Pcsk1 (proprotein convertase subtilisin/kexin type 1) - Rat Genome Database

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Gene: Pcsk1 (proprotein convertase subtilisin/kexin type 1) Rattus norvegicus
Analyze
Symbol: Pcsk1
Name: proprotein convertase subtilisin/kexin type 1
RGD ID: 3272
Description: Enables endopeptidase activity. Involved in several processes, including nervous system development; protein processing; and response to morphine. Located in several cellular components, including perikaryon; rough endoplasmic reticulum; and trans-Golgi network. Colocalizes with secretory granule. Used to study hyperglycemia and type 2 diabetes mellitus. Biomarker of glucose metabolism disease (multiple); hyperthyroidism; hypothyroidism; islet cell tumor; and visual epilepsy. Human ortholog(s) of this gene implicated in obesity and proprotein convertase 1/3 deficiency. Orthologous to human PCSK1 (proprotein convertase subtilisin/kexin type 1); PARTICIPATES IN altered energy homeostasis pathway; altered melanocortin system pathway; melanocortin system pathway; INTERACTS WITH (+)-pilocarpine; 1,2-dimethylhydrazine; 1,3-dinitrobenzene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: BDP; NEC 1; neuroendocrine convertase 1; PC1; PC3; prohormone convertase 1; prohormone convertase 3; proprotein convertase 1; Protein convertase subtilisin / kexin type I; Protein convertase subtilisin / kexin, type I
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
mRatBN7.224,395,543 - 4,442,434 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl24,395,543 - 4,442,434 (+)Ensembl
Rnor_6.0291,450,162 - 91,497,091 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl291,450,162 - 91,497,091 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.022,274,882 - 2,309,886 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.421,923,309 - 1,970,238 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.121,937,434 - 1,981,975 (+)NCBI
Celera2885,989 - 932,918 (+)NCBICelera
Cytogenetic Map2q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Alarcon C, etal., J Clin Invest. 1995 Mar;95(3):1032-9.
2. Arias AE, etal., J Cell Sci. 2000 Jun;113 ( Pt 11):2075-83.
3. Bauer R, etal., Eur J Neurosci. 2000 Aug;12(8):2746-56.
4. Billova S, etal., Neuroscience. 2007 Jun 29;147(2):403-18. Epub 2007 Jun 1.
5. Bloomquist BT, etal., Mol Endocrinol 1991 Dec;5(12):2014-24.
6. Borjesson A and Carlsson C, J Endocrinol. 2007 Feb;192(2):381-7.
7. Cain BM, etal., J Comp Neurol 2003 Dec 15;467(3):307-25.
8. Chandramohan G, etal., Pituitary. 2001 Sep;4(4):231-7.
9. Dagai L, etal., Neurochem Res. 2009 May;34(5):867-75. Epub 2008 Sep 10.
10. Davidson HW, etal., Nature. 1988 May 5;333(6168):93-6. doi: 10.1038/333093a0.
11. Dong W and Day R, Endocrinology 2002 Jan;143(1):254-62.
12. Espinosa VP, etal., Am J Physiol Endocrinol Metab. 2007 Jan;292(1):E175-86. Epub 2006 Aug 22.
13. Espinosa VP, etal., Neuroscience. 2008 Oct 15;156(3):788-99. Epub 2008 Aug 9.
14. Fodor A, etal., Diabetologia. 2007 Jan;50(1):121-30. Epub 2006 Nov 28.
15. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
16. GOA data from the GO Consortium
17. Guest PC, etal., J Endocrinol. 2002 Dec;175(3):637-47.
18. Hajebrahimi Z, etal., Neurosci Lett. 2008 Aug 29;441(3):261-6. Epub 2008 Jun 21.
19. Hakes DJ, etal., Endocrinology 1991 Dec;129(6):3053-63.
20. Jackson RS, etal., Nat Genet. 1997 Jul;16(3):303-6.
21. Kato H, etal., J Histochem Cytochem. 2004 Jul;52(7):943-57.
22. Lansac G, etal., J Neuroimmunol. 2006 Feb;171(1-2):57-71. Epub 2005 Dec 5.
23. Lee YC, etal., Mol Cell Endocrinol. 1999 Sep 10;155(1-2):27-35.
24. Li M, etal., Neuroendocrinology. 1999 Mar;69(3):217-26.
25. Li QL, etal., Mol Cell Endocrinol. 1999 Dec 20;158(1-2):143-52.
26. Lu H, etal., Mol Cell Proteomics. 2008 Aug;7(8):1434-51. Epub 2008 Apr 30.
27. Malide D, etal., J Histochem Cytochem. 1995 Jan;43(1):11-9.
28. Marcinkiewicz M, etal., Endocrinology. 1994 Oct;135(4):1651-60.
29. Marcinkiewicz M, etal., Neuroscience. 1997 Jan;76(2):425-39.
30. Marx R and Mains RE, Endocrinology. 1997 Dec;138(12):5108-18.
31. MGD data from the GO Consortium
32. Mousa SA, etal., Endocrinology. 2004 Mar;145(3):1331-41. Epub 2003 Nov 20.
33. Muller L, etal., J Histochem Cytochem. 1998 Jan;46(1):101-8.
34. Nakashima M, etal., Regul Pept. 2001 Dec 15;102(2-3):135-45.
35. NCBI rat LocusLink and RefSeq merged data July 26, 2002
36. Nilaweera KN, etal., Neuroscience. 2003;119(3):713-20.
37. Nillni EA Endocrinology. 2007 Sep;148(9):4191-200. Epub 2007 Jun 21.
38. Niquet J, etal., Brain Res Dev Brain Res. 2000 Mar 15;120(1):49-56.
39. Ohagi S, etal., Diabetes. 1996 Jul;45(7):897-901.
40. OMIM Disease Annotation Pipeline
41. Patriti A, etal., Surgery. 2007 Jul;142(1):74-85.
42. Perello M, etal., Endocrinology. 2006 Jun;147(6):2705-16. Epub 2006 Feb 23.
43. Pritchard LE, etal., J Endocrinol 2002 Mar;172(3):411-21.
44. RGD automated data pipeline
45. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
46. RGD automated import pipeline for gene-chemical interactions
47. Rhodes CJ, etal., J Biol Chem. 1992 Nov 15;267(32):22719-27.
48. Sebaai N, etal., Neuroendocrinology. 2002 Oct;76(4):243-53.
49. Seeley RJ, etal., Annu Rev Nutr 2004;24:133-49.
50. Shen X, etal., J Mol Endocrinol. 2004 Aug;33(1):21-33.
51. Ueda K, etal., Proc Natl Acad Sci U S A 2003 May 13;100(10):5622-7.
52. Wang H, etal., Diabetologia. 2007 Feb;50(2):348-58. Epub 2006 Dec 6.
53. Wen JH, etal., Diabetologia. 2009 Mar;52(3):504-13. Epub 2008 Nov 26.
54. Wideman RD, etal., Diabetes. 2007 Nov;56(11):2744-52. Epub 2007 Aug 13.
55. Wideman RD, etal., Mol Ther. 2009 Jan;17(1):191-8. Epub 2008 Oct 21.
56. Wideman RD, etal., Proc Natl Acad Sci U S A. 2006 Sep 5;103(36):13468-73. Epub 2006 Aug 28.
57. Winsky-Sommerer R, etal., J Comp Neurol. 2000 Aug 28;424(3):439-60.
58. Zertal-Zidani S, etal., Diabetologia. 2007 Mar;50(3):585-95. Epub 2007 Jan 13.
59. Zheng M, etal., J Neurosci. 1994 Aug;14(8):4656-73.
60. Zhou A, etal., J Biol Chem. 1998 May 1;273(18):11107-14.
61. Zhu X, etal., Proc Natl Acad Sci U S A 2002 Aug 6;99(16):10293-8. Epub 2002 Jul 26.
Additional References at PubMed
PMID:8262946   PMID:8397508   PMID:9242664   PMID:15146101   PMID:15286802   PMID:16204236   PMID:16221685   PMID:16274843   PMID:16384863   PMID:16476726   PMID:17240044   PMID:17531155  
PMID:17556096   PMID:18784614   PMID:19376969   PMID:19628676   PMID:23050949   PMID:23637853   PMID:26778167  


Genomics

Comparative Map Data
Pcsk1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.224,395,543 - 4,442,434 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl24,395,543 - 4,442,434 (+)Ensembl
Rnor_6.0291,450,162 - 91,497,091 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl291,450,162 - 91,497,091 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.022,274,882 - 2,309,886 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.421,923,309 - 1,970,238 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.121,937,434 - 1,981,975 (+)NCBI
Celera2885,989 - 932,918 (+)NCBICelera
Cytogenetic Map2q23NCBI
PCSK1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl596,390,333 - 96,434,143 (-)EnsemblGRCh38hg38GRCh38
GRCh38596,390,333 - 96,433,248 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37595,726,037 - 95,768,952 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36595,751,875 - 95,794,708 (-)NCBINCBI36hg18NCBI36
Build 34595,751,874 - 95,794,708NCBI
Celera591,608,060 - 91,651,008 (-)NCBI
Cytogenetic Map5q15NCBI
HuRef590,916,038 - 90,958,959 (-)NCBIHuRef
CHM1_1595,158,671 - 95,201,600 (-)NCBICHM1_1
Pcsk1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391375,237,407 - 75,282,980 (+)NCBIGRCm39mm39
GRCm39 Ensembl1375,237,945 - 75,282,980 (+)Ensembl
GRCm381375,089,420 - 75,134,861 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1375,089,826 - 75,134,861 (+)EnsemblGRCm38mm10GRCm38
MGSCv371375,227,435 - 75,269,946 (+)NCBIGRCm37mm9NCBIm37
MGSCv361375,555,989 - 75,598,500 (+)NCBImm8
Celera1377,413,324 - 77,455,835 (+)NCBICelera
Cytogenetic Map13C1NCBI
cM Map1340.63NCBI
Pcsk1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541816,181,771 - 16,224,603 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541816,181,809 - 16,224,274 (+)NCBIChiLan1.0ChiLan1.0
PCSK1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1519,064,004 - 19,106,486 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl519,064,004 - 19,106,486 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0518,917,488 - 18,960,102 (+)NCBIMhudiblu_PPA_v0panPan3
PCSK1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1313,233,342 - 13,276,921 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl313,233,594 - 13,274,094 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha314,573,263 - 14,616,624 (+)NCBI
ROS_Cfam_1.0313,112,863 - 13,155,997 (+)NCBI
ROS_Cfam_1.0 Ensembl313,112,897 - 13,155,993 (+)Ensembl
UMICH_Zoey_3.1313,076,913 - 13,120,227 (+)NCBI
UNSW_CanFamBas_1.0313,073,463 - 13,116,776 (+)NCBI
UU_Cfam_GSD_1.0313,272,840 - 13,316,211 (+)NCBI
Pcsk1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213168,824,505 - 168,864,179 (+)NCBI
SpeTri2.0NW_0049365237,009,966 - 7,050,300 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCSK1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2103,004,794 - 103,050,839 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12103,004,794 - 103,050,707 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Pig Cytomap2qNCBI
PCSK1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1490,246,413 - 90,289,148 (-)NCBIChlSab1.1chlSab2
ChlSab1.1490,246,413 - 90,289,148 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl490,248,598 - 90,289,089 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604938,898,564 - 38,941,574 (-)NCBIVero_WHO_p1.0
Pcsk1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474314,993,436 - 15,036,512 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
M58589  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.224,439,925 - 4,440,044 (-)MAPPERmRatBN7.2
Rnor_6.0291,452,552 - 91,452,670NCBIRnor6.0
Rnor_5.022,307,378 - 2,307,496UniSTSRnor5.0
Rnor_5.02111,213,493 - 111,213,611UniSTSRnor5.0
RGSC_v3.421,967,730 - 1,967,848UniSTSRGSC3.4
Celera2930,410 - 930,528UniSTS
Cytogenetic Map2q11-q12UniSTS
AU049217  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.224,431,894 - 4,432,100 (-)MAPPERmRatBN7.2
Rnor_6.0291,460,496 - 91,460,701NCBIRnor6.0
Rnor_5.022,299,347 - 2,299,552UniSTSRnor5.0
Rnor_5.02111,221,437 - 111,221,642UniSTSRnor5.0
RGSC_v3.421,959,699 - 1,959,904UniSTSRGSC3.4
Celera2922,379 - 922,584UniSTS
Cytogenetic Map2q11-q12UniSTS
BE119208  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.224,439,827 - 4,439,977 (-)MAPPERmRatBN7.2
Rnor_6.0291,452,619 - 91,452,768NCBIRnor6.0
Rnor_5.022,307,280 - 2,307,429UniSTSRnor5.0
Rnor_5.02111,213,560 - 111,213,709UniSTSRnor5.0
RGSC_v3.421,967,632 - 1,967,781UniSTSRGSC3.4
Celera2930,312 - 930,461UniSTS
Cytogenetic Map2q11-q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:240
Count of miRNA genes:160
Interacting mature miRNAs:184
Transcripts:ENSRNOT00000015185
Prediction methods:Miranda
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
Low 2 8 27 2 7
Below cutoff 2 1 27 16 8 16 1 3 45 3 10 4 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000015185   ⟹   ENSRNOP00000015185
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl24,395,543 - 4,442,434 (+)Ensembl
Rnor_6.0 Ensembl291,450,162 - 91,497,091 (-)Ensembl
RefSeq Acc Id: NM_017091   ⟹   NP_058787
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.224,395,543 - 4,442,434 (+)NCBI
Rnor_6.0291,450,162 - 91,497,091 (-)NCBI
Rnor_5.022,274,882 - 2,309,886 (+)NCBI
RGSC_v3.421,923,309 - 1,970,238 (+)RGD
Celera2885,989 - 932,918 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_058787 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA40945 (Get FASTA)   NCBI Sequence Viewer  
  AAA41476 (Get FASTA)   NCBI Sequence Viewer  
  EDM09905 (Get FASTA)   NCBI Sequence Viewer  
  P28840 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_058787   ⟸   NM_017091
- Peptide Label: precursor
- UniProtKB: P28840 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000015185   ⟸   ENSRNOT00000015185
Protein Domains
P/Homo B   Peptidase S8

Transcriptome

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

Promoters
RGD ID:13691229
Promoter ID:EPDNEW_R1752
Type:single initiation site
Name:Pcsk1_1
Description:proprotein convertase subtilisin/kexin type 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_6.0291,497,093 - 91,497,153EPDNEW

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)
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-Lx/CubMcwi (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
BN/NHsdMcwi (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
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)
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
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 (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
BXH2/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
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)
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)
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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)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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)
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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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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)
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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)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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)
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)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (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
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:3272 AgrOrtholog
Ensembl Genes ENSRNOG00000011107 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000015185 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000015185 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.70.850 UniProtKB/Swiss-Prot
  3.40.50.200 UniProtKB/Swiss-Prot
InterPro Galactose-bd-like_sf UniProtKB/Swiss-Prot
  Kexin/furin UniProtKB/Swiss-Prot
  P_dom UniProtKB/Swiss-Prot
  Peptidase_S8/S53_dom UniProtKB/Swiss-Prot
  Peptidase_S8/S53_dom_sf UniProtKB/Swiss-Prot
  Peptidase_S8_Asp-AS UniProtKB/Swiss-Prot
  Peptidase_S8_His-AS UniProtKB/Swiss-Prot
  Peptidase_S8_Ser-AS UniProtKB/Swiss-Prot
  Peptidase_S8_subtilisin-rel UniProtKB/Swiss-Prot
  Proho_convert UniProtKB/Swiss-Prot
  S8_pro-domain UniProtKB/Swiss-Prot
  S8_pro-domain_sf UniProtKB/Swiss-Prot
KEGG Report rno:25204 UniProtKB/Swiss-Prot
NCBI Gene 25204 ENTREZGENE
Pfam P_proprotein UniProtKB/Swiss-Prot
  Peptidase_S8 UniProtKB/Swiss-Prot
  Proho_convert UniProtKB/Swiss-Prot
  S8_pro-domain UniProtKB/Swiss-Prot
PhenoGen Pcsk1 PhenoGen
PRINTS SUBTILISIN UniProtKB/Swiss-Prot
PROSITE P_HOMO_B UniProtKB/Swiss-Prot
  SUBTILASE UniProtKB/Swiss-Prot
  SUBTILASE_ASP UniProtKB/Swiss-Prot
  SUBTILASE_HIS UniProtKB/Swiss-Prot
  SUBTILASE_SER UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49785 UniProtKB/Swiss-Prot
  SSF52743 UniProtKB/Swiss-Prot
UniProt NEC1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Pcsk1  Protein convertase subtilisin / kexin, type I      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in endocrine and neuroendocrine tissues 70278
gene_process has a role in the maturation of mammalian hormones 70278
gene_process may function in secretory pathway 70278
gene_product 752 aa protein 70278