predicted to have several functions, including DNA binding activity; DNA-binding transcription activator activity, RNA polymerase II-specific; and protein domain specific binding activity. Involved in several processes, including animal organ development; odontoblast differentiation; and response to lithium ion. Localizes to nucleus. Human ortholog(s) of this gene implicated in ovarian cancer. Orthologous to human LEF1 (lymphoid enhancer binding factor 1); PARTICIPATES IN Wnt signaling, canonical pathway; acute myeloid leukemia pathway; arrhythmogenic right ventricular cardiomyopathy pathway; INTERACTS WITH 1,2-dimethylhydrazine; 1,3-dinitrobenzene; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LEF-1; lymphoid enhancer binding factor 1 short isoform; lymphoid enhancer-binding factor 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22219,666,549 - 219,779,815 (+)NCBI
Rnor_6.0 Ensembl2236,233,239 - 236,345,056 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02236,232,115 - 236,345,061 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02254,781,171 - 254,893,756 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42228,550,263 - 228,673,131 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12228,537,002 - 228,659,871 (+)NCBI
Celera2211,924,784 - 212,018,812 (+)NCBICelera
Cytogenetic Map2q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dibromoethane  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1,3-dinitrobenzene  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2-butoxyethanol  (ISO)
2-hydroxypropanoic acid  (ISO)
2-nitrotoluene  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-methylcholanthrene  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-formyltetrahydrofolic acid  (EXP)
8-Br-cAMP  (ISO)
acetaldehyde  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
buta-1,3-diene  (ISO)
Butylbenzyl phthalate  (ISO)
Butylparaben  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
casticin  (ISO)
choline  (ISO)
cobalt dichloride  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
curcumin  (EXP)
cyclophosphamide  (ISO)
D-glucose  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dibutyl phthalate  (EXP,ISO)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
emodin  (ISO)
endosulfan  (ISO)
entinostat  (ISO)
etacrynic acid  (ISO)
ethosuximide  (EXP)
flavonoids  (EXP)
flusilazole  (ISO)
folic acid  (ISO)
gentamycin  (EXP)
glucose  (ISO)
glycidol  (ISO)
hydralazine  (ISO)
hydroquinone  (ISO)
L-methionine  (ISO)
lamivudine  (ISO)
lithium chloride  (ISO)
lovastatin  (ISO)
menadione  (ISO)
methapyrilene  (ISO)
methimazole  (ISO)
methotrexate  (EXP)
methyl carbamate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-Vinyl-2-pyrrolidone  (EXP)
nickel atom  (ISO)
nickel dichloride  (EXP)
nickel subsulfide  (EXP)
nitrofen  (EXP)
ouabain  (ISO)
oxaliplatin  (EXP)
paracetamol  (ISO)
paraquat  (ISO)
PCB138  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
quercetin  (ISO)
quercitrin  (ISO)
quinolin-8-ol  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
saquinavir  (ISO)
SB 415286  (EXP)
SB 431542  (ISO)
silicon dioxide  (ISO)
simvastatin  (EXP)
sodium arsenite  (ISO)
Soman  (EXP)
sulindac  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
thymoquinone  (ISO)
titanium dioxide  (ISO)
toluene  (EXP)
topotecan  (EXP)
trichostatin A  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
zidovudine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
alpha-beta T cell differentiation  (ISO)
anatomical structure regression  (IEA,ISO)
animal organ regeneration  (IEP)
apoptotic process involved in blood vessel morphogenesis  (IEA,ISO)
apoptotic process involved in morphogenesis  (ISO)
B cell proliferation  (IEA,ISO)
BMP signaling pathway  (IEA,ISO)
branching involved in blood vessel morphogenesis  (IEA,ISO)
canonical Wnt signaling pathway  (IBA,IEA,ISO)
cell adhesion  (IEP)
cell chemotaxis  (IEA,ISO)
cell development  (ISO)
cellular response to cytokine stimulus  (ISO)
cellular response to interleukin-4  (IEA,ISO)
chorio-allantoic fusion  (IEA,ISO)
dentate gyrus development  (IEA,ISO)
embryonic limb morphogenesis  (IEA,ISO)
epithelial to mesenchymal transition  (IEA,ISO)
face morphogenesis  (IEA,ISO)
forebrain neuroblast division  (IEA,ISO)
forebrain radial glial cell differentiation  (IEA,ISO)
formation of radial glial scaffolds  (IEA,ISO)
hippocampus development  (ISO)
histone H3 acetylation  (IEA,ISO)
histone H3-K56 acetylation  (ISO)
histone H4 acetylation  (IEA,ISO)
kidney development  (IEP)
mammary gland development  (IEA,ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of apoptotic process in bone marrow cell  (IEA,ISO)
negative regulation of cell-cell adhesion  (ISO)
negative regulation of DNA binding  (IEA,ISO)
negative regulation of interleukin-13 production  (IEA,ISO)
negative regulation of interleukin-4 production  (IEA,ISO)
negative regulation of interleukin-5 production  (IEA,ISO)
negative regulation of striated muscle tissue development  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
negative regulation of transcription, DNA-templated  (ISO)
neutrophil differentiation  (IEA,ISO)
odontoblast differentiation  (IMP)
odontogenesis of dentin-containing tooth  (IEA,ISO)
osteoblast differentiation  (IEA,ISO)
paraxial mesoderm formation  (IEA,ISO)
positive regulation by host of viral transcription  (IEA,ISO)
positive regulation of cell cycle process  (ISO)
positive regulation of cell migration  (IEA,ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of cell proliferation in bone marrow  (IEA,ISO)
positive regulation of cell-cell adhesion  (ISO)
positive regulation of chondrocyte proliferation  (ISO)
positive regulation of epithelial to mesenchymal transition  (IEA,ISO)
positive regulation of gamma-delta T cell differentiation  (IEA,ISO,ISS)
positive regulation of gene expression  (IEA,ISO)
positive regulation of granulocyte differentiation  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
positive regulation of transcription, DNA-templated  (ISO)
positive regulation of Wnt signaling pathway  (ISO)
regulation of cell-cell adhesion  (ISO)
regulation of transcription by RNA polymerase II  (IBA,ISO)
regulation of transcription, DNA-templated  (ISO,ISS)
regulation of Wnt signaling pathway  (IEA,ISO)
response to lithium ion  (IEP)
response to organic cyclic compound  (IEP)
secondary palate development  (IEA,ISO)
sensory perception of taste  (IEA,ISO)
skin development  (IEP)
somitogenesis  (IEA,ISO)
sprouting angiogenesis  (IEA,ISO)
steroid hormone mediated signaling pathway  (IEA)
T cell receptor V(D)J recombination  (IEA,ISO)
T-helper 1 cell differentiation  (IEA,ISO)
tongue development  (IEA,ISO)
trachea gland development  (IEA,ISO)
vasculature development  (ISO)

Cellular Component

References

References - curated
1. Bauman TM, etal., Hum Pathol. 2016 May;51:124-33. doi: 10.1016/j.humpath.2015.12.024. Epub 2016 Jan 19.
2. Chen W, etal., Wound Repair Regen. 2007 Jan-Feb;15(1):147-55.
3. Chen X, etal., Mol Cell Biol. 2006 Jun;26(12):4462-73.
4. Dong T, etal., Oncol Rep. 2017 Aug;38(2):1287-1294. doi: 10.3892/or.2017.5777. Epub 2017 Jul 3.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. GOA data from the GO Consortium
7. Juskeviciute E, etal., BMC Genomics. 2008 Nov 6;9:527.
8. Kahler RA and Westendorf JJ, J Biol Chem 2003 Apr 4;278(14):11937-44. Epub 2003 Jan 27.
9. Klaus A and Birchmeier W, Nat Rev Cancer. 2008 May;8(5):387-98.
10. Kobielak K, etal., Acta Biochim Pol 1999;46(4):885-8.
11. Kuure S, etal., J Am Soc Nephrol. 2007 Apr;18(4):1130-9. Epub 2007 Feb 28.
12. MGD data from the GO Consortium
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. Novak A, etal., Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4374-9.
15. OMIM Disease Annotation Pipeline
16. Pipeline to import KEGG annotations from KEGG into RGD
17. Rask K, etal., Br J Cancer. 2003 Oct 6;89(7):1298-304.
18. RGD automated data pipeline
19. RGD automated import pipeline for gene-chemical interactions
20. Rider V, etal., J Endocrinol. 2006 Dec;191(3):537-48.
21. Roose J and Clevers H, Biochim Biophys Acta. 1999 Oct 29;1424(2-3):M23-37.
22. Yokose S and Naka T, J Bone Miner Metab. 2010 Apr 28.
23. Young CS, etal., Differentiation 2003 Oct;71(8):477-85.
24. Zhong N, etal., Bone. 2006 Jul;39(1):5-16. Epub 2006 Feb 3.
Additional References at PubMed
PMID:7537238   PMID:7657162   PMID:7774816   PMID:9308964   PMID:9462507   PMID:9488439   PMID:9769173   PMID:10090727   PMID:10498680   PMID:10498690   PMID:10631168   PMID:10644691  
PMID:10825188   PMID:10933391   PMID:11696550   PMID:11751639   PMID:12244173   PMID:12408825   PMID:12475749   PMID:12502739   PMID:14623238   PMID:14661054   PMID:14691138   PMID:14715945  
PMID:15024079   PMID:15094381   PMID:15545629   PMID:15649466   PMID:15668231   PMID:15729346   PMID:16163358   PMID:16344550   PMID:16510873   PMID:16678101   PMID:16678815   PMID:16818445  
PMID:16936075   PMID:17063141   PMID:17284610   PMID:17699607   PMID:18158920   PMID:18202148   PMID:18445004   PMID:18579517   PMID:18794125   PMID:18936100   PMID:19056892   PMID:19154719  
PMID:19351848   PMID:19402906   PMID:19576624   PMID:19620402   PMID:19653274   PMID:20018240   PMID:20093419   PMID:20123964   PMID:20128911   PMID:20360943   PMID:20363964   PMID:20371816  
PMID:21464233   PMID:21718540   PMID:21750544   PMID:22235033   PMID:22935613   PMID:23001182   PMID:23562159   PMID:23611378   PMID:23630438   PMID:24681597   PMID:33422572  


Genomics

Candidate Gene Status
Lef1 is a candidate Gene for QTL Eau5
Comparative Map Data
Lef1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22219,666,549 - 219,779,815 (+)NCBI
Rnor_6.0 Ensembl2236,233,239 - 236,345,056 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02236,232,115 - 236,345,061 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02254,781,171 - 254,893,756 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42228,550,263 - 228,673,131 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12228,537,002 - 228,659,871 (+)NCBI
Celera2211,924,784 - 212,018,812 (+)NCBICelera
Cytogenetic Map2q43NCBI
LEF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl4108,047,545 - 108,168,956 (-)EnsemblGRCh38hg38GRCh38
GRCh384108,047,548 - 108,168,932 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh374108,968,704 - 109,090,088 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364109,188,150 - 109,309,027 (-)NCBINCBI36hg18NCBI36
Build 344109,326,304 - 109,447,182NCBI
Celera4106,263,513 - 106,384,975 (-)NCBI
Cytogenetic Map4q25NCBI
HuRef4104,700,344 - 104,821,596 (-)NCBIHuRef
CHM1_14108,945,152 - 109,066,566 (-)NCBICHM1_1
Lef1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393130,903,946 - 131,018,006 (+)NCBIGRCm39mm39
GRCm39 Ensembl3130,904,120 - 131,018,005 (+)Ensembl
GRCm383131,110,297 - 131,224,357 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3131,110,471 - 131,224,356 (+)EnsemblGRCm38mm10GRCm38
MGSCv373130,813,389 - 130,926,252 (+)NCBIGRCm37mm9NCBIm37
MGSCv363131,099,626 - 131,212,489 (+)NCBImm8
Celera3137,630,007 - 137,744,454 (+)NCBICelera
Cytogenetic Map3G3NCBI
cM Map360.78NCBI
Lef1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554961,728,840 - 1,828,698 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554961,728,840 - 1,827,749 (+)NCBIChiLan1.0ChiLan1.0
LEF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.14111,125,312 - 111,245,980 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4111,125,312 - 111,245,980 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v04100,552,959 - 100,674,156 (-)NCBIMhudiblu_PPA_v0panPan3
LEF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13228,516,002 - 28,633,759 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3228,517,108 - 28,634,019 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3213,389,033 - 13,506,807 (+)NCBI
ROS_Cfam_1.03228,744,891 - 28,862,596 (-)NCBI
UMICH_Zoey_3.13228,737,873 - 28,855,560 (-)NCBI
UNSW_CanFamBas_1.03228,482,671 - 28,600,623 (-)NCBI
UU_Cfam_GSD_1.03211,256,345 - 11,374,064 (+)NCBI
Lef1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530112,484,346 - 12,597,999 (+)NCBI
SpeTri2.0NW_004936818453,635 - 569,194 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LEF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8113,824,547 - 113,944,078 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18113,824,511 - 113,944,078 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28122,085,854 - 122,204,415 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LEF1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1755,974,770 - 56,096,214 (-)NCBI
ChlSab1.1 Ensembl755,990,621 - 56,094,110 (-)Ensembl
Lef1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248301,320,034 - 1,422,774 (+)NCBI

Position Markers
D2Rat62  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22219,753,301 - 219,753,474 (+)MAPPER
Rnor_6.02236,318,496 - 236,318,668NCBIRnor6.0
Rnor_5.02254,867,191 - 254,867,363UniSTSRnor5.0
RGSC_v3.42228,663,949 - 228,664,122RGDRGSC3.4
RGSC_v3.42228,663,950 - 228,664,122UniSTSRGSC3.4
RGSC_v3.12228,650,690 - 228,650,862RGD
Celera2212,009,629 - 212,009,815UniSTS
RH 3.4 Map21548.6RGD
RH 3.4 Map21548.6UniSTS
RH 2.0 Map21101.3RGD
SHRSP x BN Map290.8698RGD
Cytogenetic Map2q34-q45UniSTS
RH69431  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22219,760,126 - 219,760,717 (+)MAPPER
Rnor_6.02236,325,321 - 236,325,911NCBIRnor6.0
Rnor_5.02254,874,016 - 254,874,606UniSTSRnor5.0
RGSC_v3.42228,670,775 - 228,671,365UniSTSRGSC3.4
Celera2212,016,468 - 212,017,058UniSTS
Cytogenetic Map2q34-q45UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)216679272245624402Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828236243550655Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)283754907237610852Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)283819608239166203Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)283819608243901375Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147122993240020001Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2147122993240020001Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557237742948Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557254121739Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2169852670243026643Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2175403337239166203Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2177680772243901375Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2181990297240020001Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2194378622239378622Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2194998627239998627Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2197253963242253963Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2197253963242253963Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2197253963242253963Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2197253963242253963Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2199380312244380312Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2200453324236318668Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2200453324236318668Rat
1581499Esta2Estrogen-induced thymic atrophy QTL 2thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2204585642243689611Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2204585642249585642Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2204585642249585642Rat
2301408Kidm36Kidney mass QTL 360.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2205583921243562243Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2208594330263179188Rat
1598813Memor9Memory QTL 92.7exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)2214870793251212353Rat
2298479Eau5Experimental allergic uveoretinitis QTL 50.0021uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)2217498545254132424Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2217743855262743855Rat
1302789Stl26Serum triglyceride level QTL 263.10.0035blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)2218957047240977220Rat
2299161Iddm33Insulin dependent diabetes mellitus QTL 332.98blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2221488355254121739Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2228712271266435125Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2228712271266435125Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2228712271266435125Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2228712271266435125Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2228712271266435125Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2229606682264899009Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2229793522266435125Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2231224020254132424Rat
631514Scl8Serum cholesterol level QTL84.4blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)2231621666266435125Rat
8693697Alc36Alcohol consumption QTL 3620.592drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2233013605253626471Rat
1331767Hrtrt12Heart rate QTL 123.373heart pumping trait (VT:2000009)heart rate (CMO:0000002)2235289967257110527Rat
1359019Hrtrt19Heart rate QTL 192.9heart pumping trait (VT:2000009)heart rate (CMO:0000002)2236318496243026643Rat
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2236318496264899009Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2236318496264899009Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:92
Count of miRNA genes:77
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000013694
Prediction methods:Microtar, Miranda, Rnahybrid
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 2 4 13 2 17 2 50 18 31 5
Low 1 34 35 30 2 30 8 8 24 14 10 6 8
Below cutoff 5 9 9 9 3 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_130429 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233302 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233303 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233306 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233309 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761489 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761490 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761491 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761492 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101602 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101603 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101604 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF198533 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF519319 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000079 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000013694   ⟹   ENSRNOP00000013694
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2236,233,239 - 236,345,056 (+)Ensembl
RefSeq Acc Id: NM_130429   ⟹   NP_569113
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22219,667,790 - 219,762,482 (+)NCBI
Rnor_6.02236,233,438 - 236,327,731 (+)NCBI
Rnor_5.02254,781,171 - 254,893,756 (+)NCBI
RGSC_v3.42228,550,263 - 228,673,131 (+)RGD
Celera2211,924,784 - 212,018,812 (+)RGD
Sequence:
RefSeq Acc Id: XM_006233302   ⟹   XP_006233364
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22219,666,549 - 219,779,815 (+)NCBI
Rnor_6.02236,232,120 - 236,345,061 (+)NCBI
Rnor_5.02254,781,171 - 254,893,756 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233303   ⟹   XP_006233365
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22219,666,549 - 219,779,503 (+)NCBI
Rnor_6.02236,232,119 - 236,344,143 (+)NCBI
Rnor_5.02254,781,171 - 254,893,756 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233305   ⟹   XP_006233367
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22219,666,549 - 219,778,886 (+)NCBI
Rnor_6.02236,232,119 - 236,344,132 (+)NCBI
Rnor_5.02254,781,171 - 254,893,756 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233306   ⟹   XP_006233368
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22219,666,549 - 219,778,886 (+)NCBI
Rnor_6.02236,232,119 - 236,344,143 (+)NCBI
Rnor_5.02254,781,171 - 254,893,756 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233309   ⟹   XP_006233371
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22219,667,853 - 219,779,503 (+)NCBI
Rnor_6.02236,233,830 - 236,344,143 (+)NCBI
Rnor_5.02254,781,171 - 254,893,756 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008761489   ⟹   XP_008759711
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02236,232,116 - 236,326,329 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008761490   ⟹   XP_008759712
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02236,232,115 - 236,326,329 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008761491   ⟹   XP_008759713
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22219,667,853 - 219,778,886 (+)NCBI
Rnor_6.02236,233,551 - 236,326,329 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008761492   ⟹   XP_008759714
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02236,233,830 - 236,326,329 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039101602   ⟹   XP_038957530
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22219,666,549 - 219,779,815 (+)NCBI
RefSeq Acc Id: XM_039101603   ⟹   XP_038957531
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22219,667,853 - 219,778,886 (+)NCBI
RefSeq Acc Id: XM_039101604   ⟹   XP_038957532
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22219,667,853 - 219,778,886 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_569113   ⟸   NM_130429
- UniProtKB: Q9QXN1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006233365   ⟸   XM_006233303
- Peptide Label: isoform X2
- UniProtKB: G3V7C1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233364   ⟸   XM_006233302
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006233368   ⟸   XM_006233306
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006233367   ⟸   XM_006233305
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006233371   ⟸   XM_006233309
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_008759711   ⟸   XM_008761489
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008759712   ⟸   XM_008761490
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008759713   ⟸   XM_008761491
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_008759714   ⟸   XM_008761492
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: ENSRNOP00000013694   ⟸   ENSRNOT00000013694
RefSeq Acc Id: XP_038957530   ⟸   XM_039101602
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038957531   ⟸   XM_039101603
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038957532   ⟸   XM_039101604
- Peptide Label: isoform X8
Protein Domains
CTNNB1_binding   HMG box

Transcriptome

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

Promoters
RGD ID:13691758
Promoter ID:EPDNEW_R2282
Type:single initiation site
Name:Lef1_1
Description:lymphoid enhancer binding factor 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02236,233,207 - 236,233,267EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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/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 (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)
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
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
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/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
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 (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
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
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
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
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
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 (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
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
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 (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 (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
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 (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 (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 (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:620241 AgrOrtholog
Ensembl Genes ENSRNOG00000010121 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000013694 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013694 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  4.10.900.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Catenin_binding_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CTNNB1-bd_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_box_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LEF1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TCF/LEF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:161452 UniProtKB/Swiss-Prot
NCBI Gene 161452 ENTREZGENE
PANTHER PTHR10373 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10373:SF11 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CTNNB1_binding UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lef1 PhenoGen
PROSITE HMG_BOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HMG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47095 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A5A1E7_RAT UniProtKB/TrEMBL
  G3V7C1 ENTREZGENE, UniProtKB/TrEMBL
  LEF1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Lef1  lymphoid enhancer binding factor 1      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Lef1        Symbol and Name status set to provisional 70820 PROVISIONAL