Gtf2i (general transcription factor II I) - Rat Genome Database

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Gene: Gtf2i (general transcription factor II I) Rattus norvegicus
Analyze
Symbol: Gtf2i
Name: general transcription factor II I
RGD ID: 727961
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II-specific DNA-binding transcription factor binding activity; and mitogen-activated protein kinase binding activity. Involved in negative regulation of cytosolic calcium ion concentration. Predicted to be located in cell projection; neuronal cell body; and nucleoplasm. Predicted to be active in nucleus. Orthologous to human GTF2I (general transcription factor IIi); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: general transcription factor II-I; Gtf2ird1; GTFII-I; MGC94055; TFII-I
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   DA.ACI-(D12Mit2-Gtf2i)/Nsi  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21222,400,933 - 22,476,243 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1222,401,431 - 22,476,243 (+)Ensembl
Rnor_6.01225,410,804 - 25,487,970 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1225,411,207 - 25,488,156 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01227,420,618 - 27,497,928 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41223,470,042 - 23,545,621 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11223,350,478 - 23,408,833 (+)NCBI
Celera1224,164,158 - 24,238,521 (+)NCBICelera
Cytogenetic Map12q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2-hydroxypropanoic acid  (ISO)
2-methylcholine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
acetylsalicylic acid  (ISO)
aldehydo-D-glucose  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
aristolochic acid  (ISO)
benzo[a]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
cadmium dichloride  (EXP,ISO)
carbon nanotube  (ISO)
cerium trichloride  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
D-glucose  (ISO)
diethylstilbestrol  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
ethanol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
furan  (EXP)
glafenine  (EXP)
glucose  (ISO)
hexadecanoic acid  (ISO)
ivermectin  (ISO)
menadione  (ISO)
methapyrilene  (EXP)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
perfluorooctanoic acid  (ISO)
phosgene  (ISO)
pirinixic acid  (ISO)
propiconazole  (ISO)
rac-lactic acid  (ISO)
reactive oxygen species  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
topotecan  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vincaleukoblastine  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zoledronic acid  (ISO)

References

Additional References at PubMed
PMID:12477932   PMID:14751286   PMID:17052463   PMID:19109438   PMID:19242469   PMID:19946888   PMID:22082260   PMID:22899722   PMID:25913238   PMID:25931508  


Genomics

Comparative Map Data
Gtf2i
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21222,400,933 - 22,476,243 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1222,401,431 - 22,476,243 (+)Ensembl
Rnor_6.01225,410,804 - 25,487,970 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1225,411,207 - 25,488,156 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01227,420,618 - 27,497,928 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41223,470,042 - 23,545,621 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11223,350,478 - 23,408,833 (+)NCBI
Celera1224,164,158 - 24,238,521 (+)NCBICelera
Cytogenetic Map12q12NCBI
GTF2I
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl774,650,231 - 74,760,692 (+)EnsemblGRCh38hg38GRCh38
GRCh38774,657,718 - 74,760,692 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37774,072,044 - 74,175,022 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36773,709,966 - 73,812,958 (+)NCBINCBI36hg18NCBI36
Build 34773,516,680 - 73,619,673NCBI
Celera769,551,230 - 69,623,844 (+)NCBI
Cytogenetic Map7q11.23NCBI
HuRef769,950,614 - 70,053,622 (+)NCBIHuRef
CHM1_1774,217,081 - 74,320,108 (+)NCBICHM1_1
CRA_TCAGchr7v2773,405,063 - 73,508,086 (+)NCBI
Gtf2i
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395134,266,686 - 134,346,571 (-)NCBIGRCm39mm39
GRCm39 Ensembl5134,266,688 - 134,343,614 (-)Ensembl
GRCm385134,237,832 - 134,317,678 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5134,237,834 - 134,314,760 (-)EnsemblGRCm38mm10GRCm38
MGSCv375134,713,704 - 134,790,616 (-)NCBIGRCm37mm9NCBIm37
MGSCv365134,522,471 - 134,599,320 (-)NCBImm8
Celera5131,241,157 - 131,318,055 (-)NCBICelera
Cytogenetic Map5G2NCBI
cM Map574.48NCBI
Gtf2i
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545613,369,772 - 13,446,815 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545613,371,306 - 13,461,846 (-)NCBIChiLan1.0ChiLan1.0
GTF2I
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1781,816,945 - 81,903,784 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl781,831,442 - 81,901,926 (+)Ensemblpanpan1.1panPan2
GTF2I
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.165,726,652 - 5,840,740 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl65,727,665 - 5,811,965 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha67,428,530 - 7,541,766 (-)NCBI
ROS_Cfam_1.065,543,745 - 5,657,006 (-)NCBI
UMICH_Zoey_3.165,535,568 - 5,648,801 (-)NCBI
UNSW_CanFamBas_1.065,482,175 - 5,596,064 (-)NCBI
UU_Cfam_GSD_1.065,644,547 - 5,758,859 (-)NCBI
Gtf2i
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344130,425,157 - 130,514,806 (-)NCBI
SpeTri2.0NW_0049365433,521,763 - 3,611,410 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GTF2I
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl311,671,575 - 11,811,423 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1311,656,928 - 11,811,426 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2311,424,644 - 11,529,984 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GTF2I
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1288,361,187 - 8,463,469 (-)NCBI
ChlSab1.1 Ensembl288,363,057 - 8,435,750 (-)Ensembl
Vero_WHO_p1.0NW_0236660708,139,034 - 8,242,152 (+)NCBI
Gtf2i
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474013,446,811 - 13,547,050 (-)NCBI

Position Markers
BE117132  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21222,430,668 - 22,430,818 (+)MAPPERmRatBN7.2
Rnor_6.01225,440,651 - 25,440,800NCBIRnor6.0
Rnor_5.01227,450,607 - 27,450,756UniSTSRnor5.0
RGSC_v3.41223,498,080 - 23,498,229UniSTSRGSC3.4
Celera1224,193,035 - 24,193,184UniSTS
RH 3.4 Map12346.7UniSTS
Cytogenetic Map12q12UniSTS
RH143085  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21222,432,665 - 22,432,916 (+)MAPPERmRatBN7.2
Rnor_6.01225,442,648 - 25,442,898NCBIRnor6.0
Rnor_5.01227,452,604 - 27,452,854UniSTSRnor5.0
RGSC_v3.41223,500,077 - 23,500,327UniSTSRGSC3.4
Celera1224,195,032 - 24,195,282UniSTS
RH 3.4 Map12347.3UniSTS
Cytogenetic Map12q12UniSTS
RH138602  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21222,474,593 - 22,475,256 (+)MAPPERmRatBN7.2
Rnor_6.01225,486,329 - 25,486,991NCBIRnor6.0
Rnor_5.01227,496,285 - 27,496,947UniSTSRnor5.0
RGSC_v3.41223,543,980 - 23,544,642UniSTSRGSC3.4
Celera1224,236,880 - 24,237,542UniSTS
RH 3.4 Map12354.8UniSTS
Cytogenetic Map12q12UniSTS
BI274753  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21222,475,857 - 22,476,062 (+)MAPPERmRatBN7.2
Rnor_6.01225,487,593 - 25,487,797NCBIRnor6.0
Rnor_5.01227,497,549 - 27,497,753UniSTSRnor5.0
RGSC_v3.41223,545,244 - 23,545,448UniSTSRGSC3.4
Celera1224,238,144 - 24,238,348UniSTS
RH 3.4 Map12356.0UniSTS
Cytogenetic Map12q12UniSTS
Gtf2i  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera1224,231,405 - 24,233,916UniSTS
Cytogenetic Map12q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12844949028302290Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12852542328064601Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)12931821632103380Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121107382524234895Rat
1331755Bp219Blood pressure QTL 2193.041arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382528064557Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382545055165Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121235161946669029Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121281238546669029Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121281238546669029Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121318273646669029Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101318273646669029Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121319815746669029Rat
61416Pia4Pristane induced arthritis QTL 48.4joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)121363552330827399Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121363552335682913Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121555082638478808Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)121587265332974238Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)121914436246669029Rat
2306789Ean6Experimental allergic neuritis QTL 64.9nervous system integrity trait (VT:0010566)experimental autoimmune neuritis severity score (CMO:0001528)121961087024139202Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)121961087040218516Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961087042828880Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)121961087046669029Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961088935682913Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121983578938193007Rat
631521Pia12Pristane induced arthritis QTL 128.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122025941723672083Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122032881946669029Rat


Related Rat Strains
The following Strains have been annotated to Gtf2i

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:305
Count of miRNA genes:118
Interacting mature miRNAs:138
Transcripts:ENSRNOT00000002020, ENSRNOT00000040356
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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001001512 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249170 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598365 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598369 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598370 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089535 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089536 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089537 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF547390 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF547391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC085815 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ294706 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ294707 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000002020   ⟹   ENSRNOP00000002020
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,401,465 - 22,476,234 (+)Ensembl
Rnor_6.0 Ensembl1225,430,464 - 25,487,966 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000040356   ⟹   ENSRNOP00000040835
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,401,481 - 22,476,234 (+)Ensembl
Rnor_6.0 Ensembl1225,411,292 - 25,487,978 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077189   ⟹   ENSRNOP00000073166
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,401,439 - 22,476,243 (+)Ensembl
Rnor_6.0 Ensembl1225,411,207 - 25,488,156 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092754
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1225,469,545 - 25,469,726 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092870
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1225,481,273 - 25,483,792 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092881
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1225,484,515 - 25,485,666 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092956   ⟹   ENSRNOP00000075949
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1225,450,286 - 25,462,426 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092982   ⟹   ENSRNOP00000075956
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,401,431 - 22,474,641 (+)Ensembl
Rnor_6.0 Ensembl1225,435,567 - 25,462,451 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092988
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1225,475,504 - 25,480,132 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092995
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1225,477,616 - 25,478,407 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098927   ⟹   ENSRNOP00000096595
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,401,439 - 22,476,243 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099403   ⟹   ENSRNOP00000076791
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,401,465 - 22,476,229 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099547   ⟹   ENSRNOP00000093772
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,468,422 - 22,476,232 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104703   ⟹   ENSRNOP00000080788
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,401,465 - 22,476,234 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000107220   ⟹   ENSRNOP00000077117
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,401,465 - 22,476,234 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109966   ⟹   ENSRNOP00000095456
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,401,465 - 22,476,234 (+)Ensembl
RefSeq Acc Id: NM_001001512   ⟹   NP_001001512
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,401,619 - 22,476,235 (+)NCBI
Rnor_6.01225,411,494 - 25,487,970 (+)NCBI
Rnor_5.01227,420,618 - 27,497,928 (+)NCBI
RGSC_v3.41223,470,042 - 23,545,621 (+)RGD
Celera1224,164,158 - 24,238,521 (+)RGD
Sequence:
RefSeq Acc Id: XM_006249170   ⟹   XP_006249232
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,401,413 - 22,476,243 (+)NCBI
Rnor_6.01225,411,297 - 25,487,970 (+)NCBI
Rnor_5.01227,420,618 - 27,497,928 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769141   ⟹   XP_008767363
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,400,933 - 22,476,243 (+)NCBI
Rnor_6.01225,410,804 - 25,487,970 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598360   ⟹   XP_017453849
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,420,772 - 22,476,243 (+)NCBI
Rnor_6.01225,430,459 - 25,487,970 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598361   ⟹   XP_017453850
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,420,772 - 22,476,243 (+)NCBI
Rnor_6.01225,430,459 - 25,487,970 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598362   ⟹   XP_017453851
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,420,772 - 22,476,243 (+)NCBI
Rnor_6.01225,430,459 - 25,487,970 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598363   ⟹   XP_017453852
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,420,772 - 22,476,243 (+)NCBI
Rnor_6.01225,430,459 - 25,487,970 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598365   ⟹   XP_017453854
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,420,772 - 22,476,243 (+)NCBI
Rnor_6.01225,430,459 - 25,487,970 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598366   ⟹   XP_017453855
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,420,772 - 22,476,243 (+)NCBI
Rnor_6.01225,430,459 - 25,487,970 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598368   ⟹   XP_017453857
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,420,772 - 22,476,243 (+)NCBI
Rnor_6.01225,430,459 - 25,487,970 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598369   ⟹   XP_017453858
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,420,772 - 22,476,243 (+)NCBI
Rnor_6.01225,430,459 - 25,487,970 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598370   ⟹   XP_017453859
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,420,772 - 22,476,243 (+)NCBI
Rnor_6.01225,430,459 - 25,487,970 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039089535   ⟹   XP_038945463
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,401,413 - 22,476,243 (+)NCBI
RefSeq Acc Id: XM_039089536   ⟹   XP_038945464
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,439,794 - 22,476,243 (+)NCBI
RefSeq Acc Id: XM_039089537   ⟹   XP_038945465
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,439,794 - 22,476,243 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001001512   ⟸   NM_001001512
- UniProtKB: Q5U2Y1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006249232   ⟸   XM_006249170
- Peptide Label: isoform X7
- UniProtKB: A0A0G2K4T7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008767363   ⟸   XM_008769141
- Peptide Label: isoform X7
- UniProtKB: A0A0G2K4T7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017453851   ⟸   XM_017598362
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017453849   ⟸   XM_017598360
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453852   ⟸   XM_017598363
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017453850   ⟸   XM_017598361
- Peptide Label: isoform X2
- UniProtKB: Q5U2Y1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017453854   ⟸   XM_017598365
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017453857   ⟸   XM_017598368
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017453855   ⟸   XM_017598366
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017453859   ⟸   XM_017598370
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017453858   ⟸   XM_017598369
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: ENSRNOP00000073166   ⟸   ENSRNOT00000077189
RefSeq Acc Id: ENSRNOP00000002020   ⟸   ENSRNOT00000002020
RefSeq Acc Id: ENSRNOP00000075956   ⟸   ENSRNOT00000092982
RefSeq Acc Id: ENSRNOP00000075949   ⟸   ENSRNOT00000092956
RefSeq Acc Id: ENSRNOP00000040835   ⟸   ENSRNOT00000040356
RefSeq Acc Id: XP_038945463   ⟸   XM_039089535
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038945464   ⟸   XM_039089536
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038945465   ⟸   XM_039089537
- Peptide Label: isoform X13
RefSeq Acc Id: ENSRNOP00000093772   ⟸   ENSRNOT00000099547
RefSeq Acc Id: ENSRNOP00000077117   ⟸   ENSRNOT00000107220
RefSeq Acc Id: ENSRNOP00000095456   ⟸   ENSRNOT00000109966
RefSeq Acc Id: ENSRNOP00000096595   ⟸   ENSRNOT00000098927
RefSeq Acc Id: ENSRNOP00000080788   ⟸   ENSRNOT00000104703
RefSeq Acc Id: ENSRNOP00000076791   ⟸   ENSRNOT00000099403

Transcriptome

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

Promoters
RGD ID:13698572
Promoter ID:EPDNEW_R9097
Type:initiation region
Name:Gtf2i_1
Description:general transcription factor II I
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_6.01225,411,337 - 25,411,397EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/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
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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
BN/SsN (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
BN/SsN (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
BUF/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
BXH2/CubMcwi (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
BXH3/CubMcwi (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
Buf/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
COP/CrCrl (MCW & UW)
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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)
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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
F344/DuCrl (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
F344/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
F344/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
F344/NCrl (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
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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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)
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)
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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)
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)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727961 AgrOrtholog
Ensembl Genes ENSRNOG00000001479 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002020 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000040835 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000073166 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075949 UniProtKB/TrEMBL
  ENSRNOP00000075956 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002020 UniProtKB/Swiss-Prot
  ENSRNOT00000040356 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000077189 UniProtKB/TrEMBL
  ENSRNOT00000092956 UniProtKB/TrEMBL
  ENSRNOT00000092982 UniProtKB/TrEMBL
Gene3D-CATH 3.90.1460.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7123295 IMAGE-MGC_LOAD
InterPro GTF2I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GTF2I-like_rpt_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TF_II-I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:353256 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94055 IMAGE-MGC_LOAD
NCBI Gene 353256 ENTREZGENE
Pfam GTF2I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Gtf2i PhenoGen
PIRSF TF_II-I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE GTF2I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF117773 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K4T7 ENTREZGENE, UniProtKB/TrEMBL
  A0A1B0GWM4_RAT UniProtKB/TrEMBL
  A0A1B0GWN0_RAT UniProtKB/TrEMBL
  GTF2I_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q80SX4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-07-08 Gtf2i  general transcription factor II I      Symbol and Name status set to approved 1299863 APPROVED