Upp1 (uridine phosphorylase 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Upp1 (uridine phosphorylase 1) Rattus norvegicus
Analyze
Symbol: Upp1
Name: uridine phosphorylase 1
RGD ID: 1305566
Description: Predicted to have identical protein binding activity and transferase activity, transferring pentosyl groups. Involved in cellular response to glucose starvation. Predicted to localize to cytosol and nucleoplasm. Biomarker of middle cerebral artery infarction. Orthologous to human UPP1 (uridine phosphorylase 1); PARTICIPATES IN pyrimidine metabolic pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,4-dinitrotoluene; 4-(ethoxymethylene)-2-phenyloxazol-5-one.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC289801; MGC124655
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21483,809,495 - 83,829,299 (+)NCBI
Rnor_6.0 Ensembl1489,314,176 - 89,334,276 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01489,314,234 - 89,334,060 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01489,112,302 - 89,132,102 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41489,651,264 - 89,669,630 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11489,669,068 - 89,688,775 (+)NCBI
Celera1482,846,265 - 82,864,631 (+)NCBICelera
Cytogenetic Map14q21NCBI
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
(S)-nicotine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-diaminotoluene  (ISO)
2,4-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-benzyl-1-(2-hydroxyethoxymethyl)uracil  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aconitine  (EXP)
adenosine  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
bicalutamide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A5  (ISO)
bortezomib  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
calciol  (ISO)
calyculin a  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
cefaloridine  (EXP)
chloropicrin  (ISO)
chloroprene  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
crotonaldehyde  (ISO)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
cytidine  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dioxygen  (ISO)
diquat  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxifluridine  (ISO)
doxorubicin  (ISO)
endosulfan  (ISO)
ethanol  (ISO)
formaldehyde  (ISO)
guanosine  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
indometacin  (ISO)
manganese(II) chloride  (EXP)
menadione  (ISO)
mercury dichloride  (EXP)
methamphetamine  (EXP)
methotrexate  (ISO)
methylmercury chloride  (EXP,ISO)
methylparaben  (ISO)
Monobutylphthalate  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-methyl-N-nitrosourea  (EXP,ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
nicotine  (ISO)
obeticholic acid  (ISO)
oxaliplatin  (EXP)
paracetamol  (ISO)
pentobarbital  (ISO)
perfluorononanoic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
pyrimidine  (ISO)
rac-lactic acid  (ISO)
resveratrol  (EXP)
SB 431542  (ISO)
SCH 23390  (EXP)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
succimer  (ISO)
sulforaphane  (ISO)
sulindac sulfide  (ISO)
tert-butyl hydroperoxide  (ISO)
thalidomide  (ISO)
thimerosal  (ISO)
topotecan  (EXP)
tributylstannane  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (EXP)
Triptolide  (EXP)
tris(2-butoxyethyl) phosphate  (ISO)
trovafloxacin  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
uridine  (ISO)
valproic acid  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytosol  (ISO)
nucleoplasm  (IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:7488099   PMID:7744869   PMID:12477932   PMID:15772079   PMID:19291308   PMID:20856879   PMID:23355744  


Genomics

Comparative Map Data
Upp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21483,809,495 - 83,829,299 (+)NCBI
Rnor_6.0 Ensembl1489,314,176 - 89,334,276 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01489,314,234 - 89,334,060 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01489,112,302 - 89,132,102 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41489,651,264 - 89,669,630 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11489,669,068 - 89,688,775 (+)NCBI
Celera1482,846,265 - 82,864,631 (+)NCBICelera
Cytogenetic Map14q21NCBI
UPP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl748,088,628 - 48,108,736 (+)EnsemblGRCh38hg38GRCh38
GRCh38748,088,308 - 48,108,736 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37748,128,301 - 48,148,333 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36748,094,880 - 48,114,855 (+)NCBINCBI36hg18NCBI36
Celera748,227,538 - 48,247,515 (+)NCBI
Cytogenetic Map7p12.3NCBI
HuRef748,013,948 - 48,033,924 (+)NCBIHuRef
CHM1_1748,131,900 - 48,152,030 (+)NCBICHM1_1
CRA_TCAGchr7v2748,168,224 - 48,188,201 (+)NCBI
Upp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39119,068,008 - 9,086,170 (+)NCBIGRCm39mm39
GRCm39 Ensembl119,068,103 - 9,086,170 (+)Ensembl
GRCm38119,118,008 - 9,136,170 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl119,118,103 - 9,136,170 (+)EnsemblGRCm38mm10GRCm38
MGSCv37119,018,011 - 9,036,173 (+)NCBIGRCm37mm9NCBIm37
MGSCv36119,018,106 - 9,036,167 (+)NCBImm8
Celera119,551,715 - 9,569,878 (+)NCBICelera
Cytogenetic Map11A1NCBI
Upp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554565,365,877 - 5,385,336 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554565,365,912 - 5,385,336 (-)NCBIChiLan1.0ChiLan1.0
UPP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1748,838,901 - 48,858,189 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl748,838,893 - 48,858,185 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0748,729,975 - 48,749,598 (+)NCBIMhudiblu_PPA_v0panPan3
UPP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.118108,215 - 120,213 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1867,812 - 89,151 (+)NCBI
ROS_Cfam_1.018133,593 - 154,855 (+)NCBI
UMICH_Zoey_3.118108,433 - 129,715 (+)NCBI
UNSW_CanFamBas_1.018111,361 - 132,570 (+)NCBI
UU_Cfam_GSD_1.018246,479 - 267,730 (+)NCBI
Upp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118103,296,840 - 103,319,396 (+)NCBI
SpeTri2.0NW_00493647822,508,602 - 22,531,604 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UPP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1848,418,385 - 48,440,736 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11848,418,385 - 48,440,414 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
UPP1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12110,686,600 - 10,707,181 (-)NCBI
ChlSab1.1 Ensembl2110,686,093 - 10,706,347 (-)Ensembl
Upp1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247405,517,387 - 5,531,594 (-)NCBI

Position Markers
RH131849  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01489,333,857 - 89,334,044NCBIRnor6.0
Rnor_5.01489,131,899 - 89,132,086UniSTSRnor5.0
RGSC_v3.41489,669,431 - 89,669,618UniSTSRGSC3.4
Celera1482,864,432 - 82,864,619UniSTS
RH 3.4 Map14617.2UniSTS
Cytogenetic Map14q21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1442442731108833671Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1443910761105074364Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1451818462105074364Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1460980905105980905Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1460980905105980905Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1461993178106993178Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1463548095108548095Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)1478172765102549388Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1478172765102549388Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765106641756Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1478446303110402569Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1480049285115493446Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1480049285115493446Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)1485307663106641756Rat
4889951Bss92Bone structure and strength QTL 923.9tibia area (VT:1000281)tibia-fibula cortical bone total cross-sectional area (CMO:0001721)1487458772106641756Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:82
Count of miRNA genes:71
Interacting mature miRNAs:73
Transcripts:ENSRNOT00000006765
Prediction methods:Microtar, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 18 8 11
Low 1 25 57 41 19 41 8 11 68 35 32 8
Below cutoff 6 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006765   ⟹   ENSRNOP00000006765
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1489,314,176 - 89,334,276 (+)Ensembl
RefSeq Acc Id: NM_001030025   ⟹   NP_001025196
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21483,810,924 - 83,829,292 (+)NCBI
Rnor_6.01489,315,690 - 89,334,056 (+)NCBI
Rnor_5.01489,112,302 - 89,132,102 (+)NCBI
RGSC_v3.41489,651,264 - 89,669,630 (+)RGD
Celera1482,846,265 - 82,864,631 (+)RGD
Sequence:
RefSeq Acc Id: XM_006251483   ⟹   XP_006251545
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21483,809,830 - 83,829,299 (+)NCBI
Rnor_6.01489,314,520 - 89,334,060 (+)NCBI
Rnor_5.01489,112,302 - 89,132,102 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006251484   ⟹   XP_006251546
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21483,809,584 - 83,829,299 (+)NCBI
Rnor_6.01489,314,234 - 89,334,060 (+)NCBI
Rnor_5.01489,112,302 - 89,132,102 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006251485   ⟹   XP_006251547
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21483,809,552 - 83,829,299 (+)NCBI
Rnor_6.01489,314,234 - 89,334,060 (+)NCBI
Rnor_5.01489,112,302 - 89,132,102 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006251487   ⟹   XP_006251549
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21483,809,817 - 83,829,299 (+)NCBI
Rnor_6.01489,314,520 - 89,334,060 (+)NCBI
Rnor_5.01489,112,302 - 89,132,102 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008770270   ⟹   XP_008768492
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01489,314,901 - 89,334,060 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599126   ⟹   XP_017454615
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01489,315,106 - 89,334,060 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039091760   ⟹   XP_038947688
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21483,809,495 - 83,829,299 (+)NCBI
RefSeq Acc Id: XM_039091762   ⟹   XP_038947690
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21483,809,595 - 83,829,299 (+)NCBI
RefSeq Acc Id: XM_039091763   ⟹   XP_038947691
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21483,809,820 - 83,829,299 (+)NCBI
RefSeq Acc Id: XM_039091764   ⟹   XP_038947692
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21483,809,550 - 83,829,299 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001025196   ⟸   NM_001030025
- UniProtKB: Q499V1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251546   ⟸   XM_006251484
- Peptide Label: isoform X1
- UniProtKB: Q499V1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251547   ⟸   XM_006251485
- Peptide Label: isoform X1
- UniProtKB: Q499V1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251549   ⟸   XM_006251487
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006251545   ⟸   XM_006251483
- Peptide Label: isoform X1
- UniProtKB: Q499V1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008768492   ⟸   XM_008770270
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017454615   ⟸   XM_017599126
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000006765   ⟸   ENSRNOT00000006765
RefSeq Acc Id: XP_038947688   ⟸   XM_039091760
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947692   ⟸   XM_039091764
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947690   ⟸   XM_039091762
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947691   ⟸   XM_039091763
- Peptide Label: isoform X1
Protein Domains
PNP_UDP_1

Transcriptome

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

Promoters
RGD ID:13699490
Promoter ID:EPDNEW_R10013
Type:single initiation site
Name:Upp1_2
Description:uridine phosphorylase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10014  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01489,314,249 - 89,314,309EPDNEW
RGD ID:13699491
Promoter ID:EPDNEW_R10014
Type:multiple initiation site
Name:Upp1_1
Description:uridine phosphorylase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10013  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01489,314,861 - 89,314,921EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 89127035 89127036 G A snv HTX/Kyo (KyushuU)
14 89131899 89131900 T G snv SR/JrHsd (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 89328993 89328994 G A snv MR/N (MCW)
14 89333953 89333954 T G snv F344/NCrl (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 89664567 89664568 G A snv MR/N (KNAW)
14 89669431 89669432 T G snv SR/JrHsd (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305566 AgrOrtholog
Ensembl Genes ENSRNOG00000004972 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006765 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006765 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.1580 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5623209 IMAGE-MGC_LOAD
InterPro Nucleoside_phosphorylase UniProtKB/TrEMBL
  Nucleoside_phosphorylase_CS UniProtKB/TrEMBL
  Nucleoside_phosphorylase_sf UniProtKB/TrEMBL
  Uridine_phosphorylase_euk UniProtKB/TrEMBL
KEGG Report rno:289801 UniProtKB/TrEMBL
MGC_CLONE MGC:124655 IMAGE-MGC_LOAD
NCBI Gene 289801 ENTREZGENE
Pfam PNP_UDP_1 UniProtKB/TrEMBL
PharmGKB UPP1 RGD
PhenoGen Upp1 PhenoGen
PROSITE PNP_UDP_1 UniProtKB/TrEMBL
Superfamily-SCOP SSF53167 UniProtKB/TrEMBL
TIGRFAMs euk_UDPppase UniProtKB/TrEMBL
UniProt Q499V1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Upp1  uridine phosphorylase 1  Upp1_predicted  uridine phosphorylase 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Upp1_predicted  uridine phosphorylase 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED