Fubp1 (far upstream element binding protein 1) - Rat Genome Database

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Gene: Fubp1 (far upstream element binding protein 1) Rattus norvegicus
Analyze
Symbol: Fubp1
Name: far upstream element binding protein 1
RGD ID: 1591892
Description: Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and mRNA binding activity. Involved in cellular response to lipopolysaccharide and positive regulation of Schwann cell migration. Located in nucleus. Biomarker of sciatic neuropathy. Orthologous to human FUBP1 (far upstream element binding protein 1); INTERACTS WITH (+)-schisandrin B; 2,4-dibromophenyl 2,4,5-tribromophenyl ether; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: far upstream element (FUSE) binding protein 1; far upstream element-binding protein 1; FBP; FUSE-binding protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22241,159,481 - 241,186,591 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2241,159,512 - 241,186,602 (+)Ensembl
Rnor_6.02257,425,676 - 257,452,745 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2257,425,679 - 257,449,568 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02276,102,238 - 276,129,492 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42250,749,095 - 250,777,521 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2233,094,240 - 233,117,161 (+)NCBICelera
Cytogenetic Map2q45NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP)
2,4-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper(II) chloride  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
finasteride  (EXP)
flutamide  (EXP)
folic acid  (ISO)
geraniol  (ISO)
hexadecanoic acid  (ISO)
hyaluronic acid  (EXP)
hydrogen peroxide  (EXP)
indometacin  (ISO)
ivermectin  (ISO)
ketamine  (EXP)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
miconazole  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nickel atom  (ISO)
ochratoxin A  (ISO)
oxaliplatin  (EXP)
paracetamol  (ISO)
pentachlorophenol  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
quinoline  (ISO)
rac-lactic acid  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
succimer  (ISO)
sunitinib  (ISO)
T-2 toxin  (EXP)
tamoxifen  (ISO)
tanespimycin  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
topotecan  (EXP)
trichostatin A  (ISO)
Triptolide  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IDA,ISO)
synapse  (ISO)

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:16452087   PMID:18836447   PMID:19087307   PMID:22658674   PMID:22681889   PMID:26095368  


Genomics

Comparative Map Data
Fubp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22241,159,481 - 241,186,591 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2241,159,512 - 241,186,602 (+)Ensembl
Rnor_6.02257,425,676 - 257,452,745 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2257,425,679 - 257,449,568 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02276,102,238 - 276,129,492 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42250,749,095 - 250,777,521 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2233,094,240 - 233,117,161 (+)NCBICelera
Cytogenetic Map2q45NCBI
FUBP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl177,944,055 - 77,979,110 (-)EnsemblGRCh38hg38GRCh38
GRCh38177,944,055 - 77,979,435 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37178,409,740 - 78,444,756 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36178,186,179 - 78,217,365 (-)NCBINCBI36hg18NCBI36
Build 34178,126,110 - 78,156,735NCBI
Celera176,652,669 - 76,683,855 (-)NCBI
Cytogenetic Map1p31.1NCBI
HuRef176,545,210 - 76,576,401 (-)NCBIHuRef
CHM1_1178,529,931 - 78,561,136 (-)NCBICHM1_1
Fubp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393151,916,059 - 151,942,467 (+)NCBIGRCm39mm39
GRCm39 Ensembl3151,916,059 - 151,942,463 (+)Ensembl
GRCm383152,210,422 - 152,236,830 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3152,210,422 - 152,236,826 (+)EnsemblGRCm38mm10GRCm38
MGSCv373151,873,422 - 151,899,794 (+)NCBIGRCm37mm9NCBIm37
MGSCv363152,147,907 - 152,174,212 (+)NCBImm8
Celera3158,688,293 - 158,714,689 (+)NCBICelera
Cytogenetic Map3H3NCBI
cM Map377.05NCBI
Fubp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542315,245,610 - 15,278,628 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542315,245,645 - 15,278,628 (+)NCBIChiLan1.0ChiLan1.0
FUBP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1179,244,892 - 79,280,448 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0177,162,675 - 77,198,486 (-)NCBIMhudiblu_PPA_v0panPan3
FUBP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1668,923,215 - 68,963,766 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha671,580,919 - 71,621,261 (+)NCBI
ROS_Cfam_1.0669,508,282 - 69,548,642 (+)NCBI
UMICH_Zoey_3.1669,015,218 - 69,054,818 (+)NCBI
UNSW_CanFamBas_1.0668,959,769 - 69,000,118 (+)NCBI
UU_Cfam_GSD_1.0669,446,187 - 69,486,514 (+)NCBI
Fubp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505889,218,777 - 89,250,519 (-)NCBI
SpeTri2.0NW_0049365714,729,135 - 4,760,943 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FUBP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6135,281,521 - 135,318,714 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16135,281,474 - 135,319,055 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26125,463,226 - 125,500,521 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FUBP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12055,194,681 - 55,233,666 (+)NCBI
ChlSab1.12055,194,681 - 55,233,666 (+)NCBI
ChlSab1.12055,194,681 - 55,233,666 (+)NCBI
ChlSab1.12055,194,681 - 55,233,666 (+)NCBI
ChlSab1.1 Ensembl2055,194,743 - 55,230,277 (+)Ensembl
Vero_WHO_p1.0NW_02366603362,279,926 - 62,320,345 (-)NCBI
Fubp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474219,279,544 - 19,313,139 (+)NCBI

Position Markers
D2Rat106  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22241,180,224 - 241,180,458 (+)MAPPERmRatBN7.2
Rnor_6.02257,446,379 - 257,446,612NCBIRnor6.0
Rnor_5.02276,123,126 - 276,123,359UniSTSRnor5.0
RGSC_v3.42250,755,359 - 250,755,592UniSTSRGSC3.4
RGSC_v3.42250,755,328 - 250,755,690RGDRGSC3.4
RGSC_v3.12250,769,966 - 250,770,199RGD
Celera2233,114,890 - 233,115,123UniSTS
RH 3.4 Map21650.32RGD
RH 3.4 Map21650.32UniSTS
RH 2.0 Map21224.5RGD
SHRSP x BN Map2110.2099RGD
FHH x ACI Map2112.8599RGD
Cytogenetic Map2q45UniSTS
RH130397  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22226,377,844 - 226,378,048 (+)MAPPERmRatBN7.2
mRatBN7.22241,186,236 - 241,186,430 (+)MAPPERmRatBN7.2
Rnor_6.02257,452,391 - 257,452,584NCBIRnor6.0
Rnor_6.02243,127,299 - 243,127,502NCBIRnor6.0
Rnor_5.02276,129,138 - 276,129,331UniSTSRnor5.0
Rnor_5.02261,675,035 - 261,675,238UniSTSRnor5.0
RGSC_v3.42235,375,102 - 235,375,305UniSTSRGSC3.4
RGSC_v3.42250,760,862 - 250,761,055UniSTSRGSC3.4
Celera2233,120,904 - 233,121,097UniSTS
Celera2218,544,327 - 218,544,530UniSTS
RH 3.4 Map21607.5UniSTS
Cytogenetic Map2q44UniSTS
Cytogenetic Map2q45UniSTS
AA799423  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22241,186,902 - 241,186,998 (+)MAPPERmRatBN7.2
Rnor_6.02257,453,057 - 257,453,152NCBIRnor6.0
Rnor_5.02276,129,804 - 276,129,899UniSTSRnor5.0
RGSC_v3.42250,761,528 - 250,761,623UniSTSRGSC3.4
Celera2233,121,570 - 233,121,665UniSTS
RH 3.4 Map21650.31UniSTS
Cytogenetic Map2q45UniSTS
A62227834FB73  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22241,184,233 - 241,185,481 (+)MAPPERmRatBN7.2
mRatBN7.22241,184,233 - 241,185,515 (+)MAPPERmRatBN7.2
Rnor_6.02257,450,388 - 257,451,669NCBIRnor6.0
Rnor_6.02257,450,388 - 257,451,635NCBIRnor6.0
Rnor_5.02276,127,135 - 276,128,416UniSTSRnor5.0
Rnor_5.02276,127,135 - 276,128,382UniSTSRnor5.0
RGSC_v3.42250,758,861 - 250,760,106UniSTSRGSC3.4
RGSC_v3.42250,758,861 - 250,760,140UniSTSRGSC3.4
Celera2233,118,899 - 233,120,182UniSTS
Celera2233,118,899 - 233,120,146UniSTS
Cytogenetic Map2q45UniSTS
UniSTS:234848  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22241,183,678 - 241,183,917 (+)MAPPERmRatBN7.2
Rnor_6.02257,449,833 - 257,450,071NCBIRnor6.0
Rnor_5.02276,126,580 - 276,126,818UniSTSRnor5.0
RGSC_v3.42250,758,306 - 250,758,544UniSTSRGSC3.4
Celera2233,118,344 - 233,118,582UniSTS
Cytogenetic Map2q45UniSTS
FUBP1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22241,182,320 - 241,182,476 (+)MAPPERmRatBN7.2
Rnor_6.02257,448,475 - 257,448,630NCBIRnor6.0
Rnor_5.02276,125,222 - 276,125,377UniSTSRnor5.0
Celera2233,116,986 - 233,117,141UniSTS
Cytogenetic Map2q45UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2211744537249053267Rat
631563Hcuc3Hepatic copper content QTL 33.87hepatic copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)2229059610249053267Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2212828222249053267Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2214226044247136170Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2200990457245990457Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2211744537249053267Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2193452645245889826Rat
9587428Epfw6Epididymal fat weight QTL 67.470.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)2223389739249053267Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2211744537249053267Rat
7411555Bw132Body weight QTL 1320.001body mass (VT:0001259)body weight gain (CMO:0000420)2223389739249053267Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2211744537249053267Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2211744537249053267Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:61
Count of miRNA genes:43
Interacting mature miRNAs:56
Transcripts:ENSRNOT00000066199
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 52 36 19 36 8 8 74 35 41 11 8
Low 5 5 5 3
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001037653 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233507 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233511 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233512 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233513 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761553 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761554 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761555 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761556 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761557 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103100 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103101 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103102 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103105 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103106 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103107 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103108 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103109 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103110 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103111 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103113 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001836493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001836494 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005500367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005500368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_591394 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC107942 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226465 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000079 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000066199   ⟹   ENSRNOP00000061544
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2241,159,528 - 241,182,495 (+)Ensembl
Rnor_6.0 Ensembl2257,425,679 - 257,449,568 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094623   ⟹   ENSRNOP00000077531
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2241,159,512 - 241,186,602 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000110491   ⟹   ENSRNOP00000095243
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2241,159,512 - 241,182,511 (+)Ensembl
RefSeq Acc Id: NM_001037653   ⟹   NP_001032742
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,576 - 241,182,496 (+)NCBI
Rnor_6.02257,425,729 - 257,448,650 (+)NCBI
Rnor_5.02276,102,238 - 276,129,492 (+)NCBI
RGSC_v3.42250,749,095 - 250,777,521 (+)RGD
Celera2233,094,240 - 233,117,161 (+)RGD
Sequence:
RefSeq Acc Id: XM_006233507   ⟹   XP_006233569
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
Rnor_6.02257,425,691 - 257,452,745 (+)NCBI
Rnor_5.02276,102,238 - 276,129,492 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233511   ⟹   XP_006233573
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
Rnor_6.02257,425,692 - 257,452,745 (+)NCBI
Rnor_5.02276,102,238 - 276,129,492 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233512   ⟹   XP_006233574
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
Rnor_6.02257,425,692 - 257,452,745 (+)NCBI
Rnor_5.02276,102,238 - 276,129,492 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233513   ⟹   XP_006233575
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
Rnor_6.02257,425,692 - 257,452,745 (+)NCBI
Rnor_5.02276,102,238 - 276,129,492 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008761555   ⟹   XP_008759777
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
Rnor_6.02257,425,692 - 257,452,745 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008761556   ⟹   XP_008759778
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
Rnor_6.02257,425,692 - 257,452,745 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039103100   ⟹   XP_038959028
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
RefSeq Acc Id: XM_039103101   ⟹   XP_038959029
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
RefSeq Acc Id: XM_039103102   ⟹   XP_038959030
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
RefSeq Acc Id: XM_039103103   ⟹   XP_038959031
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
RefSeq Acc Id: XM_039103105   ⟹   XP_038959033
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
RefSeq Acc Id: XM_039103106   ⟹   XP_038959034
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
RefSeq Acc Id: XM_039103107   ⟹   XP_038959035
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
RefSeq Acc Id: XM_039103108   ⟹   XP_038959036
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
RefSeq Acc Id: XM_039103109   ⟹   XP_038959037
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
RefSeq Acc Id: XM_039103110   ⟹   XP_038959038
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
RefSeq Acc Id: XM_039103111   ⟹   XP_038959039
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
RefSeq Acc Id: XM_039103113   ⟹   XP_038959041
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
RefSeq Acc Id: XR_005500367
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
RefSeq Acc Id: XR_005500368
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
RefSeq Acc Id: XR_591394
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22241,159,481 - 241,186,591 (+)NCBI
Rnor_6.02257,425,691 - 257,452,745 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001032742   ⟸   NM_001037653
- UniProtKB: Q32PX7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006233569   ⟸   XM_006233507
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_006233573   ⟸   XM_006233511
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_006233574   ⟸   XM_006233512
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_006233575   ⟸   XM_006233513
- Peptide Label: isoform X18
- Sequence:
RefSeq Acc Id: XP_008759777   ⟸   XM_008761555
- Peptide Label: isoform X16
- Sequence:
RefSeq Acc Id: XP_008759778   ⟸   XM_008761556
- Peptide Label: isoform X17
- Sequence:
RefSeq Acc Id: ENSRNOP00000061544   ⟸   ENSRNOT00000066199
RefSeq Acc Id: XP_038959028   ⟸   XM_039103100
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038959033   ⟸   XM_039103105
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038959030   ⟸   XM_039103102
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038959039   ⟸   XM_039103111
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038959029   ⟸   XM_039103101
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038959038   ⟸   XM_039103110
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038959041   ⟸   XM_039103113
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038959031   ⟸   XM_039103103
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038959034   ⟸   XM_039103106
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038959036   ⟸   XM_039103108
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038959035   ⟸   XM_039103107
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038959037   ⟸   XM_039103109
- Peptide Label: isoform X10
RefSeq Acc Id: ENSRNOP00000077531   ⟸   ENSRNOT00000094623
RefSeq Acc Id: ENSRNOP00000095243   ⟸   ENSRNOT00000110491
Protein Domains
KH

Transcriptome

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

Promoters
RGD ID:13691824
Promoter ID:EPDNEW_R2349
Type:initiation region
Name:Fubp1_1
Description:far upstream element binding protein 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02257,425,679 - 257,425,739EPDNEW

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)
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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)
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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
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)
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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/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)
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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
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)
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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/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)
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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
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:1591892 AgrOrtholog
Ensembl Genes ENSRNOG00000043370 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061544 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066199 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.1370.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7389449 IMAGE-MGC_LOAD
InterPro FUBP_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KH_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KH_dom_type_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KH_dom_type_1_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:654496 UniProtKB/Swiss-Prot
MGC_CLONE MGC:125009 IMAGE-MGC_LOAD
NCBI Gene 654496 ENTREZGENE
Pfam DUF1897 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KH_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Fubp1 PhenoGen
PROSITE KH_TYPE_1 UniProtKB/Swiss-Prot
SMART SM00322 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54791 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A140TAJ3_RAT UniProtKB/TrEMBL
  FUBP1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Fubp1  far upstream element binding protein 1  Fubp1  far upstream element (FUSE) binding protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-11 Fubp1  far upstream element binding protein 1  Fubp1  far upstream element binding protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 Fubp1  far upstream element (FUSE) binding protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL