Nfib (nuclear factor I/B) - Rat Genome Database

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Gene: Nfib (nuclear factor I/B) Rattus norvegicus
Analyze
Symbol: Nfib
Name: nuclear factor I/B
RGD ID: 62015
Description: Enables double-stranded DNA binding activity. Involved in positive regulation of transcription, DNA-templated. Predicted to be located in cerebellar mossy fiber; fibrillar center; and nucleoplasm. Predicted to be active in nucleus. Orthologous to human NFIB (nuclear factor I B); PARTICIPATES IN forkhead class A signaling pathway; INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: nuclear factor 1 B-type; olfactory epithelium nuclear factor I-B
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
mRatBN7.2596,759,208 - 96,973,092 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl596,764,653 - 96,975,479 (-)Ensembl
Rnor_6.05100,436,343 - 100,647,962 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5100,439,082 - 100,647,727 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05104,464,121 - 104,676,709 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45101,184,253 - 101,409,907 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15101,189,483 - 101,283,030 (-)NCBI
Celera595,320,913 - 95,528,007 (-)NCBICelera
Cytogenetic Map5q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
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-hydroxypropanoic acid  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
acetamide  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (EXP,ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
Benzo[ghi]perylene  (ISO)
bis(2-chloroethyl) sulfide  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Brodifacoum  (EXP)
butanal  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
chlordecone  (ISO)
chlorpyrifos  (EXP)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
cyproconazole  (ISO)
cytarabine  (ISO)
dibenzo[a,l]pyrene  (ISO)
dichloromethane  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
epoxiconazole  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
ethylbenzene  (ISO)
flutamide  (EXP)
formaldehyde  (ISO)
gamma-hexachlorocyclohexane  (EXP)
genistein  (EXP)
glafenine  (EXP)
iron atom  (ISO)
iron(0)  (ISO)
L-ascorbic acid  (ISO)
leflunomide  (ISO)
maneb  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
mercury dibromide  (ISO)
methapyrilene  (EXP)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
nimesulide  (EXP)
o-xylene  (ISO)
oxaliplatin  (EXP,ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
PCB138  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (EXP,ISO)
phenol red  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
Ptaquiloside  (ISO)
pyridaben  (ISO)
rac-lactic acid  (ISO)
SB 431542  (ISO)
sodium arsenate  (ISO)
sulindac  (EXP)
sunitinib  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP,ISO)
titanium dioxide  (ISO)
toluene  (ISO)
topotecan  (EXP)
trichloroethene  (EXP,ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
troglitazone  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cerebellar mossy fiber  (ISO,ISS)
fibrillar center  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,ISO,ISS)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9056636   PMID:9099724   PMID:11850179   PMID:12477932   PMID:15632069   PMID:16147868   PMID:17904922   PMID:18384814   PMID:19107796   PMID:19540848   PMID:19706729   PMID:19961580  
PMID:21513708   PMID:23012479   PMID:25403566   PMID:30388402   PMID:33275244   PMID:33506922  


Genomics

Comparative Map Data
Nfib
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2596,759,208 - 96,973,092 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl596,764,653 - 96,975,479 (-)Ensembl
Rnor_6.05100,436,343 - 100,647,962 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5100,439,082 - 100,647,727 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05104,464,121 - 104,676,709 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45101,184,253 - 101,409,907 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15101,189,483 - 101,283,030 (-)NCBI
Celera595,320,913 - 95,528,007 (-)NCBICelera
Cytogenetic Map5q31NCBI
NFIB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl914,081,843 - 14,398,983 (-)EnsemblGRCh38hg38GRCh38
GRCh38914,081,843 - 14,532,077 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37914,081,842 - 14,532,075 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36914,071,847 - 14,303,945 (-)NCBINCBI36hg18NCBI36
Build 34914,077,372 - 14,303,719NCBI
Celera914,015,384 - 14,332,471 (-)NCBI
Cytogenetic Map9p23-p22.3NCBI
HuRef914,045,221 - 14,362,372 (-)NCBIHuRef
CHM1_1914,081,962 - 14,399,030 (-)NCBICHM1_1
Nfib
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39482,208,410 - 82,424,988 (-)NCBIGRCm39mm39
GRCm39 Ensembl482,208,410 - 82,623,987 (-)Ensembl
GRCm38482,290,173 - 82,506,751 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl482,290,173 - 82,705,750 (-)EnsemblGRCm38mm10GRCm38
MGSCv37481,936,077 - 82,151,212 (-)NCBIGRCm37mm9NCBIm37
MGSCv36481,766,962 - 81,976,354 (-)NCBImm8
Celera480,824,138 - 81,039,259 (-)NCBICelera
Cytogenetic Map4C3NCBI
cM Map438.4NCBI
Nfib
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543417,198,571 - 17,415,084 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543417,192,188 - 17,603,503 (-)NCBIChiLan1.0ChiLan1.0
NFIB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1914,432,239 - 14,664,424 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0913,923,516 - 14,376,264 (-)NCBIMhudiblu_PPA_v0panPan3
NFIB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11134,573,136 - 35,010,319 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1134,579,431 - 34,901,322 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1133,281,491 - 33,523,124 (-)NCBI
ROS_Cfam_1.01135,477,680 - 35,719,587 (-)NCBI
UMICH_Zoey_3.11134,182,236 - 34,423,934 (-)NCBI
UNSW_CanFamBas_1.01133,974,417 - 34,216,067 (-)NCBI
UU_Cfam_GSD_1.01134,631,192 - 34,872,773 (-)NCBI
Nfib
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947149,310,349 - 149,730,717 (-)NCBI
SpeTri2.0NW_0049365397,763,036 - 8,185,001 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NFIB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1208,175,194 - 208,421,643 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11208,182,397 - 208,427,504 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21231,957,992 - 232,197,794 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103219433
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11265,043,819 - 65,487,832 (+)NCBI
ChlSab1.1 Ensembl1265,256,407 - 65,481,485 (+)Ensembl
Vero_WHO_p1.0NW_02366603853,635,229 - 53,707,627 (+)NCBI
Nfib
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473618,372,418 - 18,586,390 (-)NCBI

Position Markers
D5Rat149  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2597,059,760 - 97,059,958 (+)MAPPERmRatBN7.2
Rnor_6.05100,745,417 - 100,745,614NCBIRnor6.0
Rnor_6.05100,723,739 - 100,723,936NCBIRnor6.0
Rnor_5.05104,770,864 - 104,771,061UniSTSRnor5.0
Rnor_5.05104,751,414 - 104,751,611UniSTSRnor5.0
RGSC_v3.45101,506,464 - 101,506,661UniSTSRGSC3.4
RGSC_v3.45101,506,332 - 101,506,667RGDRGSC3.4
RGSC_v3.15101,511,690 - 101,511,887RGD
Celera595,614,587 - 95,614,784UniSTS
RH 3.4 Map5723.5UniSTS
RH 3.4 Map5723.5RGD
SHRSP x BN Map553.6299RGD
SHRSP x BN Map553.6299UniSTS
Cytogenetic Map5q31UniSTS
D5Got128  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2596,824,138 - 96,824,374 (+)MAPPERmRatBN7.2
Rnor_6.05100,497,947 - 100,498,184NCBIRnor6.0
Rnor_5.05104,528,723 - 104,528,960UniSTSRnor5.0
RGSC_v3.45101,243,911 - 101,244,149RGDRGSC3.4
RGSC_v3.45101,243,912 - 101,244,149UniSTSRGSC3.4
RGSC_v3.15101,249,138 - 101,249,375RGD
Celera595,379,682 - 95,379,941UniSTS
RH 3.4 Map5750.39UniSTS
RH 3.4 Map5750.39RGD
RH 2.0 Map5614.0RGD
Cytogenetic Map5q31UniSTS
D5Got240  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.45101,228,767 - 101,228,906UniSTSRGSC3.4
Celera595,364,459 - 95,364,598UniSTS
Cytogenetic Map5q31UniSTS
D9S2012  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2596,759,223 - 96,759,349 (+)MAPPERmRatBN7.2
Rnor_6.05100,433,284 - 100,433,409NCBIRnor6.0
Rnor_5.05104,464,137 - 104,464,262UniSTSRnor5.0
RGSC_v3.45101,178,460 - 101,178,585UniSTSRGSC3.4
Celera595,314,996 - 95,315,121UniSTS
Cytogenetic Map5q31UniSTS
RH132021  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2597,013,981 - 97,014,171 (+)MAPPERmRatBN7.2
Rnor_6.05100,687,980 - 100,688,169NCBIRnor6.0
Rnor_5.05104,715,494 - 104,715,683UniSTSRnor5.0
RGSC_v3.45101,456,449 - 101,456,638UniSTSRGSC3.4
Celera595,568,856 - 95,569,045UniSTS
RH 3.4 Map5727.1UniSTS
Cytogenetic Map5q31UniSTS
RH142928  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2596,786,688 - 96,786,855 (+)MAPPERmRatBN7.2
Rnor_6.05100,460,751 - 100,460,917NCBIRnor6.0
Rnor_5.05104,491,527 - 104,491,693UniSTSRnor5.0
RGSC_v3.45101,206,745 - 101,206,911UniSTSRGSC3.4
Celera595,342,271 - 95,342,437UniSTS
RH 3.4 Map5724.11UniSTS
Cytogenetic Map5q31UniSTS
RH143568  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2596,787,691 - 96,787,905 (+)MAPPERmRatBN7.2
Rnor_6.05100,461,754 - 100,461,967NCBIRnor6.0
Rnor_5.05104,492,530 - 104,492,743UniSTSRnor5.0
RGSC_v3.45101,207,748 - 101,207,961UniSTSRGSC3.4
Celera595,343,274 - 95,343,487UniSTS
Cytogenetic Map5q31UniSTS
RH138459  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2596,786,197 - 96,786,401 (+)MAPPERmRatBN7.2
Rnor_6.05100,460,260 - 100,460,463NCBIRnor6.0
Rnor_5.05104,491,036 - 104,491,239UniSTSRnor5.0
RGSC_v3.45101,206,254 - 101,206,457UniSTSRGSC3.4
Celera595,341,780 - 95,341,983UniSTS
RH 3.4 Map5748.5UniSTS
Cytogenetic Map5q31UniSTS
MARC_17865-17866:1025013775:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2596,765,165 - 96,765,652 (+)MAPPERmRatBN7.2
Rnor_6.05100,439,226 - 100,439,712NCBIRnor6.0
Rnor_5.05104,470,079 - 104,470,565UniSTSRnor5.0
RGSC_v3.45101,184,402 - 101,184,888UniSTSRGSC3.4
Celera595,321,062 - 95,321,548UniSTS
Cytogenetic Map5q31UniSTS
Nfib  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2596,963,422 - 96,963,474 (+)MAPPERmRatBN7.2
Rnor_6.05100,637,407 - 100,637,458NCBIRnor6.0
Rnor_5.05104,666,462 - 104,666,513UniSTSRnor5.0
RGSC_v3.45101,400,404 - 101,400,455UniSTSRGSC3.4
Celera595,518,449 - 95,518,500UniSTS
Cytogenetic Map5q31UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)55349671998496719Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)555715622100715622Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)56029343498603051Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
2290005Mcs24Mammary carcinoma susceptibility QTL 24mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)564719390109719390Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)566174080124160948Rat
2312671Scl64Serum cholesterol level QTL 640.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)568984307104251008Rat
61380Edpm5Estrogen-dependent pituitary mass QTL 54.50.92pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)568984307104251008Rat
1357396Bw44Body weight QTL 444.19body mass (VT:0001259)body weight (CMO:0000012)568984307104251008Rat
1357402Bw46Body weight QTL 464.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
2302381Bw84Body weight QTL 844.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1298070Scl18Serum cholesterol level QTL 183.7blood LDL cholesterol amount (VT:0000181)calculated plasma low density lipoprotein cholesterol level (CMO:0001245)579584860124584860Rat
1598846Bp293Blood pressure QTL 2933.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)579584860124584860Rat
1598859Cm66Cardiac mass QTL 662heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)579584860124584860Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1331782Rf36Renal function QTL 363.296kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)58384059897059958Rat
1298086Bp156Blood pressure QTL 156arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)584132602129132602Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)587468046132468046Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)587765973132765973Rat
1358889Bp261Blood pressure QTL 2612.86arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)590067849128034027Rat
1358909Kidm25Kidney mass QTL 251.87kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)590067849128034027Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)590450144135450144Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:450
Count of miRNA genes:204
Interacting mature miRNAs:252
Transcripts:ENSRNOT00000013092, ENSRNOT00000067435, ENSRNOT00000067538
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 41 33 19 15 19 8 10 68 35 41 11 8
Low 2 24 22 4 22 1 6
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_031566 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238335 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238336 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238339 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593197 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593198 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109354 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109355 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109357 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB012230 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB012231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB012232 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF112457 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC089062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473978 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000013092   ⟹   ENSRNOP00000013092
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl596,764,653 - 96,972,982 (-)Ensembl
Rnor_6.0 Ensembl5100,439,082 - 100,647,298 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000067435   ⟹   ENSRNOP00000060839
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl596,765,022 - 96,975,479 (-)Ensembl
Rnor_6.0 Ensembl5100,439,476 - 100,647,727 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000067538   ⟹   ENSRNOP00000063791
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl596,790,074 - 96,972,982 (-)Ensembl
Rnor_6.0 Ensembl5100,439,082 - 100,647,298 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104453   ⟹   ENSRNOP00000087113
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl596,764,653 - 96,975,479 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110522   ⟹   ENSRNOP00000084432
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl596,765,022 - 96,975,479 (-)Ensembl
RefSeq Acc Id: NM_031566   ⟹   NP_113754
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2596,765,017 - 96,972,982 (-)NCBI
Rnor_6.05100,439,077 - 100,647,298 (-)NCBI
Rnor_5.05104,464,121 - 104,676,709 (-)NCBI
RGSC_v3.45101,184,253 - 101,409,907 (-)RGD
Celera595,320,913 - 95,528,007 (-)RGD
Sequence:
RefSeq Acc Id: XM_006238335   ⟹   XP_006238397
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2596,759,208 - 96,973,092 (-)NCBI
Rnor_6.05100,436,343 - 100,647,962 (-)NCBI
Rnor_5.05104,464,121 - 104,676,709 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238336   ⟹   XP_006238398
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2596,759,208 - 96,973,092 (-)NCBI
Rnor_6.05100,436,343 - 100,647,962 (-)NCBI
Rnor_5.05104,464,121 - 104,676,709 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238339   ⟹   XP_006238401
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2596,759,208 - 96,973,092 (-)NCBI
Rnor_6.05100,436,343 - 100,647,960 (-)NCBI
Rnor_5.05104,464,121 - 104,676,709 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763762   ⟹   XP_008761984
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2596,759,208 - 96,967,788 (-)NCBI
Rnor_6.05100,436,343 - 100,641,811 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593197   ⟹   XP_017448686
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2596,759,208 - 96,967,789 (-)NCBI
Rnor_6.05100,436,343 - 100,641,811 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593198   ⟹   XP_017448687
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2596,759,208 - 96,967,790 (-)NCBI
Rnor_6.05100,439,693 - 100,641,811 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593199   ⟹   XP_017448688
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2596,759,208 - 96,967,788 (-)NCBI
Rnor_6.05100,436,343 - 100,641,811 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593200   ⟹   XP_017448689
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2596,759,208 - 96,967,776 (-)NCBI
Rnor_6.05100,436,343 - 100,641,811 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039109354   ⟹   XP_038965282
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2596,759,208 - 96,967,783 (-)NCBI
RefSeq Acc Id: XM_039109355   ⟹   XP_038965283
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2596,759,208 - 96,973,092 (-)NCBI
RefSeq Acc Id: XM_039109356   ⟹   XP_038965284
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2596,759,208 - 96,851,576 (-)NCBI
RefSeq Acc Id: XM_039109357   ⟹   XP_038965285
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2596,759,208 - 96,966,513 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_113754   ⟸   NM_031566
- UniProtKB: O70186 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238401   ⟸   XM_006238339
- Peptide Label: isoform X10
- UniProtKB: O70187 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238398   ⟸   XM_006238336
- Peptide Label: isoform X5
- UniProtKB: O70185 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238397   ⟸   XM_006238335
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008761984   ⟸   XM_008763762
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017448689   ⟸   XM_017593200
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017448688   ⟸   XM_017593199
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017448686   ⟸   XM_017593197
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017448687   ⟸   XM_017593198
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000060839   ⟸   ENSRNOT00000067435
RefSeq Acc Id: ENSRNOP00000063791   ⟸   ENSRNOT00000067538
RefSeq Acc Id: ENSRNOP00000013092   ⟸   ENSRNOT00000013092
RefSeq Acc Id: XP_038965283   ⟸   XM_039109355
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038965282   ⟸   XM_039109354
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038965285   ⟸   XM_039109357
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038965284   ⟸   XM_039109356
- Peptide Label: isoform X11
RefSeq Acc Id: ENSRNOP00000084432   ⟸   ENSRNOT00000110522
RefSeq Acc Id: ENSRNOP00000087113   ⟸   ENSRNOT00000104453
Protein Domains
CTF/NF-I

Transcriptome

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

Promoters
RGD ID:13693820
Promoter ID:EPDNEW_R4341
Type:single initiation site
Name:Nfib_1
Description:nuclear factor I/B
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_6.05100,647,698 - 100,647,758EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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:62015 AgrOrtholog
Ensembl Genes ENSRNOG00000009795 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000013092 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000060839 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000063791 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013092 UniProtKB/TrEMBL
  ENSRNOT00000067435 UniProtKB/TrEMBL
  ENSRNOT00000067538 ENTREZGENE, UniProtKB/TrEMBL
InterPro CTF/NFI UniProtKB/TrEMBL
  CTF/NFI_DNA-bd-dom UniProtKB/TrEMBL
  CTF/NFI_DNA-bd_CS UniProtKB/TrEMBL
  CTF/NFI_DNA-bd_N UniProtKB/TrEMBL
  MAD_homology1_Dwarfin-type UniProtKB/TrEMBL
KEGG Report rno:29227 UniProtKB/TrEMBL
NCBI Gene 29227 ENTREZGENE
PANTHER CTF_NFI UniProtKB/TrEMBL
Pfam CTF_NFI UniProtKB/TrEMBL
  MH1 UniProtKB/TrEMBL
  NfI_DNAbd_pre-N UniProtKB/TrEMBL
PhenoGen Nfib PhenoGen
PROSITE CTF_NFI_1 UniProtKB/TrEMBL
  CTF_NFI_2 UniProtKB/TrEMBL
SMART DWA UniProtKB/TrEMBL
TIGR TC229476
UniProt O70185 ENTREZGENE, UniProtKB/TrEMBL
  O70186 ENTREZGENE, UniProtKB/TrEMBL
  O70187 ENTREZGENE, UniProtKB/TrEMBL
  Q9QY88_RAT UniProtKB/TrEMBL
UniProt Secondary F1LLY9 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Nfib  nuclear factor I/B      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_product member of a family of olfactory epithelium transcription factors 633408