Ppia (peptidylprolyl isomerase A) - Rat Genome Database

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Gene: Ppia (peptidylprolyl isomerase A) Rattus norvegicus
Analyze
Symbol: Ppia
Name: peptidylprolyl isomerase A
RGD ID: 3372
Description: Enables cyclosporin A binding activity. Involved in negative regulation of phosphoprotein phosphatase activity. Predicted to be located in cytosol; extracellular region; and nucleus. Predicted to be part of protein-containing complex. Predicted to be active in cytoplasm and intracellular membrane-bounded organelle. Used to study epilepsy. Orthologous to human PPIA (peptidylprolyl isomerase A); INTERACTS WITH (+)-alpha-tocopherol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CYCA; cyclophilin A; cyclosporin A-binding protein; CyP-A; MGC72881; p1B15; p31; peptidyl-prolyl cis-trans isomerase A; peptidylprolyl isomerase A (cyclophilin A); PPIase A; rotamase A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: LOC100911593  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21481,279,292 - 81,282,960 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1481,275,091 - 81,299,601 (+)Ensembl
Rnor_6.01486,673,775 - 86,677,443 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1486,673,775 - 86,677,443 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01480,306,923 - 80,310,652 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41487,165,998 - 87,169,995 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11487,185,142 - 87,189,140 (+)NCBI
Celera1480,161,152 - 80,164,810 (+)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(R,R,R)-alpha-tocopherol  (EXP)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
1H-pyrazole  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2,2-tetramine  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP)
2-amino-2-deoxy-D-galactopyranose  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
5-aza-2'-deoxycytidine  (ISO)
acrylamide  (EXP)
all-trans-retinoic acid  (ISO)
alprazolam  (ISO)
ammonium chloride  (EXP)
arsenous acid  (ISO)
Bandrowski's base  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP)
bucladesine  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
CU-O LINKAGE  (ISO)
cumene hydroperoxide  (EXP)
cyclosporin A  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dihydroartemisinin  (ISO)
disulfiram  (ISO)
doxorubicin  (EXP,ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
fenvalerate  (EXP)
ferric ammonium citrate  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
fumonisin B1  (ISO)
genistein  (EXP)
gentamycin  (EXP)
hyaluronic acid  (EXP)
hydrogen peroxide  (EXP)
ibuprofen  (ISO)
indometacin  (ISO)
iodide salt  (EXP)
iron(III) nitrilotriacetate  (EXP)
ivermectin  (ISO)
L-glutamic acid  (EXP)
limonene  (EXP)
lithium atom  (EXP)
lithium hydride  (EXP)
medroxyprogesterone acetate  (ISO)
megestrol acetate  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methamphetamine  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
morphine  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-ethyl-N-nitrosourea  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
nickel sulfate  (ISO)
okadaic acid  (ISO)
paracetamol  (ISO)
picoxystrobin  (ISO)
potassium dichromate  (EXP)
Propiverine  (EXP)
quercetin  (ISO)
Rebamipide  (EXP)
rotenone  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (EXP,ISO)
T-2 toxin  (EXP)
tamoxifen  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP)
thimerosal  (ISO)
torcetrapib  (ISO)
trichostatin A  (ISO)
uranium atom  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. An P, etal., PLoS Pathog. 2007 Jun;3(6):e88. doi: 10.1371/journal.ppat.0030088.
2. Bouybayoune I, etal., Neurobiol Dis. 2019 Oct;130:104498. doi: 10.1016/j.nbd.2019.104498. Epub 2019 Jun 8.
3. Danielson PE, etal., DNA 1988 May;7(4):261-7.
4. Demir B, etal., J Craniofac Surg. 2020 Jun;31(4):e368-e370. doi: 10.1097/SCS.0000000000006308.
5. Dorner M, etal., Nature. 2013 Sep 12;501(7466):237-41. doi: 10.1038/nature12427. Epub 2013 Jul 31.
6. Eren G, etal., Arch Oral Biol. 2016 Aug;68:162-6. doi: 10.1016/j.archoralbio.2016.05.004. Epub 2016 May 4.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Jiang J, etal., Int Immunopharmacol. 2018 Jun;59:347-353. doi: 10.1016/j.intimp.2018.03.039. Epub 2018 Apr 19.
9. Li J, etal., Sci Rep. 2016 Jun 29;6:28978. doi: 10.1038/srep28978.
10. Liu L, etal., Cancer Med. 2019 Jun;8(6):3142-3151. doi: 10.1002/cam4.2185. Epub 2019 May 7.
11. Liu W, etal., Elife. 2017 Jun 8;6. doi: 10.7554/eLife.24425.
12. Lo WY, etal., Am J Chin Med. 2010;38(4):745-59.
13. Malouitre S, etal., Biochem J. 2009 Dec 14;425(1):137-48. doi: 10.1042/BJ20090332.
14. MGD data from the GO Consortium
15. NCBI rat LocusLink and RefSeq merged data July 26, 2002
16. Obchoei S, etal., Mol Cancer. 2011 Aug 26;10:102. doi: 10.1186/1476-4598-10-102.
17. RGD automated data pipeline
18. RGD automated import pipeline for gene-chemical interactions
19. Seizer P, etal., J Mol Cell Cardiol. 2012 Jul;53(1):6-14. doi: 10.1016/j.yjmcc.2012.03.004. Epub 2012 Mar 15.
20. Theodor L, etal., Biochim Biophys Acta 1985 Nov 13;826(2-3):137-46.
Additional References at PubMed
PMID:1599421   PMID:1851525   PMID:11250896   PMID:12218175   PMID:12357034   PMID:12477932   PMID:14993672   PMID:15489334   PMID:16352598   PMID:16502470   PMID:16780588   PMID:17634366  
PMID:19056867   PMID:19190083   PMID:19199708   PMID:19932913   PMID:19946888   PMID:19968957   PMID:20458337   PMID:20676357   PMID:21330604   PMID:21423176   PMID:21711559   PMID:22139963  
PMID:22658674   PMID:22681889   PMID:22871113   PMID:23106098   PMID:23376485   PMID:23533145   PMID:23846495   PMID:24006456   PMID:24434144   PMID:26173747   PMID:27825172   PMID:29476059  
PMID:29914983   PMID:30221707  


Genomics

Comparative Map Data
Ppia
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21481,279,292 - 81,282,960 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1481,275,091 - 81,299,601 (+)Ensembl
Rnor_6.01486,673,775 - 86,677,443 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1486,673,775 - 86,677,443 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01480,306,923 - 80,310,652 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41487,165,998 - 87,169,995 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11487,185,142 - 87,189,140 (+)NCBI
Celera1480,161,152 - 80,164,810 (+)NCBICelera
Cytogenetic Map14q21NCBI
PPIA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl744,796,680 - 44,824,564 (+)EnsemblGRCh38hg38GRCh38
GRCh38744,795,960 - 44,803,117 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37744,836,280 - 44,842,716 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36744,802,766 - 44,809,241 (+)NCBINCBI36hg18NCBI36
Build 34744,609,504 - 44,615,343NCBI
Celera744,935,095 - 44,941,571 (+)NCBI
Cytogenetic Map7p13NCBI
HuRef744,721,292 - 44,727,768 (+)NCBIHuRef
CHM1_1744,840,586 - 44,847,069 (+)NCBICHM1_1
CRA_TCAGchr7v2744,875,748 - 44,882,224 (+)NCBI
Ppia
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39116,365,867 - 6,369,817 (+)NCBIGRCm39mm39
GRCm39 Ensembl116,365,443 - 6,369,817 (+)Ensembl
GRCm38116,415,867 - 6,419,817 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl116,415,443 - 6,419,817 (+)EnsemblGRCm38mm10GRCm38
MGSCv37116,315,873 - 6,319,813 (+)NCBIGRCm37mm9NCBIm37
MGSCv36116,315,873 - 6,319,813 (+)NCBImm8
Celera116,899,520 - 6,903,460 (+)NCBICelera
Cytogenetic Map11A1NCBI
cM Map113.97NCBI
Ppia
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554567,381,923 - 7,383,203 (-)NCBIChiLan1.0ChiLan1.0
PPIA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1745,578,764 - 45,583,516 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl745,578,765 - 45,605,545 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0745,510,450 - 45,515,448 (+)NCBIMhudiblu_PPA_v0panPan3
LOC403581
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1780,937,433 - 80,938,175 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
ROS_Cfam_1.0781,027,063 - 81,027,805 (-)NCBI
UMICH_Zoey_3.1780,741,873 - 80,742,615 (-)NCBI
UNSW_CanFamBas_1.01764,379,529 - 64,380,271 (-)NCBI
UU_Cfam_GSD_1.0781,058,591 - 81,059,333 (-)NCBI
Ppia
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118100,457,966 - 100,461,621 (+)NCBI
SpeTri2.0NW_00493647819,669,727 - 19,673,355 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PPIA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11850,563,130 - 50,566,857 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21855,286,994 - 55,290,557 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PPIA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12113,876,099 - 13,883,546 (-)NCBI
ChlSab1.1 Ensembl2113,876,099 - 13,883,462 (-)Ensembl
Vero_WHO_p1.0NW_0236660628,652,515 - 8,658,073 (+)NCBI
Ppia
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247407,447,554 - 7,450,707 (-)NCBI

Position Markers
UniSTS:265677  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21421,006,765 - 21,007,058 (+)MAPPERmRatBN7.2
mRatBN7.2441,829,100 - 41,829,392 (+)MAPPERmRatBN7.2
Rnor_6.01422,707,130 - 22,707,422NCBIRnor6.0
Rnor_5.01422,609,939 - 22,610,231UniSTSRnor5.0
RGSC_v3.41422,613,076 - 22,613,368UniSTSRGSC3.4
Cytogenetic Map14q21UniSTS
Ppia  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21421,006,634 - 21,006,784 (+)MAPPERmRatBN7.2
Rnor_6.01422,706,999 - 22,707,148NCBIRnor6.0
Rnor_5.01422,609,808 - 22,609,957UniSTSRnor5.0
Cytogenetic Map14q21UniSTS


QTLs in Region (mRatBN7.2)
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)141103062295876975Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)146875779683368335Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147341532392554092Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147341532392554092Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)147995092195876975Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:26
Count of miRNA genes:22
Interacting mature miRNAs:26
Transcripts:ENSRNOT00000009179
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 1 20 16 16 16 51 20 27
Medium 3 39 58 42 21 42 8 11 67 24 28 12 8
Low 2 24 40 24 17 24 5 8 30 26 27 10 5
Below cutoff 3 3 3 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_017101 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599085 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC106663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC059141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC091153 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210843 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221386 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222826 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223330 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227889 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228411 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228450 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231674 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233894 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234872 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M19533 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M25637 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000038275
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1481,278,349 - 81,282,951 (+)Ensembl
Rnor_6.0 Ensembl1486,675,818 - 86,677,438 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079015   ⟹   ENSRNOP00000071920
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1481,278,928 - 81,299,601 (+)Ensembl
Rnor_6.0 Ensembl1486,673,817 - 86,677,237 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091873   ⟹   ENSRNOP00000073930
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1481,275,091 - 81,282,954 (+)Ensembl
Rnor_6.0 Ensembl1486,673,775 - 86,677,443 (+)Ensembl
RefSeq Acc Id: NM_017101   ⟹   NP_058797
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21481,279,292 - 81,282,960 (+)NCBI
Rnor_6.01486,673,775 - 86,677,443 (+)NCBI
Rnor_5.01480,306,923 - 80,310,652 (+)NCBI
RGSC_v3.41487,165,998 - 87,169,995 (+)RGD
Celera1480,161,152 - 80,164,810 (+)RGD
Sequence:
RefSeq Acc Id: XM_017599085   ⟹   XP_017454574
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21481,279,733 - 81,282,959 (+)NCBI
Rnor_6.01486,674,258 - 86,677,443 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_058797   ⟸   NM_017101
- UniProtKB: P10111 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017454574   ⟸   XM_017599085
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000071920   ⟸   ENSRNOT00000079015
RefSeq Acc Id: ENSRNOP00000073930   ⟸   ENSRNOT00000091873
Protein Domains
PPIase cyclophilin-type

Transcriptome

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

Promoters
RGD ID:13699474
Promoter ID:EPDNEW_R9998
Type:multiple initiation site
Name:Ppia_1
Description:peptidylprolyl isomerase A
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_6.01486,673,774 - 86,673,834EPDNEW

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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: 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)
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
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)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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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:3372 AgrOrtholog
Ensembl Genes ENSRNOG00000027864 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00000055068 UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000071404 UniProtKB/Swiss-Prot
  ENSRNOP00000071920 UniProtKB/TrEMBL
  ENSRNOP00000073930 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000079015 UniProtKB/TrEMBL
  ENSRNOT00000088798 UniProtKB/Swiss-Prot
  ENSRNOT00000091873 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.40.100.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6919594 IMAGE-MGC_LOAD
  IMAGE:7308693 IMAGE-MGC_LOAD
InterPro Cyclophilin-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclophilin-type_PPIase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclophilin-type_PPIase_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclophilin-type_PPIase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:100360977 UniProtKB/Swiss-Prot
  rno:25518 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108714 IMAGE-MGC_LOAD
  MGC:72881 IMAGE-MGC_LOAD
NCBI Gene 25518 ENTREZGENE
Pfam Pro_isomerase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ppia PhenoGen
PIRSF Peptidylpro_ismrse UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS CSAPPISMRASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CSA_PPIASE_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CSA_PPIASE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50891 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K1P0_RAT UniProtKB/TrEMBL
  P10111 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary P18303 UniProtKB/Swiss-Prot
  Q5BK98 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-21 Ppia  peptidylprolyl isomerase A  Ppia  peptidylprolyl isomerase A (cyclophilin A)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-24 Ppia  peptidylprolyl isomerase A (cyclophilin A)  Ppia  peptidylprolyl isomerase A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Ppia  Peptidylprolyl isomerase A (cyclophilin A)      Symbol and Name status set to approved 70586 APPROVED