Prf1 (perforin 1) - Rat Genome Database

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Gene: Prf1 (perforin 1) Rattus norvegicus
Analyze
Symbol: Prf1
Name: perforin 1
RGD ID: 708463
Description: Predicted to enable calcium ion binding activity; identical protein binding activity; and wide pore channel activity. Involved in apoptotic process; circadian rhythm; and response to ethanol. Located in cytoplasmic vesicle and extracellular space. Used to study asthma; colon carcinoma; and glomerulonephritis. Biomarker of membranoproliferative glomerulonephritis. Human ortholog(s) of this gene implicated in several diseases, including Crohn's disease; familial hemophagocytic lymphohistiocytosis 2; human immunodeficiency virus infectious disease; multiple sclerosis; and non-Langerhans-cell histiocytosis. Orthologous to human PRF1 (perforin 1); PARTICIPATES IN allograft rejection pathway; autoimmune thyroiditis pathway; graft-versus-host disease pathway; INTERACTS WITH 1,2-dimethylhydrazine; 1-naphthyl isothiocyanate; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Cyta; cytolysin; lymphocyte pore-forming protein; MGC108712; P1; perforin 1 (pore forming protein); perforin-1; RATCYTA
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22029,246,202 - 29,251,712 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2029,246,202 - 29,251,701 (+)Ensembl
Rnor_6.02030,915,294 - 30,920,804 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2030,915,213 - 30,921,382 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02032,706,313 - 32,711,823 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42028,658,367 - 28,663,877 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12028,672,166 - 28,677,670 (+)NCBI
Celera2030,679,378 - 30,684,888 (+)NCBICelera
Cytogenetic Map20q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (EXP)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (EXP)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-dinitrotoluene  (EXP)
2-tert-butylhydroquinone  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3,7-dihydropurine-6-thione  (EXP)
5-azacytidine  (ISO)
acetamide  (EXP)
adenosine  (ISO)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP)
bortezomib  (ISO)
bromodichloromethane  (ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
coformycin  (ISO)
dichloroacetic acid  (ISO)
dichlorvos  (ISO)
ethanol  (ISO)
ferric oxide  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
gentamycin  (EXP)
halothane  (ISO)
ionomycin  (ISO)
L-ascorbic acid  (ISO)
mercaptopurine  (EXP)
N,N-diethyl-m-toluamide  (EXP)
nevirapine  (EXP)
nickel atom  (ISO)
oxaliplatin  (EXP)
p-menthan-3-ol  (ISO)
Pentoxifylline  (ISO)
permethrin  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
poly(I:C)  (ISO)
purine-6-thiol  (EXP)
pyrrolidine dithiocarbamate  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
tamoxifen  (ISO)
testosterone  (EXP)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP)
thalidomide  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
triclosan  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
urethane  (ISO)
valproic acid  (ISO)
ziram  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Arjona A and Sarkar DK, Brain Behav Immun. 2006 Sep;20(5):469-76. Epub 2005 Nov 23.
2. Arjona A, etal., J Immunol. 2004 Mar 1;172(5):2811-7.
3. Beeston T, etal., J Neuroimmunol. 2010 Dec 15;229(1-2):91-7. Epub 2010 Aug 12.
4. Brenu EW, etal., J Transl Med. 2011 May 28;9:81.
5. Camina-Tato M, etal., J Immunol. 2010 Nov 1;185(9):5392-404. Epub 2010 Oct 4.
6. Cosgrove C, etal., PLoS One. 2014 Aug 22;9(8):e105950. doi: 10.1371/journal.pone.0105950. eCollection 2014.
7. Daca A, etal., Hum Immunol. 2011 Dec;72(12):1160-7. Epub 2011 Aug 26.
8. de Alencar BC, etal., Infect Immun. 2009 Oct;77(10):4383-95. Epub 2009 Aug 3.
9. Deb C, etal., J Neuropathol Exp Neurol. 2009 Sep;68(9):1037-48.
10. Enomoto N, etal., J Immunol. 2012 Feb 15;188(4):1734-41. Epub 2012 Jan 16.
11. Feldmann J, etal., Br J Haematol. 2002 Jun;117(4):965-72.
12. Fujinaka H, etal., Kidney Int. 2007 Oct;72(7):823-30. Epub 2007 Jul 11.
13. Giovanni F, etal., J Neuroimmunol. 2011 Dec 15;240-241:137-41. Epub 2011 Oct 15.
14. GOA data from the GO Consortium
15. Goransdotter Ericson K, etal., Am J Hum Genet. 2001 Mar;68(3):590-7. Epub 2001 Feb 6.
16. Haque A, etal., J Immunol. 2011 Jun 1;186(11):6148-56. Epub 2011 Apr 27.
17. Hersperger AR, etal., PLoS Pathog. 2010 May 27;6(5):e1000917.
18. Ikezumi Y, etal., Kidney Int. 2000 Jul;58(1):100-14.
19. Ishikawa H, etal., J Immunol 1989 Nov 1;143(9):3069-73.
20. Kitaura K, etal., J Immunol. 2011 Oct 15;187(8):3919-30. Epub 2011 Sep 9.
21. Kremer M, etal., PLoS Pathog. 2012 Mar;8(3):e1002557. Epub 2012 Mar 1.
22. MGD data from the GO Consortium
23. Myers KC, etal., Br J Haematol. 2011 Jul;154(2):234-40. doi: 10.1111/j.1365-2141.2011.08721.x. Epub 2011 May 4.
24. Nimmo ER, etal., Inflamm Bowel Dis. 2012 May;18(5):889-99. doi: 10.1002/ibd.21912. Epub 2011 Oct 21.
25. OMIM Disease Annotation Pipeline
26. Pachlopnik Schmid J, etal., EMBO Mol Med. 2009 May;1(2):112-24.
27. Padovan L, etal., AIDS. 2011 Feb 20;25(4):535-7.
28. Pipeline to import KEGG annotations from KEGG into RGD
29. RGD automated data pipeline
30. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
31. RGD automated import pipeline for gene-chemical interactions
32. RGD comprehensive gene curation
33. Shi L, etal., J Immunol. 2005 May 1;174(9):5456-61.
34. Sotosek Tokmadzic V, etal., Injury. 2012 May;43(5):624-31. Epub 2010 May 26.
35. Vastert SJ, etal., Rheumatology (Oxford). 2010 Mar;49(3):441-9. Epub 2009 Dec 17.
36. Waldner MJ, etal., Inflamm Bowel Dis. 2010 Apr;16(4):559-67.
37. Xie Y, etal., Virology. 2011 Dec 5;421(1):78-84. Epub 2011 Oct 11.
38. Zhu M, etal., Nutr Cancer. 2012 Apr;64(3):464-72. Epub 2012 Mar 16.
39. Zou LP, etal., Zhongguo Dang Dai Er Ke Za Zhi. 2011 Mar;13(3):223-6.
Additional References at PubMed
PMID:8164737   PMID:9756476   PMID:11856751   PMID:12477932   PMID:15454490   PMID:15576364   PMID:15755897   PMID:19915045   PMID:19946888   PMID:20450731   PMID:20889983   PMID:21037563  
PMID:21438968   PMID:21685908   PMID:24070258   PMID:24506670  


Genomics

Comparative Map Data
Prf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22029,246,202 - 29,251,712 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2029,246,202 - 29,251,701 (+)Ensembl
Rnor_6.02030,915,294 - 30,920,804 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2030,915,213 - 30,921,382 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02032,706,313 - 32,711,823 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42028,658,367 - 28,663,877 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12028,672,166 - 28,677,670 (+)NCBI
Celera2030,679,378 - 30,684,888 (+)NCBICelera
Cytogenetic Map20q11NCBI
PRF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1070,597,348 - 70,602,759 (-)EnsemblGRCh38hg38GRCh38
GRCh381070,597,348 - 70,602,741 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371072,357,104 - 72,362,497 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361072,027,110 - 72,032,537 (-)NCBINCBI36hg18NCBI36
Build 341072,027,110 - 72,032,520NCBI
Celera1065,638,863 - 65,644,316 (-)NCBI
Cytogenetic Map10q22.1NCBI
HuRef1066,350,612 - 66,356,064 (-)NCBIHuRef
CHM1_11072,639,251 - 72,644,703 (-)NCBICHM1_1
Prf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391061,133,530 - 61,140,463 (+)NCBIGRCm39mm39
GRCm39 Ensembl1061,133,612 - 61,140,459 (+)Ensembl
GRCm381061,297,751 - 61,304,684 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1061,297,833 - 61,304,680 (+)EnsemblGRCm38mm10GRCm38
MGSCv371060,760,584 - 60,767,011 (+)NCBIGRCm37mm9NCBIm37
MGSCv361060,693,191 - 60,699,667 (+)NCBImm8
Celera1062,399,002 - 62,405,430 (+)NCBICelera
Cytogenetic Map10B4NCBI
cM Map1032.18NCBI
Prf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543720,700,718 - 20,706,929 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543720,700,912 - 20,705,076 (+)NCBIChiLan1.0ChiLan1.0
PRF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11069,597,574 - 69,603,070 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1069,597,574 - 69,603,070 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01067,071,141 - 67,078,057 (-)NCBIMhudiblu_PPA_v0panPan3
PRF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1421,497,865 - 21,502,429 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl421,498,249 - 21,500,864 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha421,630,717 - 21,633,264 (-)NCBI
ROS_Cfam_1.0421,771,953 - 21,776,587 (-)NCBI
UMICH_Zoey_3.1421,669,548 - 21,672,095 (-)NCBI
UNSW_CanFamBas_1.0421,875,818 - 21,878,365 (-)NCBI
UU_Cfam_GSD_1.0422,227,730 - 22,230,277 (-)NCBI
Prf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721359,564,718 - 59,568,196 (+)NCBI
SpeTri2.0NW_0049365218,057,874 - 8,060,695 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1473,512,769 - 73,520,202 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11473,515,306 - 73,520,256 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21479,363,495 - 79,368,376 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PRF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1960,692,544 - 60,698,000 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl960,692,600 - 60,698,465 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604821,417,046 - 21,423,720 (+)NCBIVero_WHO_p1.0
Prf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247544,679,451 - 4,681,627 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D20Rat27  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22029,244,388 - 29,244,578 (+)MAPPERmRatBN7.2
Rnor_6.02030,913,481 - 30,913,670NCBIRnor6.0
Rnor_5.02032,704,500 - 32,704,689UniSTSRnor5.0
RGSC_v3.42028,656,553 - 28,656,743RGDRGSC3.4
RGSC_v3.42028,656,554 - 28,656,743UniSTSRGSC3.4
RGSC_v3.12028,670,353 - 28,670,543RGD
Celera2030,677,565 - 30,677,754UniSTS
FHH x ACI Map2014.6699UniSTS
FHH x ACI Map2014.6699RGD
Cytogenetic Map20q11UniSTS
D20Got111  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22029,249,873 - 29,250,013 (+)MAPPERmRatBN7.2
Rnor_6.02030,918,966 - 30,919,105NCBIRnor6.0
Rnor_5.02032,709,985 - 32,710,124UniSTSRnor5.0
RGSC_v3.42028,662,039 - 28,662,178UniSTSRGSC3.4
Celera2030,683,050 - 30,683,189UniSTS
Cytogenetic Map20q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:17
Count of miRNA genes:14
Interacting mature miRNAs:15
Transcripts:ENSRNOT00000000681
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 8 18 9
Low 2 15 29 21 1 21 5 6 7 21 18 2 5
Below cutoff 16 18 18 18 3 5 16 10 18 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000681   ⟹   ENSRNOP00000000681
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2029,246,202 - 29,251,486 (+)Ensembl
Rnor_6.0 Ensembl2030,915,213 - 30,921,382 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000100131   ⟹   ENSRNOP00000078379
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2029,247,792 - 29,251,701 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117051   ⟹   ENSRNOP00000076990
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2029,246,202 - 29,251,701 (+)Ensembl
RefSeq Acc Id: NM_017330   ⟹   NP_059026
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,246,202 - 29,251,712 (+)NCBI
Rnor_6.02030,915,294 - 30,920,804 (+)NCBI
Rnor_5.02032,706,313 - 32,711,823 (+)NCBI
RGSC_v3.42028,658,367 - 28,663,877 (+)RGD
Celera2030,679,378 - 30,684,888 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_059026 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41071 (Get FASTA)   NCBI Sequence Viewer  
  AAH89808 (Get FASTA)   NCBI Sequence Viewer  
  EDL93028 (Get FASTA)   NCBI Sequence Viewer  
  EDL93029 (Get FASTA)   NCBI Sequence Viewer  
  P35763 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_059026   ⟸   NM_017330
- Peptide Label: precursor
- UniProtKB: Q5FVS5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000681   ⟸   ENSRNOT00000000681
RefSeq Acc Id: ENSRNOP00000078379   ⟸   ENSRNOT00000100131
RefSeq Acc Id: ENSRNOP00000076990   ⟸   ENSRNOT00000117051
Protein Domains
C2   EGF-like   MACPF

Transcriptome

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

Promoters
RGD ID:13701601
Promoter ID:EPDNEW_R12125
Type:single initiation site
Name:Prf1_1
Description:perforin 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02030,915,271 - 30,915,331EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
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)
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
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (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
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)
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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)
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
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)
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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)
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
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)
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
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)
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
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)
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
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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
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
LEXF10A/StmMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/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
LEXF1A/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (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: 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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
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)
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/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)
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: 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)
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/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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
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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:708463 AgrOrtholog
Ensembl Genes ENSRNOG00000000562 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000681 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000681 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7378633 IMAGE-MGC_LOAD
InterPro C2_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MACPF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MACPF_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Perforin-1_C2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:50669 UniProtKB/TrEMBL
MGC_CLONE MGC:108712 IMAGE-MGC_LOAD
NCBI Gene 50669 ENTREZGENE
Pfam MACPF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00168 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PRF1 RGD
PhenoGen Prf1 PhenoGen
PROSITE MACPF_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MACPF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PS50004 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART MACPF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00239 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F7EPF5_RAT UniProtKB/TrEMBL
  P35763 ENTREZGENE, UniProtKB/Swiss-Prot
  Q5FVS5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Prf1  perforin 1  Prf1  perforin 1 (pore forming protein)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-04-22 Prf1  perforin 1 (pore forming protein)  Cyta  cytolysin  Symbol and Name updated to reflect Human and Mouse nomenclature 625702 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in lymphocytes 1299461