Ppat (phosphoribosyl pyrophosphate amidotransferase) - Rat Genome Database

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Gene: Ppat (phosphoribosyl pyrophosphate amidotransferase) Rattus norvegicus
Analyze
Symbol: Ppat
Name: phosphoribosyl pyrophosphate amidotransferase
RGD ID: 620237
Description: Exhibits amidophosphoribosyltransferase activity and identical protein binding activity. Involved in several processes, including animal organ development; cellular response to insulin stimulus; and glutamine catabolic process. Biomarker of hepatocellular carcinoma and renal cell carcinoma. Orthologous to human PPAT (phosphoribosyl pyrophosphate amidotransferase); PARTICIPATES IN 2-hydroxyglutaric aciduria pathway; adenine phoshoribosyltransferase deficiency pathway; adenosine monophosphate deaminase deficiency pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: amidophosphoribosyltransferase; Atase; glutamine phosphoribosylpyrophosphate amidotransferase; GPAT; MGC93251
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
mRatBN7.21431,215,741 - 31,250,144 (+)NCBI
Rnor_6.0 Ensembl1433,580,541 - 33,614,919 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01433,580,541 - 33,614,919 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01433,371,454 - 33,405,854 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41433,509,364 - 33,543,743 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11433,509,363 - 33,543,743 (+)NCBI
Celera1430,529,492 - 30,563,868 (+)NCBICelera
Cytogenetic Map14p11NCBI
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
References

Additional References at PubMed
PMID:12477932   PMID:15489334  


Genomics

Comparative Map Data
Ppat
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21431,215,741 - 31,250,144 (+)NCBI
Rnor_6.0 Ensembl1433,580,541 - 33,614,919 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01433,580,541 - 33,614,919 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01433,371,454 - 33,405,854 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41433,509,364 - 33,543,743 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11433,509,363 - 33,543,743 (+)NCBI
Celera1430,529,492 - 30,563,868 (+)NCBICelera
Cytogenetic Map14p11NCBI
PPAT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl456,393,362 - 56,435,615 (-)EnsemblGRCh38hg38GRCh38
GRCh38456,393,362 - 56,435,615 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37457,259,528 - 57,301,781 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36456,954,285 - 56,996,602 (-)NCBINCBI36hg18NCBI36
Build 34457,100,458 - 57,142,773NCBI
Celera454,765,911 - 54,808,216 (-)NCBI
Cytogenetic Map4q12NCBI
HuRef453,213,663 - 53,255,937 (-)NCBIHuRef
CHM1_1457,294,641 - 57,336,915 (-)NCBICHM1_1
Ppat
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39577,061,096 - 77,099,425 (-)NCBIGRCm39mm39
GRCm39 Ensembl577,061,096 - 77,099,425 (-)Ensembl
GRCm38576,913,249 - 76,951,578 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl576,913,249 - 76,951,578 (-)EnsemblGRCm38mm10GRCm38
MGSCv37577,342,274 - 77,380,603 (-)NCBIGRCm37mm9NCBIm37
MGSCv36577,987,920 - 78,026,353 (-)NCBImm8
Celera574,190,125 - 74,219,445 (-)NCBICelera
Cytogenetic Map5C3.3NCBI
Ppat
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544714,574,407 - 14,607,416 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544714,552,846 - 14,607,416 (+)NCBIChiLan1.0ChiLan1.0
PPAT
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1474,059,967 - 74,102,002 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl474,059,966 - 74,102,002 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0467,491,407 - 67,533,822 (+)NCBIMhudiblu_PPA_v0panPan3
PPAT
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11348,618,460 - 48,656,164 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1348,620,714 - 48,655,780 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1348,509,175 - 48,546,691 (-)NCBI
ROS_Cfam_1.01349,233,071 - 49,270,374 (-)NCBI
UMICH_Zoey_3.11348,904,984 - 48,942,482 (-)NCBI
UNSW_CanFamBas_1.01348,433,951 - 48,471,441 (-)NCBI
UU_Cfam_GSD_1.01349,380,077 - 49,417,387 (-)NCBI
Ppat
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528527,649,519 - 27,693,748 (+)NCBI
SpeTri2.0NW_00493648218,606,124 - 18,648,989 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PPAT
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl855,652,201 - 55,701,077 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1855,652,194 - 55,701,077 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2857,820,418 - 57,896,880 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PPAT
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1712,201,434 - 12,242,418 (+)NCBI
ChlSab1.1 Ensembl712,191,784 - 12,243,488 (+)Ensembl
Ppat
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476112,980,508 - 13,017,818 (+)NCBI

Position Markers
RH141568  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21431,249,660 - 31,249,860 (+)MAPPER
Rnor_6.01433,614,458 - 33,614,657NCBIRnor6.0
Rnor_5.01433,405,371 - 33,405,570UniSTSRnor5.0
RGSC_v3.41433,543,282 - 33,543,481UniSTSRGSC3.4
Celera1430,563,407 - 30,563,606UniSTS
RH 3.4 Map14382.98UniSTS
Cytogenetic Map14p11UniSTS
PMC312758P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21431,216,183 - 31,216,360 (+)MAPPER
Rnor_6.01433,580,984 - 33,581,160NCBIRnor6.0
Rnor_5.01433,371,897 - 33,372,073UniSTSRnor5.0
RGSC_v3.41433,509,807 - 33,509,983UniSTSRGSC3.4
Celera1430,529,935 - 30,530,111UniSTS
Cytogenetic Map14p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14134403399Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14141333960Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14141333960Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14142766285Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14975643572854397Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin141053997755539977Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)141053997755539977Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)141072926861873323Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
631528Scl11Serum cholesterol level QTL 114.9blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)141915991938289187Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141916189343957503Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141919154143957628Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)142018938665189386Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)142026622343957628Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)142145756566457565Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143259392686191589Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143303991261783215Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143316331673391571Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1313
Count of miRNA genes:350
Interacting mature miRNAs:483
Transcripts:ENSRNOT00000002905
Prediction methods:Microtar, Miranda, 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 57 41 19 41 8 10 74 35 35 11 8
Low 1 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002905   ⟹   ENSRNOP00000002905
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1433,580,541 - 33,614,919 (+)Ensembl
RefSeq Acc Id: NM_057198   ⟹   NP_476546
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,215,741 - 31,250,122 (+)NCBI
Rnor_6.01433,580,541 - 33,614,919 (+)NCBI
Rnor_5.01433,371,454 - 33,405,854 (+)NCBI
RGSC_v3.41433,509,364 - 33,543,743 (+)RGD
Celera1430,529,492 - 30,563,868 (+)RGD
Sequence:
RefSeq Acc Id: XM_039091566   ⟹   XP_038947494
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,216,234 - 31,250,144 (+)NCBI
RefSeq Acc Id: XM_039091567   ⟹   XP_038947495
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,232,734 - 31,250,144 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_476546   ⟸   NM_057198
- UniProtKB: P35433 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002905   ⟸   ENSRNOT00000002905
RefSeq Acc Id: XP_038947494   ⟸   XM_039091566
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947495   ⟸   XM_039091567
- Peptide Label: isoform X2
Transcriptome

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

Promoters
RGD ID:13699271
Promoter ID:EPDNEW_R9796
Type:single initiation site
Name:Ppat_1
Description:phosphoribosyl pyrophosphate amidotransferase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R9798  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01433,580,527 - 33,580,587EPDNEW
RGD ID:13699273
Promoter ID:EPDNEW_R9798
Type:initiation region
Name:Ppat_2
Description:phosphoribosyl pyrophosphate amidotransferase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R9796  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01433,580,995 - 33,581,055EPDNEW

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)
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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
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 (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 (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
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 (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 (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/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 (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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 33372027 33372028 A G snv NIG-III/Hok (KyushuU)
14 33375605 33375606 A T snv COP/CrCrl (MCW & UW), Crl:SD (UDEL), LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL), WN/N (KNAW), MNS/Gib (KNAW), M520/N (KNAW), LEW/NCrl (KNAW), LEW/Crl (KNAW), GK/Ox (KNAW), FHL/EurMcwi (KNAW), FHH/EurMcwi (KNAW), F344/NHsd (KNAW), F344/NCrl (KNAW), F344/NRrrc (SOLiD) (KNAW), BUF/N (KNAW), WKY/NHsd (KNAW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SS/JrHsdMcwi (MCW), LL/MavRrrc (KNAW), MHS/Gib (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), WAG/Rij (KNAW), BBDP/WorN (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW)
14 33388086 33388087 A G snv ACI/EurMcwi (MCW), BDIX.Cg-Tal/NemOda (KyushuU), DOB/Oda (KyushuU), SR/JrHsd (KNAW), MR/N (KNAW), SBN/Ygl (KNAW), LN/MavRrrc (KNAW), SBH/Ygl (KNAW), LH/MavRrrc (KNAW), BDIX/NemOda (KyushuU), SR/JrHsd (MCW), SBN/Ygl (MCW), ACI/EurMcwi (KNAW), ACI/N (KNAW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), Crl:SD (UDEL)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 33584692 33584693 A T snv COP/CrCrl (MCW & UW), WKY/Gcrc (RGD), FHL/EurMcwi (MCW), SS/JrHsdMcwi (MCW), CDR, Buf/N (MCW), F344/NRrrc (MCW), M520/N (MCW), WKY/N (MCW), WN/N (MCW), FHL/EurMcwi (RGD), BBDP/Wor (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), GK/Ox (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), LL/MavRrrc (RGD), MHS/Gib (RGD), MNS/Gib (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WAG/Rij (RGD), WKY/NCrl (RGD), FHH/EurMcwi (MCW)
14 33587989 33587990 T G snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), CDR, CDS, ACI/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), M520/N (MCW), MR/N (MCW), WKY/N (MCW), WN/N (MCW), FHL/EurMcwi (RGD), ACI/EurMcwi (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), GK/Ox (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), MHS/Gib (RGD), MNS/Gib (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), SR/JrHsd (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WAG/Rij (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), WKY/NHsd (RGD)
14 33597173 33597174 A G snv ACI/EurMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), CDS, SR/JrHsd (RGD), MR/N (MCW), ACI/EurMcwi (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), ACI/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620237 AgrOrtholog
Ensembl Genes ENSRNOG00000002128 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000002905 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000002905 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7189259 IMAGE-MGC_LOAD
InterPro GATase_2_dom UniProtKB/Swiss-Prot
  Ntn_hydrolases_N UniProtKB/Swiss-Prot
  PRibTrfase_dom UniProtKB/Swiss-Prot
  PRTase-like UniProtKB/Swiss-Prot
  PurF UniProtKB/Swiss-Prot
  PurF_N UniProtKB/Swiss-Prot
KEGG Report rno:117544 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93251 IMAGE-MGC_LOAD
NCBI Gene 117544 ENTREZGENE
PharmGKB PPAT RGD
PhenoGen Ppat PhenoGen
PIRSF Amd_phspho_trans UniProtKB/Swiss-Prot
PROSITE GATASE_TYPE_2 UniProtKB/Swiss-Prot
  PUR_PYR_PR_TRANSFER UniProtKB/Swiss-Prot
Superfamily-SCOP SSF53271 UniProtKB/Swiss-Prot
  SSF56235 UniProtKB/Swiss-Prot
TIGRFAMs purF UniProtKB/Swiss-Prot
UniProt P35433 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Ppat  phosphoribosyl pyrophosphate amidotransferase      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Ppat  phosphoribosyl pyrophosphate amidotransferase      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression ubiquitously expressed; enriched in brain, heart, liver, and stomach 633710
gene_protein 517 amino acids; 57.4 kDa 633710