Psen1 (presenilin 1) - Rat Genome Database

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Gene: Psen1 (presenilin 1) Rattus norvegicus
Analyze
Symbol: Psen1
Name: presenilin 1
RGD ID: 3425
Description: Enables endopeptidase activity. Involved in several processes, including negative regulation of neuron apoptotic process; neural retina development; and proteolysis. Located in several cellular components, including cytoplasmic vesicle; lysosomal membrane; and sarcolemma. Part of protein-containing complex. Is integral component of presynaptic membrane. Human ortholog(s) of this gene implicated in Alzheimer's disease (multiple); Pick's disease; dilated cardiomyopathy 1U; frontotemporal dementia; and hidradenitis suppurativa. Orthologous to human PSEN1 (presenilin 1); PARTICIPATES IN Notch signaling pathway; syndecan signaling pathway; Alzheimer's disease pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-hydroxy-5alpha-androstan-3-one; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: presenilin-1; PS-1
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
mRatBN7.26103,323,014 - 103,375,088 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl6103,323,120 - 103,371,650 (+)Ensembl
Rnor_6.06107,169,514 - 107,221,000 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6107,169,528 - 107,216,798 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06118,324,910 - 118,373,090 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46107,737,543 - 107,776,357 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16107,729,188 - 107,781,021 (+)NCBI
Celera6101,163,513 - 101,199,486 (+)NCBICelera
Cytogenetic Map6q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
all-trans-retinoic acid  (ISO)
aminoguanidine  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP,ISO)
antirheumatic drug  (ISO)
arsane  (EXP)
arsenic atom  (EXP)
arsenite(3-)  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP)
bortezomib  (ISO)
cadmium atom  (EXP)
cadmium dichloride  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cycloheximide  (ISO)
cypermethrin  (EXP)
cyproconazole  (ISO)
deguelin  (ISO)
dextran sulfate  (ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP)
diethyldithiocarbamic acid  (ISO)
dioxygen  (EXP)
disodium selenite  (ISO)
diuron  (EXP)
enzalutamide  (ISO)
epoxiconazole  (ISO)
fenofibrate  (ISO)
flutamide  (EXP)
folic acid  (ISO)
folpet  (ISO)
fulvestrant  (EXP)
glycine betaine  (ISO)
Goe 6976  (ISO)
isoflurane  (EXP)
isoniazide  (ISO)
isoprenaline  (ISO)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
lipopolysaccharide  (ISO)
maneb  (ISO)
melatonin  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
Methysticin  (ISO)
miconazole  (EXP)
N,N-diethyl-m-toluamide  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nickel atom  (ISO)
nickel dichloride  (EXP)
notoginsenoside R1  (ISO)
ochratoxin A  (EXP)
oxaliplatin  (ISO)
ozone  (ISO)
p-menthan-3-ol  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
permethrin  (EXP)
phenobarbital  (ISO)
phorbol 12,13-dibutanoate  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
S-adenosyl-L-homocysteine  (ISO)
sarin  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP)
sulindac sulfide  (ISO)
tauroursodeoxycholic acid  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
toluene  (EXP)
Trenbolone  (EXP)
triadimefon  (ISO)
trichostatin A  (ISO)
trilostane  (EXP)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
amyloid precursor protein catabolic process  (IBA,ISO)
amyloid precursor protein metabolic process  (ISO,ISS)
amyloid-beta formation  (ISO,ISS)
amyloid-beta metabolic process  (IBA,ISO)
astrocyte activation  (ISO)
astrocyte activation involved in immune response  (ISO)
autophagosome assembly  (ISO)
autophagy  (ISO)
blood vessel development  (ISO)
brain development  (ISO)
brain morphogenesis  (ISO)
Cajal-Retzius cell differentiation  (ISO)
calcium ion transmembrane transport  (IEA)
calcium ion transport  (IBA)
cell fate specification  (ISO)
cell-cell adhesion  (ISO)
cellular calcium ion homeostasis  (ISO)
cellular protein metabolic process  (ISO)
cellular response to amyloid-beta  (ISO)
cellular response to DNA damage stimulus  (ISO)
cerebellum development  (IEP)
cerebral cortex cell migration  (ISO)
cerebral cortex development  (ISO)
choline transport  (ISO)
dorsal/ventral neural tube patterning  (ISO)
embryonic limb morphogenesis  (ISO)
endoplasmic reticulum calcium ion homeostasis  (ISO,ISS)
epithelial cell proliferation  (ISO)
eye photoreceptor cell development  (NAS)
forebrain development  (ISO)
gene expression  (ISO)
heart development  (ISO)
heart looping  (ISO)
hematopoietic progenitor cell differentiation  (ISO)
intracellular signal transduction  (IEA)
L-glutamate import across plasma membrane  (ISO)
learning or memory  (ISO)
locomotion  (ISO)
membrane protein ectodomain proteolysis  (IBA,IMP,ISO,ISS)
membrane protein intracellular domain proteolysis  (ISO)
memory  (ISO)
mitochondrial transport  (ISO)
modulation of age-related behavioral decline  (ISO)
myeloid dendritic cell differentiation  (ISO)
myeloid leukocyte differentiation  (ISO)
negative regulation of apoptotic process  (IBA,IDA,ISO)
negative regulation of apoptotic signaling pathway  (ISO)
negative regulation of axonogenesis  (ISO)
negative regulation of core promoter binding  (ISO)
negative regulation of epidermal growth factor-activated receptor activity  (ISO)
negative regulation of gene expression  (ISO)
negative regulation of low-density lipoprotein receptor activity  (ISO)
negative regulation of neuron apoptotic process  (IMP)
negative regulation of protein kinase activity  (ISO)
negative regulation of protein phosphorylation  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
negative regulation of ubiquitin-dependent protein catabolic process  (ISO)
negative regulation of ubiquitin-protein transferase activity  (ISO)
neural retina development  (IEP)
neurogenesis  (ISO)
neuron apoptotic process  (ISO)
neuron development  (ISO)
neuron differentiation  (ISO)
neuron migration  (ISO)
neuron projection maintenance  (ISO)
Notch receptor processing  (IBA,ISO)
Notch signaling pathway  (ISO)
positive regulation of amyloid fibril formation  (ISO)
positive regulation of apoptotic process  (ISO)
positive regulation of catalytic activity  (ISO,ISS)
positive regulation of coagulation  (ISO)
positive regulation of dendritic spine development  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of glycolytic process  (ISO)
positive regulation of L-glutamate import across plasma membrane  (ISO)
positive regulation of MAP kinase activity  (ISO)
positive regulation of phosphorylation  (ISO)
positive regulation of proteasomal ubiquitin-dependent protein catabolic process  (ISO)
positive regulation of protein binding  (ISO)
positive regulation of protein import into nucleus  (ISO)
positive regulation of protein kinase activity  (ISO)
positive regulation of protein phosphorylation  (ISO)
positive regulation of receptor recycling  (ISO)
positive regulation of transcription, DNA-templated  (ISO)
positive regulation of tumor necrosis factor production  (ISO)
post-embryonic development  (ISO)
protein glycosylation  (ISO)
protein maturation  (ISO)
protein processing  (IDA,ISO,ISS)
protein transport  (ISO)
regulation of canonical Wnt signaling pathway  (ISO,ISS)
regulation of epidermal growth factor-activated receptor activity  (ISO)
regulation of gene expression  (ISO)
regulation of neuron projection development  (ISO,ISS)
regulation of phosphorylation  (ISO)
regulation of protein binding  (ISO)
regulation of resting membrane potential  (ISO)
regulation of synaptic plasticity  (ISO)
regulation of synaptic transmission, glutamatergic  (ISO)
response to oxidative stress  (ISO)
segmentation  (ISO)
sequestering of calcium ion  (ISO)
skeletal system morphogenesis  (ISO)
skin morphogenesis  (ISO)
smooth endoplasmic reticulum calcium ion homeostasis  (IBA,ISO)
somitogenesis  (ISO)
synapse organization  (ISO)
synaptic vesicle targeting  (ISO)
T cell activation involved in immune response  (ISO)
T cell receptor signaling pathway  (ISO)
thymus development  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Ankarcrona M and Hultenby K, Biochem Biophys Res Commun 2002 Jul 19;295(3):766-70.
2. Becker KG, etal., Nat Genet. 2004 May;36(5):431-2.
3. Benussi L, etal., Exp Cell Res 2001 Oct 1;269(2):256-65.
4. Bresciani LG, etal., Mol Cell Neurosci 2002 Oct;21(2):239-49.
5. Fiuza UM and Arias AM, J Endocrinol. 2007 Sep;194(3):459-74.
6. Frykman S, etal., PLoS One. 2010 Jan 28;5(1):e8948. doi: 10.1371/journal.pone.0008948.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Gil C, etal., FEBS Lett. 2007 May 1;581(9):1851-8. Epub 2007 Apr 9.
9. GOA data from the GO Consortium
10. Hansson CA, etal., J Biol Chem 2004 Dec 3;279(49):51654-60. Epub 2004 Sep 28.
11. KEGG
12. Klakotskaia D, etal., PLoS One. 2018 Apr 11;13(4):e0195469. doi: 10.1371/journal.pone.0195469. eCollection 2018.
13. Lee SF, etal., J Biol Chem 2002 Nov 22;277(47):45013-9. Epub 2002 Sep 23.
14. Leong DW, etal., J Biol Chem. 2012 Jun 8;287(24):20652-63. Epub 2012 Apr 25.
15. MGD data from the GO Consortium
16. Nadler Y, etal., Glia. 2008 Apr;56(5):552-67. doi: 10.1002/glia.20638.
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. OMIM Disease Annotation Pipeline
19. Pasternak SH, etal., J Biol Chem 2003 Jul 18;278(29):26687-94.
20. Pipeline to import KEGG annotations from KEGG into RGD
21. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
22. RGD automated data pipeline
23. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
24. RGD automated import pipeline for gene-chemical interactions
25. Sakuma K, etal., Biochim Biophys Acta. 2006 Jun;1760(6):980-7. Epub 2006 Mar 7.
26. Shen J, etal., Cell 1997 May 16;89(4):629-39.
27. Sherrington R, etal., Nature 1995 Jun 29;375(6534):754-60.
28. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
29. Takahashi H, etal., Neurosci Lett 1996 Mar 15;206(2-3):113-6.
30. Taniguchi T, etal., Gene 1997 Feb 20;186(1):73-5.
31. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
32. Uchihara T, etal., Neurobiol Aging. 2006 Jan;27(1):88-97. doi: 10.1016/j.neurobiolaging.2004.12.011. Epub 2005 Mar 31.
33. Wen PH, etal., Development. 2005 Sep;132(17):3873-83. Epub 2005 Aug 3.
34. Zhou Y, etal., Neurobiol Dis 2002 Mar;9(2):126-38.
Additional References at PubMed
PMID:8755489   PMID:8922407   PMID:9153393   PMID:9246482   PMID:9298903   PMID:9632714   PMID:9689133   PMID:10097174   PMID:10206645   PMID:10421573   PMID:10508860   PMID:10518543  
PMID:10551805   PMID:10557208   PMID:10662826   PMID:10801983   PMID:10805794   PMID:10821758   PMID:10854253   PMID:11104755   PMID:11262239   PMID:11517342   PMID:11567612   PMID:11738035  
PMID:11740561   PMID:11814648   PMID:11880515   PMID:11943765   PMID:11953314   PMID:12377771   PMID:12391611   PMID:12431992   PMID:12460542   PMID:12646573   PMID:12684521   PMID:12794186  
PMID:12805290   PMID:15004326   PMID:15009636   PMID:15066262   PMID:15122901   PMID:15123735   PMID:15148382   PMID:15163631   PMID:15192701   PMID:15254914   PMID:15274632   PMID:15280425  
PMID:15452145   PMID:15474363   PMID:15489334   PMID:15525534   PMID:15548218   PMID:15623526   PMID:15634781   PMID:15886206   PMID:15896720   PMID:16018997   PMID:16169548   PMID:16478525  
PMID:16511561   PMID:16715081   PMID:16959576   PMID:17097608   PMID:17196556   PMID:17428795   PMID:17431506   PMID:17512915   PMID:17543552   PMID:17556541   PMID:17614943   PMID:17698590  
PMID:17913918   PMID:17920016   PMID:18927449   PMID:18996842   PMID:19318429   PMID:19376115   PMID:19549834   PMID:19779553   PMID:19932144   PMID:20005821   PMID:20130175   PMID:20208556  
PMID:20299451   PMID:20445063   PMID:21143716   PMID:21179780   PMID:21325529   PMID:21559374   PMID:21951279   PMID:22375059   PMID:22771797   PMID:23152628   PMID:23794287   PMID:23913046  
PMID:24012003   PMID:24052308   PMID:25394380   PMID:25707991   PMID:26094765   PMID:26200696   PMID:26280335   PMID:26401782   PMID:27278235   PMID:27601731   PMID:27804997   PMID:28008308  
PMID:29061364   PMID:29392878   PMID:32265300  


Genomics

Comparative Map Data
Psen1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26103,323,014 - 103,375,088 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl6103,323,120 - 103,371,650 (+)Ensembl
Rnor_6.06107,169,514 - 107,221,000 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6107,169,528 - 107,216,798 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06118,324,910 - 118,373,090 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46107,737,543 - 107,776,357 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16107,729,188 - 107,781,021 (+)NCBI
Celera6101,163,513 - 101,199,486 (+)NCBICelera
Cytogenetic Map6q24NCBI
PSEN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1473,136,418 - 73,223,691 (+)EnsemblGRCh38hg38GRCh38
GRCh381473,136,436 - 73,223,691 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371473,603,215 - 73,690,399 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361472,672,932 - 72,756,862 (+)NCBINCBI36hg18NCBI36
Build 341472,684,480 - 72,755,750NCBI
Celera1453,666,429 - 53,753,632 (+)NCBI
Cytogenetic Map14q24.2NCBI
HuRef1453,768,824 - 53,855,913 (+)NCBIHuRef
CHM1_11473,542,049 - 73,629,540 (+)NCBICHM1_1
Psen1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391283,734,926 - 83,781,869 (+)NCBIGRCm39mm39
GRCm39 Ensembl1283,734,926 - 83,781,973 (+)Ensembl
GRCm381283,688,152 - 83,735,095 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1283,688,152 - 83,735,199 (+)EnsemblGRCm38mm10GRCm38
MGSCv371285,029,513 - 85,076,149 (+)NCBIGRCm37mm9NCBIm37
MGSCv361284,578,311 - 84,624,947 (+)NCBImm8
Celera1285,135,054 - 85,181,689 (+)NCBICelera
Cytogenetic Map12D1NCBI
cM Map1238.84NCBI
Psen1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555232,128,529 - 2,210,737 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555232,128,529 - 2,210,737 (-)NCBIChiLan1.0ChiLan1.0
PSEN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11472,579,024 - 72,663,876 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1472,579,024 - 72,663,876 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01453,718,299 - 53,802,684 (+)NCBIMhudiblu_PPA_v0panPan3
PSEN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1846,495,551 - 46,569,532 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl846,495,624 - 46,569,532 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha846,188,004 - 46,253,311 (+)NCBI
ROS_Cfam_1.0846,719,986 - 46,800,157 (+)NCBI
UMICH_Zoey_3.1846,399,068 - 46,464,638 (+)NCBI
UNSW_CanFamBas_1.0846,414,872 - 46,480,438 (+)NCBI
UU_Cfam_GSD_1.0846,805,794 - 46,871,397 (+)NCBI
Psen1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864029,540,161 - 29,604,355 (-)NCBI
SpeTri2.0NW_0049364882,464,623 - 2,528,807 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PSEN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl796,478,181 - 96,569,132 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1796,478,179 - 96,567,884 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27102,265,830 - 102,360,301 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap7q12-q26NCBI
PSEN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12450,394,310 - 50,476,521 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2450,405,590 - 50,472,132 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605338,577,780 - 38,659,678 (+)NCBIVero_WHO_p1.0
Psen1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473428,200,358 - 28,272,684 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH130315  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26103,371,424 - 103,371,642 (+)MAPPERmRatBN7.2
Rnor_6.06107,217,418 - 107,217,635NCBIRnor6.0
Rnor_5.06118,325,241 - 118,325,458UniSTSRnor5.0
RGSC_v3.46107,777,175 - 107,777,392UniSTSRGSC3.4
Celera6101,200,304 - 101,200,521UniSTS
RH 3.4 Map6733.1UniSTS
Cytogenetic Map6q31UniSTS
BF396895  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26103,358,677 - 103,358,913 (+)MAPPERmRatBN7.2
Rnor_6.06107,204,650 - 107,204,885NCBIRnor6.0
Rnor_5.06118,337,604 - 118,337,839UniSTSRnor5.0
RGSC_v3.46107,764,135 - 107,764,370UniSTSRGSC3.4
Celera6101,187,582 - 101,187,817UniSTS
RH 3.4 Map6733.8UniSTS
Cytogenetic Map6q31UniSTS
RH138321  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26103,328,921 - 103,329,120 (+)MAPPERmRatBN7.2
Rnor_6.06107,175,743 - 107,175,941NCBIRnor6.0
Rnor_5.06118,366,671 - 118,366,869UniSTSRnor5.0
RGSC_v3.46107,731,557 - 107,731,755UniSTSRGSC3.4
Celera6101,158,740 - 101,158,938UniSTS
RH 3.4 Map6732.59UniSTS
Cytogenetic Map6q31UniSTS
RH139353  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26103,371,682 - 103,371,758 (+)MAPPERmRatBN7.2
Rnor_6.06107,217,676 - 107,217,751NCBIRnor6.0
Rnor_5.06118,325,125 - 118,325,200UniSTSRnor5.0
RGSC_v3.46107,777,433 - 107,777,508UniSTSRGSC3.4
Celera6101,200,562 - 101,200,637UniSTS
RH 3.4 Map6732.09UniSTS
Cytogenetic Map6q31UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)645790088104200226Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)657730540104085867Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)657730540104085867Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)658632962103632962Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)661747639106747639Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)667262953112262953Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)671201409116201409Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)672202632115200186Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)672202632117202632Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)672202632130729475Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)672227641130729205Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)672227641130729205Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)673463459109394713Rat
2293837Kiddil1Kidney dilation QTL 13.7kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)681132889104393926Rat
2293842Kiddil3Kidney dilation QTL 34.3kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)681132889104393926Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)682523650110548006Rat
1576302Schws4Schwannoma susceptibility QTL 40.0078nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)683190345106747639Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)684130881129130881Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)685140138130140138Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)685140138130140138Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)685311061133478515Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)686894788131894788Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)688047916133047916Rat
1331722Thshl1Thyroid stimulating hormone level QTL 111.70.0001blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)689762877106752806Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)693701310128713626Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)694968928137848904Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)694968928139968928Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)696833997140994061Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6100364669140994061Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6100671796132340886Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:133
Count of miRNA genes:109
Interacting mature miRNAs:121
Transcripts:ENSRNOT00000012495
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 3 42 57 41 19 41 8 11 74 35 41 11 8
Low 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012495   ⟹   ENSRNOP00000012495
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6103,323,120 - 103,371,650 (+)Ensembl
Rnor_6.0 Ensembl6107,169,528 - 107,216,798 (+)Ensembl
RefSeq Acc Id: NM_019163   ⟹   NP_062036
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26103,334,224 - 103,370,607 (+)NCBI
Rnor_6.06107,181,052 - 107,216,600 (+)NCBI
Rnor_5.06118,324,910 - 118,373,090 (-)NCBI
RGSC_v3.46107,737,543 - 107,776,357 (+)RGD
Celera6101,163,513 - 101,199,486 (+)RGD
Sequence:
RefSeq Acc Id: XM_006240321   ⟹   XP_006240383
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26103,323,014 - 103,375,088 (+)NCBI
Rnor_6.06107,169,514 - 107,221,000 (+)NCBI
Rnor_5.06118,324,910 - 118,373,090 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006240322   ⟹   XP_006240384
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26103,323,258 - 103,375,088 (+)NCBI
Rnor_6.06107,169,671 - 107,221,000 (+)NCBI
Rnor_5.06118,324,910 - 118,373,090 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039111826   ⟹   XP_038967754
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26103,323,608 - 103,375,088 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_062036   ⟸   NM_019163
- UniProtKB: P97887 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006240384   ⟸   XM_006240322
- Peptide Label: isoform X1
- UniProtKB: P97887 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006240383   ⟸   XM_006240321
- Peptide Label: isoform X1
- UniProtKB: P97887 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000012495   ⟸   ENSRNOT00000012495
RefSeq Acc Id: XP_038967754   ⟸   XM_039111826
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13694713
Promoter ID:EPDNEW_R5238
Type:initiation region
Name:Psen1_1
Description:presenilin 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_6.06107,169,567 - 107,169,627EPDNEW

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)
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
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (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
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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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)
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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
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)
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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
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (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)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3425 AgrOrtholog
Ensembl Genes ENSRNOG00000009110 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000012495 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000012495 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.472.100 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7098018 IMAGE-MGC_LOAD
InterPro Pept_A22A_PS1 UniProtKB/Swiss-Prot
  Peptidase_A22A UniProtKB/Swiss-Prot
  Preselin/SPP UniProtKB/Swiss-Prot
  Presenilin_C UniProtKB/Swiss-Prot
KEGG Report rno:29192 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91716 IMAGE-MGC_LOAD
NCBI Gene 29192 ENTREZGENE
PANTHER PTHR10202 UniProtKB/Swiss-Prot
Pfam Presenilin UniProtKB/Swiss-Prot
PhenoGen Psen1 PhenoGen
PRINTS PRESENILIN UniProtKB/Swiss-Prot
  PRESENILIN1 UniProtKB/Swiss-Prot
SMART PSN UniProtKB/Swiss-Prot
TIGR TC235825
UniProt P97887 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary P97529 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Psen1  presenilin 1      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to the inner membrane of mitochondria 729648
gene_expression developmentally regulated in the retina 727595
gene_function interacts with proliferation-associated gene (PAG) resulting in protection from neuronal apoptosis 1304239