Plcb1 (phospholipase C beta 1) - Rat Genome Database

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Gene: Plcb1 (phospholipase C beta 1) Rattus norvegicus
Analyze
Symbol: Plcb1
Name: phospholipase C beta 1
RGD ID: 3344
Description: Enables calcium ion binding activity; identical protein binding activity; and phosphatidylinositol phospholipase C activity. Involved in several processes, including cellular response to glyceraldehyde; cellular response to ionomycin; and learning or memory. Located in cytosol; membrane; and nucleus. Biomarker of myocardial infarction. Human ortholog(s) of this gene implicated in Alzheimer's disease; developmental and epileptic encephalopathy 12; and myelodysplastic syndrome. Orthologous to human PLCB1 (phospholipase C beta 1); PARTICIPATES IN acebutolol pharmacodynamics pathway; adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway; amiodarone pharmacodynamics pathway; INTERACTS WITH (+)-schisandrin B; (R)-noradrenaline; 1-(3-chlorophenyl)piperazine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1; 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-1; Phosphb; phosphoinositide phospholipase C; phosphoinositide phospholipase C-beta-1; phospholipase C, beta 1; phospholipase C, beta 1 (phosphoinositide-specific); phospholipase C-beta-1; Phospholipase C-beta1; phospholipase C-I; PLC'1; PLC-154; PLC-beta-1; PLC-I; PLCbeta1; RATPHOSPHB
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Plcb1Tn(pb-Bhr2)1Wmukf  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23122,059,968 - 122,772,896 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3122,060,031 - 122,772,869 (+)Ensembl
Rnor_6.03127,721,244 - 128,419,565 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3128,155,069 - 128,419,545 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03134,211,557 - 134,908,321 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43122,797,718 - 123,523,675 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13122,703,321 - 123,430,863 (+)NCBI
Celera3120,808,920 - 121,513,252 (+)NCBICelera
Cytogenetic Map3q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(R)-noradrenaline  (EXP)
1,2-dichloroethane  (ISO)
1-(3-chlorophenyl)piperazine  (EXP)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-dihydroxyphenylethyleneglycol  (EXP)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acrylamide  (EXP)
acrylonitrile  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
aldehydo-D-glucose  (EXP)
all-trans-retinoic acid  (ISO)
alprazolam  (EXP)
aluminium trifluoride  (EXP)
amphetamine  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP)
antirheumatic drug  (ISO)
apocynin  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
barium(0)  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buspirone  (EXP)
butanal  (ISO)
C60 fullerene  (EXP)
caffeine  (EXP)
calcitriol  (EXP)
Candesartan cilexetil  (EXP)
carbachol  (EXP)
carbon nanotube  (ISO)
choline  (ISO)
chrysene  (ISO)
cisplatin  (EXP)
clofibrate  (ISO)
clozapine  (ISO)
cobalt dichloride  (EXP,ISO)
cocaine  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
D-glucose  (EXP)
D-glyceraldehyde  (EXP)
desipramine  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP,ISO)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (ISO)
dieldrin  (EXP)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fipronil  (EXP)
fluoxetine  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
genistein  (ISO)
glucose  (EXP)
glyceraldehyde  (EXP)
glyphosate  (ISO)
guanosine 5'-[gamma-thio]triphosphate  (EXP)
indometacin  (ISO)
ionomycin  (EXP)
irinotecan  (EXP)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
methamphetamine  (EXP,ISO)
methapyrilene  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
morphine  (ISO)
N-nitrosodiethylamine  (ISO)
N-nitrosomorpholine  (EXP)
N-Nitrosopyrrolidine  (ISO)
nickel atom  (ISO)
nickel dichloride  (EXP)
O-methyleugenol  (ISO)
oxaliplatin  (EXP)
oxytocin  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
perfluorooctanoic acid  (ISO)
Phenelzine  (EXP)
phenylephrine  (EXP)
phenylpropanolamine  (ISO)
PhIP  (EXP)
pirinixic acid  (ISO)
poly(I:C)  (ISO)
prazosin  (EXP)
progesterone  (ISO)
quercetin  (ISO)
silicon dioxide  (EXP,ISO)
sodium dichromate  (EXP)
streptozocin  (EXP)
temozolomide  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP)
tetraphene  (ISO)
theophylline  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
topotecan  (EXP)
trichostatin A  (ISO)
U-73122  (EXP,ISO)
valproic acid  (ISO)
zearalenone  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of meiosis involved in egg activation  (IEA,ISO,ISS)
brain development  (IEA,IEP)
cellular response to fluoride  (IDA)
cellular response to glyceraldehyde  (IDA)
cellular response to ionomycin  (IDA)
cellular response to vasopressin  (IDA)
cerebral cortex development  (IEA,ISO,ISS)
fat cell differentiation  (IEA,ISO)
G protein-coupled acetylcholine receptor signaling pathway  (IEA,ISO)
G2/M transition of mitotic cell cycle  (IEA,ISO)
glutamate receptor signaling pathway  (IEA,ISO,ISS)
inositol trisphosphate metabolic process  (IDA)
insulin-like growth factor receptor signaling pathway  (IEA,ISO,ISS)
interleukin-1-mediated signaling pathway  (IEA,ISO)
interleukin-12-mediated signaling pathway  (IEA,ISO)
interleukin-15-mediated signaling pathway  (IEA,ISO)
intracellular signal transduction  (IEA)
learning  (IEP)
lipid catabolic process  (IEA)
memory  (IBA,IEA,IEP,ISO)
negative regulation of monocyte extravasation  (IEA,ISO,ISS)
negative regulation of transcription, DNA-templated  (IEA,ISO,ISS)
phosphatidylinositol catabolic process  (IDA)
phosphatidylinositol metabolic process  (IEA,IEP,ISO)
phosphatidylinositol-mediated signaling  (IBA)
positive regulation of acrosome reaction  (IEA,ISO)
positive regulation of CD24 production  (IEA,ISO,ISS)
positive regulation of developmental growth  (IEA,ISO,ISS)
positive regulation of embryonic development  (IEA,ISO)
positive regulation of G1/S transition of mitotic cell cycle  (IEA,ISO,ISS)
positive regulation of interleukin-12 production  (IEA,ISO,ISS)
positive regulation of JNK cascade  (IEA,ISO)
positive regulation of myoblast differentiation  (IEA,ISO,ISS)
positive regulation of transcription, DNA-templated  (IEA,ISO,ISS)
postsynaptic modulation of chemical synaptic transmission  (IEA,ISO)
regulation of catalytic activity  (IEA)
regulation of cell cycle  (IEA)
regulation of establishment of endothelial barrier  (IEA,ISO)
regulation of fertilization  (IEA,ISO)
regulation of G protein-coupled receptor signaling pathway  (IEA,ISO,ISS)
regulation of retrograde trans-synaptic signaling by endocanabinoid  (IEA,ISO)
response to monosaccharide  (IDA)
response to organonitrogen compound  (IEP)
response to peptide hormone  (IDA)

Cellular Component
chromatin  (IEA,ISO)
cytoplasm  (IBA,IEA,ISO,ISS)
cytosol  (IDA)
GABA-ergic synapse  (IEA,ISO)
glutamatergic synapse  (IEA,ISO)
membrane  (IDA)
nuclear membrane  (IEA)
nuclear speck  (IBA,IEA,ISO,ISS)
nucleus  (IDA,IEA,ISO,ISS)
postsynapse  (IEA)
protein-containing complex  (IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
acebutolol pharmacodynamics pathway  (ISO)
adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway  (ISO)
Alzheimer's disease pathway  (IEA)
amiodarone pharmacodynamics pathway  (ISO)
amlodipine pharmacodynamics pathway  (ISO)
atenolol pharmacodynamics pathway  (ISO)
betaxolol pharmacodynamics pathway  (ISO)
bisoprolol pharmacodynamics pathway  (ISO)
bupranolol drug pathway  (ISO)
bupranolol pharmacodynamics pathway  (ISO)
calcium/calcium-mediated signaling pathway  (IEA)
carvedilol pharmacodynamics pathway  (ISO)
Chagas disease pathway  (IEA)
chemokine mediated signaling pathway  (IEA)
diltiazem pharmacodynamics pathway  (ISO)
disopyramide pharmacodynamics pathway  (ISO)
dobutamine pharmacodynamics pathway  (ISO)
endothelin signaling pathway  (ISO)
Entamoebiasis pathway  (IEA)
esmolol pharmacodynamics pathway  (ISO)
flecainde pharmacodynamics pathway  (ISO)
fosphenytoin pharmacodynamics pathway  (ISO)
G protein mediated signaling pathway via Galphaq family  (ISO)
glutamate signaling pathway  (IEA)
gonadotropin-releasing hormone signaling pathway  (IEA)
Huntington's disease pathway  (IEA)
ibutilide pharmacodynamics pathway  (ISO)
inositol phosphate metabolic pathway  (IEA)
isoprenaline pharmacodynamics pathway  (ISO)
isradipine pharmacodynamics pathway  (ISO)
levobunolol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
long term depression  (IEA)
long term potentiation  (IEA)
metoprolol pharmacodynamics pathway  (ISO)
mexiletine pharmacodynamics pathway  (ISO)
nadolol pharmacodynamics pathway  (ISO)
nebivolol pharmacodynamics pathway  (ISO)
nifedipine pharmacodynamics pathway  (ISO)
nimodipine pharmacodynamics pathway  (ISO)
nisoldipine pharmacodynamics pathway  (ISO)
nitrendipine pharmacodynamics pathway  (ISO)
penbutolol pharmacodynamics pathway  (ISO)
phenytoin pharmacodynamics pathway  (ISO)
phosphatidylinositol 3-kinase signaling pathway  (IEA)
phosphoinositide metabolic pathway  (ISO)
pindolol pharmacodynamics pathway  (ISO)
procainamide pharmacodynamics pathway  (ISO)
propranolol pharmacodynamics pathway  (ISO)
protein kinase C (PKC) signaling pathway  (ISO)
quinidine pharmacodynamics pathway  (ISO)
sleeping sickness pathway  (IEA)
sotalol pharmacodynamics pathway  (ISO)
timolol pharmacodynamics pathway  (ISO)
verapamil pharmacodynamics pathway  (ISO)
Wnt signaling pathway  (IEA)

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Bahk YY, etal., J Biol Chem 1994 Mar 18;269(11):8240-5.
2. Cai Y, etal., Oncogene. 2005 Jun 16;24(26):4293-300.
3. Damm F, etal., J Clin Oncol. 2010 Aug 1;28(22):e384-7; author reply e388-9. doi: 10.1200/JCO.2010.28.6971. Epub 2010 Jun 1.
4. Day M, etal., J Neurophysiol 2002 May;87(5):2490-504.
5. Domenici MR, etal., Eur J Neurosci 2003 May;17(10):2047-55.
6. Drin G and Scarlata S, Cell Signal. 2007 Jul;19(7):1383-92. Epub 2007 Apr 29.
7. Dwivedi Y, etal., Neuropsychopharmacology. 2005 Mar;30(3):473-83.
8. Follo MY, etal., Int J Mol Med. 2006 Aug;18(2):267-71.
9. Follo MY, etal., Leukemia. 2011 Feb;25(2):271-80. doi: 10.1038/leu.2010.266. Epub 2010 Nov 26.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. GOA data from the GO Consortium
12. Hannan AJ, etal., Neuropharmacology. 1998 Apr-May;37(4-5):593-605.
13. Ju H, etal., Circulation. 1998 Mar 10;97(9):892-9.
14. KEGG
15. Kelley GG, etal., Mol Cell Endocrinol. 2001 May 25;177(1-2):107-15.
16. Mazzoni M, etal., Biochem Biophys Res Commun. 1992 Aug 31;187(1):114-20.
17. MGD data from the GO Consortium
18. Nagasawa K, etal., Life Sci 2003 Aug 1;73(11):1453-62.
19. NCBI rat LocusLink and RefSeq merged data July 26, 2002
20. OMIM Disease Annotation Pipeline
21. Pipeline to import KEGG annotations from KEGG into RGD
22. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
23. Pipeline to import SMPDB annotations from SMPDB into RGD
24. RGD automated data pipeline
25. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
26. RGD automated import pipeline for gene-chemical interactions
27. Rhee SG Annu Rev Biochem. 2001;70:281-312.
28. Runnels LW, etal., Science 2001 Feb 9;291(5506):1043-7.
29. Shimohama S and Matsushima H, Alzheimer Dis Assoc Disord. 1995;9 Suppl 2:15-22.
30. Singal T, etal., Biochem Biophys Res Commun. 2004 Jul 30;320(3):1015-9.
31. Smrcka AV and Sternweis PC, J Biol Chem. 1993 May 5;268(13):9667-74.
32. Vitale M, etal., Int J Mol Med. 2004 Aug;14(2):161-4.
33. Weeber EJ and Caldwell KK, Pharmacol Biochem Behav. 2004 May;78(1):155-64.
34. Zhang Y, etal., Mol Pharmacol. 2006 Sep;70(3):860-8. Epub 2006 Jun 8.
Additional References at PubMed
PMID:1322796   PMID:3390863   PMID:8454637   PMID:8872139   PMID:9187110   PMID:9305844   PMID:9444325   PMID:9500449   PMID:9762362   PMID:10913438   PMID:11118617   PMID:11224545  
PMID:11464583   PMID:11743656   PMID:12031797   PMID:12612139   PMID:12704654   PMID:12799190   PMID:12821674   PMID:14499343   PMID:15174099   PMID:15474310   PMID:15664177   PMID:15849202  
PMID:16339037   PMID:17022104   PMID:17065107   PMID:17634366   PMID:17725492   PMID:18390926   PMID:18493969   PMID:18692062   PMID:18694821   PMID:18820027   PMID:19028838   PMID:19199708  
PMID:19347873   PMID:19385066   PMID:19538471   PMID:19564249   PMID:19687358   PMID:19896516   PMID:20393598   PMID:21124736   PMID:21148417   PMID:21338571   PMID:22735577   PMID:22871113  
PMID:23376485   PMID:23503970   PMID:23665500   PMID:24760983   PMID:25185819   PMID:26521046   PMID:26747500   PMID:27353086   PMID:27379421   PMID:27624933   PMID:29401590   PMID:32247043  


Genomics

Comparative Map Data
Plcb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23122,059,968 - 122,772,896 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3122,060,031 - 122,772,869 (+)Ensembl
Rnor_6.03127,721,244 - 128,419,565 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3128,155,069 - 128,419,545 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03134,211,557 - 134,908,321 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43122,797,718 - 123,523,675 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13122,703,321 - 123,430,863 (+)NCBI
Celera3120,808,920 - 121,513,252 (+)NCBICelera
Cytogenetic Map3q36NCBI
PLCB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl208,077,251 - 8,968,360 (+)EnsemblGRCh38hg38GRCh38
GRCh38208,132,266 - 8,884,900 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37208,112,913 - 8,865,547 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36208,061,296 - 8,813,547 (+)NCBINCBI36hg18NCBI36
Build 34208,061,295 - 8,813,547NCBI
Celera208,182,881 - 8,935,778 (+)NCBI
Cytogenetic Map20p12.3NCBI
HuRef208,064,325 - 8,817,514 (+)NCBIHuRef
CHM1_1208,113,481 - 8,866,748 (+)NCBICHM1_1
Plcb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392134,628,084 - 135,317,178 (+)NCBIGRCm39mm39
GRCm39 Ensembl2134,627,987 - 135,317,178 (+)Ensembl
GRCm382134,786,164 - 135,475,258 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2134,786,067 - 135,475,258 (+)EnsemblGRCm38mm10GRCm38
MGSCv372134,611,900 - 135,300,994 (+)NCBIGRCm37mm9NCBIm37
MGSCv362134,477,971 - 135,163,863 (+)NCBImm8
Celera2135,990,426 - 136,678,579 (+)NCBICelera
Cytogenetic Map2F3NCBI
cM Map265.66NCBI
Plcb1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541518,210,662 - 18,915,158 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541518,210,608 - 18,915,099 (+)NCBIChiLan1.0ChiLan1.0
PLCB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1207,887,773 - 8,636,019 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl207,887,960 - 8,636,019 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0208,106,665 - 8,858,572 (+)NCBIMhudiblu_PPA_v0panPan3
PLCB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12413,337,285 - 13,996,218 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2413,322,296 - 13,995,539 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2413,161,289 - 13,837,418 (-)NCBI
ROS_Cfam_1.02413,744,297 - 14,413,598 (-)NCBI
UMICH_Zoey_3.12413,354,731 - 14,024,546 (-)NCBI
UNSW_CanFamBas_1.02413,455,648 - 14,132,727 (-)NCBI
UU_Cfam_GSD_1.02413,793,592 - 14,463,037 (-)NCBI
Plcb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640162,117,602 - 162,822,762 (-)NCBI
SpeTri2.0NW_00493648510,548,966 - 11,254,139 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PLCB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1717,007,261 - 17,745,312 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11717,007,197 - 17,745,314 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21719,691,473 - 19,950,043 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PLCB1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1229,242,601 - 29,994,238 (-)NCBI
ChlSab1.1 Ensembl229,242,425 - 29,496,793 (-)Ensembl
Vero_WHO_p1.0NW_02366607114,560,873 - 15,334,958 (+)NCBI
Plcb1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247419,030,817 - 9,859,597 (+)NCBI

Position Markers
D3Wox22  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23122,771,586 - 122,771,798 (+)MAPPERmRatBN7.2
mRatBN7.23122,771,586 - 122,771,840 (+)MAPPERmRatBN7.2
Rnor_6.03128,419,864 - 128,420,075NCBIRnor6.0
Rnor_6.03128,419,864 - 128,420,193NCBIRnor6.0
Rnor_5.03134,908,640 - 134,908,969UniSTSRnor5.0
Rnor_5.03134,908,640 - 134,908,851UniSTSRnor5.0
RGSC_v3.43123,523,994 - 123,524,205UniSTSRGSC3.4
Celera3121,513,571 - 121,513,784UniSTS
Cytogenetic Map3q36UniSTS
D3Rat158  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23122,457,858 - 122,458,012 (+)MAPPERmRatBN7.2
Rnor_6.03128,120,751 - 128,120,904NCBIRnor6.0
Rnor_5.03134,608,322 - 134,608,475UniSTSRnor5.0
RGSC_v3.43123,202,756 - 123,203,100RGDRGSC3.4
RGSC_v3.43123,202,807 - 123,202,960UniSTSRGSC3.4
RGSC_v3.13123,108,380 - 123,108,533RGD
Celera3121,205,948 - 121,206,101UniSTS
RH 3.4 Map31069.6RGD
RH 3.4 Map31069.6UniSTS
RH 2.0 Map3718.3RGD
SHRSP x BN Map359.6699RGD
Cytogenetic Map3q36UniSTS
D3Mco10  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23122,411,707 - 122,412,032 (+)MAPPERmRatBN7.2
Rnor_6.03128,074,425 - 128,074,746NCBIRnor6.0
Rnor_5.03134,561,996 - 134,562,317UniSTSRnor5.0
RGSC_v3.43123,156,618 - 123,156,941RGDRGSC3.4
RGSC_v3.43123,156,620 - 123,156,941UniSTSRGSC3.4
RGSC_v3.13123,062,191 - 123,062,514RGD
Celera3121,159,818 - 121,160,139UniSTS
Cytogenetic Map3q36UniSTS
A007B46  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23122,769,721 - 122,769,918 (+)MAPPERmRatBN7.2
Rnor_6.03128,417,999 - 128,418,195NCBIRnor6.0
Rnor_5.03134,906,775 - 134,906,971UniSTSRnor5.0
RGSC_v3.43123,522,129 - 123,522,325UniSTSRGSC3.4
Celera3121,511,706 - 121,511,902UniSTS
Cytogenetic Map3q36UniSTS
AI132408  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23122,772,417 - 122,772,691 (+)MAPPERmRatBN7.2
Rnor_6.03128,420,813 - 128,421,086NCBIRnor6.0
Rnor_5.03134,909,589 - 134,909,862UniSTSRnor5.0
RGSC_v3.43123,524,825 - 123,525,098UniSTSRGSC3.4
Celera3121,514,404 - 121,514,677UniSTS
Cytogenetic Map3q36UniSTS
RH143123  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23122,301,585 - 122,301,695 (+)MAPPERmRatBN7.2
Rnor_6.03127,963,136 - 127,963,245NCBIRnor6.0
Rnor_5.03134,451,872 - 134,451,981UniSTSRnor5.0
RGSC_v3.43123,042,363 - 123,042,472UniSTSRGSC3.4
Celera3121,050,653 - 121,050,762UniSTS
RH 3.4 Map31074.6UniSTS
Cytogenetic Map3q36UniSTS
BE107717  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera3121,070,507 - 121,070,663UniSTS
RH 3.4 Map31077.7UniSTS
Cytogenetic Map3q36UniSTS
RH135213  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23122,431,214 - 122,431,409 (+)MAPPERmRatBN7.2
Rnor_6.03128,093,928 - 128,094,122NCBIRnor6.0
Rnor_5.03134,581,499 - 134,581,693UniSTSRnor5.0
RGSC_v3.43123,175,965 - 123,176,159UniSTSRGSC3.4
Celera3121,179,319 - 121,179,513UniSTS
RH 3.4 Map31069.6UniSTS
Cytogenetic Map3q36UniSTS
RH138108  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23122,266,922 - 122,267,059 (+)MAPPERmRatBN7.2
Rnor_6.03127,928,459 - 127,928,595NCBIRnor6.0
Rnor_5.03134,417,629 - 134,417,765UniSTSRnor5.0
RGSC_v3.43123,004,632 - 123,004,768UniSTSRGSC3.4
Celera3121,015,901 - 121,016,037UniSTS
RH 3.4 Map31074.7UniSTS
Cytogenetic Map3q36UniSTS
RH138884  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23122,269,326 - 122,269,498 (+)MAPPERmRatBN7.2
Rnor_6.03127,930,863 - 127,931,034NCBIRnor6.0
Rnor_5.03134,420,033 - 134,420,204UniSTSRnor5.0
RGSC_v3.43123,007,036 - 123,007,207UniSTSRGSC3.4
Celera3121,018,305 - 121,018,476UniSTS
RH 3.4 Map31074.7UniSTS
Cytogenetic Map3q36UniSTS
AU048499  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23122,681,618 - 122,681,812 (+)MAPPERmRatBN7.2
Rnor_6.03128,333,610 - 128,333,805NCBIRnor6.0
Rnor_5.03134,820,853 - 134,821,048UniSTSRnor5.0
RGSC_v3.43123,432,866 - 123,433,061UniSTSRGSC3.4
Celera3121,424,544 - 121,424,739UniSTS
Cytogenetic Map3q36UniSTS
AU048959  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23122,685,104 - 122,685,277 (+)MAPPERmRatBN7.2
Rnor_6.03128,337,098 - 128,337,270NCBIRnor6.0
Rnor_5.03134,824,341 - 134,824,513UniSTSRnor5.0
RGSC_v3.43123,436,354 - 123,436,526UniSTSRGSC3.4
Celera3121,428,032 - 121,428,204UniSTS
Cytogenetic Map3q36UniSTS
D8S1807  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23122,135,471 - 122,136,109 (+)MAPPERmRatBN7.2
mRatBN7.21573,241,271 - 73,242,912 (+)MAPPERmRatBN7.2
Rnor_6.01580,810,982 - 80,812,622NCBIRnor6.0
Rnor_6.03127,796,967 - 127,797,604NCBIRnor6.0
Rnor_5.01584,349,172 - 84,350,812UniSTSRnor5.0
Rnor_5.03134,287,614 - 134,288,251UniSTSRnor5.0
RGSC_v3.43122,874,247 - 122,874,884UniSTSRGSC3.4
RGSC_v3.41579,872,788 - 79,874,428UniSTSRGSC3.4
Celera1572,522,594 - 72,524,234UniSTS
Celera3120,884,308 - 120,884,945UniSTS
Cytogenetic Map3q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)389772419134772419Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3112287552135181505Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)3115638168135181505Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)3115638168135181505Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3121056165145956249Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:98
Count of miRNA genes:60
Interacting mature miRNAs:66
Transcripts:ENSRNOT00000006389, ENSRNOT00000051184
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 16 8 8 60 27 5 9
Low 3 43 41 33 19 33 8 8 14 8 36 2 8
Below cutoff 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006389   ⟹   ENSRNOP00000006389
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3122,060,031 - 122,771,268 (+)Ensembl
Rnor_6.0 Ensembl3128,155,117 - 128,419,545 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000051184   ⟹   ENSRNOP00000042533
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3122,060,031 - 122,772,869 (+)Ensembl
Rnor_6.0 Ensembl3128,155,069 - 128,349,864 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098292   ⟹   ENSRNOP00000085919
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3122,111,601 - 122,689,381 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113879   ⟹   ENSRNOP00000078760
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3122,491,581 - 122,772,869 (+)Ensembl
RefSeq Acc Id: NM_001077641   ⟹   NP_001071109
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23122,059,968 - 122,771,268 (+)NCBI
Rnor_6.03127,721,244 - 128,419,545 (+)NCBI
Rnor_5.03134,211,557 - 134,908,321 (+)NCBI
RGSC_v3.43122,797,718 - 123,523,675 (+)RGD
Celera3120,808,920 - 121,513,252 (+)RGD
Sequence:
RefSeq Acc Id: XM_017591466   ⟹   XP_017446955
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23122,059,988 - 122,772,896 (+)NCBI
Rnor_6.03127,721,389 - 128,419,565 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017591467   ⟹   XP_017446956
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23122,059,988 - 122,772,896 (+)NCBI
Rnor_6.03127,721,389 - 128,419,565 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001071109 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446955 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446956 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41885 (Get FASTA)   NCBI Sequence Viewer  
  EDL80287 (Get FASTA)   NCBI Sequence Viewer  
  P10687 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001071109   ⟸   NM_001077641
- UniProtKB: P10687 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017446956   ⟸   XM_017591467
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017446955   ⟸   XM_017591466
- Peptide Label: isoform X1
- UniProtKB: P10687 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006389   ⟸   ENSRNOT00000006389
RefSeq Acc Id: ENSRNOP00000042533   ⟸   ENSRNOT00000051184
RefSeq Acc Id: ENSRNOP00000085919   ⟸   ENSRNOT00000098292
RefSeq Acc Id: ENSRNOP00000078760   ⟸   ENSRNOT00000113879
Protein Domains
C2   PI-PLC X-box   PI-PLC Y-box

Transcriptome

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


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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (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/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)
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
F344/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
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
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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)
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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
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)
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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
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)
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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)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (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)
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)
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:3344 AgrOrtholog
Ensembl Genes ENSRNOG00000004810 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006389 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000042533 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006389 UniProtKB/TrEMBL
  ENSRNOT00000051184 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1230.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.60.40.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.20.20.190 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro C2_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand-dom_pair UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PI-PLC_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLC-beta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLC-beta1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLC-beta_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLC-beta_C_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLC-beta_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLC-beta_PH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLC-like_Pdiesterase_TIM-brl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLC_EF-hand-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLipase_C_PInositol-sp_X_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLipase_C_Pinositol-sp_Y UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24654 UniProtKB/Swiss-Prot
NCBI Gene 24654 ENTREZGENE
PANTHER PTHR10336 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10336:SF12 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DUF1154 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand_like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00168 UniProtKB/TrEMBL
  PH_14 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PI-PLC-X UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PI-PLC-Y UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLC-beta_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Plcb1 PhenoGen
PIRSF PLC-beta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS PHPHLIPASEC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PIPLC_X_DOMAIN UniProtKB/Swiss-Prot
  PIPLC_Y_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PS50004 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PLCXc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLCYc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00239 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF51695 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F1M084_RAT UniProtKB/TrEMBL
  P10687 ENTREZGENE, UniProtKB/Swiss-Prot
  R9PXY3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-30 Plcb1  phospholipase C beta 1  Plcb1  phospholipase C, beta 1 (phosphoinositide-specific)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-09 Plcb1  phospholipase C, beta 1 (phosphoinositide-specific)  Plcb1  phospholipase C, beta 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 Plcb1  phospholipase C, beta 1  LOC688139  similar to 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 1 (Phosphoinositide phospholipase C) (Phospholipase C-beta-1) (PLC-beta-1) (PLC-I) (PLC-154)  Data Merged 1643240 APPROVED
2006-11-20 LOC688139  similar to 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 1 (Phosphoinositide phospholipase C) (Phospholipase C-beta-1) (PLC-beta-1) (PLC-I) (PLC-154)      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Plcb1  Phospholipase C-beta1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease inhibition of pathway modulated by 5-HT(2) receptor activation via atypical neuroleptics may lead to alterations in serotonergic signaling and schizophrenia 633577
gene_expression expression levels significantly reduced in old neuronal striata 1299009
gene_expression expressed in brain 1299007
gene_pathway mediates intracellular Ca(2+), activation of calcineurin and inhibition of Ca(v)1.2 L-type Ca(2+) currents via upstream stimulation of 5-HT(2) receptors in prefrontal neurons 633577
gene_pathway may be involved in oxidative stress pathways 1299008
gene_process may play a role in myoblast differentiation 1299010
gene_transcript produced by alternative splicing of 5.4 kb transcript precursor 1299007