Psen2 (presenilin 2) - Rat Genome Database
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Gene: Psen2 (presenilin 2) Rattus norvegicus
Analyze
Symbol: Psen2
Name: presenilin 2
RGD ID: 621060
Description: Predicted to have endopeptidase activity. Involved in response to hypoxia. Localizes to early endosome; synaptic membrane; and synaptic vesicle. Human ortholog(s) of this gene implicated in Alzheimer's disease; Alzheimer's disease 4; breast cancer; and dilated cardiomyopathy 1V. Orthologous to human PSEN2 (presenilin 2); PARTICIPATES IN altered Notch signaling pathway involving the macromolecules modifying the main players; Alzheimer's disease pathway; Notch signaling pathway; INTERACTS WITH (+)-schisandrin B; 2,6-dinitrotoluene; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: presenilin-2; PS-2
Orthologs:
Homo sapiens (human) : PSEN2 (presenilin 2)  HGNC  Alliance
Mus musculus (house mouse) : Psen2 (presenilin 2)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Psen2 (presenilin 2)
Pan paniscus (bonobo/pygmy chimpanzee) : PSEN2 (presenilin 2)
Canis lupus familiaris (dog) : PSEN2 (presenilin 2)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Psen2 (presenilin 2)
Sus scrofa (pig) : PSEN2 (presenilin 2)
Chlorocebus sabaeus (African green monkey) : PSEN2 (presenilin 2)
Heterocephalus glaber (naked mole-rat) : Psen2 (presenilin 2)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01398,513,600 - 98,539,347 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1398,513,570 - 98,530,724 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013103,521,460 - 103,547,174 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41395,934,674 - 95,951,836 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11396,123,177 - 96,145,989 (-)NCBI
Celera1391,515,731 - 91,532,398 (-)NCBICelera
Cytogenetic Map13q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
amyloid precursor protein catabolic process  (IBA)
amyloid-beta metabolic process  (IBA,ISO)
brain morphogenesis  (ISO)
calcium ion transport  (IBA,ISO)
cardiac muscle contraction  (ISO)
cell fate specification  (ISO)
cellular protein metabolic process  (ISO)
dorsal/ventral neural tube patterning  (ISO)
embryonic limb morphogenesis  (ISO)
endoplasmic reticulum calcium ion homeostasis  (ISO)
forebrain development  (ISO)
hair follicle development  (ISO)
hematopoietic progenitor cell differentiation  (ISO)
intracellular signal transduction  (IEA)
learning or memory  (ISO)
locomotion  (ISO)
lung alveolus development  (ISO)
membrane protein ectodomain proteolysis  (IBA,ISO)
memory  (ISO)
mitochondrion-endoplasmic reticulum membrane tethering  (ISO)
myeloid leukocyte differentiation  (ISO)
negative regulation of apoptotic process  (IBA)
negative regulation of apoptotic signaling pathway  (ISO)
negative regulation of epidermal growth factor-activated receptor activity  (ISO)
negative regulation of extrinsic apoptotic signaling pathway via death domain receptors  (ISO)
negative regulation of protein binding  (ISO)
negative regulation of protein phosphorylation  (ISO)
negative regulation of protein-containing complex assembly  (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)
neuroinflammatory response  (ISO)
neuron cellular homeostasis  (ISO)
Notch receptor processing  (IBA)
Notch signaling pathway  (ISO)
positive regulation of apoptotic process  (ISO)
positive regulation of catalytic activity  (ISO)
positive regulation of coagulation  (ISO)
positive regulation of extrinsic apoptotic signaling pathway via death domain receptors  (ISO)
positive regulation of proteasomal ubiquitin-dependent protein catabolic process  (ISO)
positive regulation of receptor recycling  (ISO)
protein maturation  (ISO)
protein processing  (ISO)
protein transport  (ISO)
regulation of calcium import into the mitochondrion  (ISO)
regulation of epidermal growth factor-activated receptor activity  (ISO)
regulation of protein binding  (ISO)
regulation of synaptic plasticity  (ISO)
response to hypoxia  (IEP)
skin morphogenesis  (ISO)
somitogenesis  (ISO)
T cell activation involved in immune response  (ISO)
T cell receptor signaling pathway  (ISO)
thymus development  (ISO)

Molecular Function

References

References - curated
1. Clark RF, etal., Cold Spring Harb Symp Quant Biol 1996;61:551-8.
2. Fiuza UM and Arias AM, J Endocrinol. 2007 Sep;194(3):459-74.
3. Fraering PC, etal., Biochemistry 2004 Aug 3;43(30):9774-89.
4. Frykman S, etal., PLoS One. 2010 Jan 28;5(1):e8948. doi: 10.1371/journal.pone.0008948.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Herreman A, etal., Proc Natl Acad Sci U S A 1999 Oct 12;96(21):11872-7.
7. KEGG
8. Lee SF, etal., J Biol Chem 2002 Nov 22;277(47):45013-9. Epub 2002 Sep 23.
9. Lippa CF, etal., Ann Neurol. 2000 Sep;48(3):376-9.
10. Lleo A, etal., Neurosci Lett 2002 Feb 1;318(3):166-8.
11. Marambaud P, etal., Biochem Biophys Res Commun 1998 Nov 9;252(1):134-8.
12. MGD data from the GO Consortium
13. Mohuczy D, etal., Regul Pept 2002 Dec 31;110(1):1-7.
14. NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. OMIM Disease Annotation Pipeline
16. Pipeline to import KEGG annotations from KEGG into RGD
17. RGD automated data pipeline
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. RGD comprehensive gene curation
21. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
22. Takahashi H, etal., Gene 1997 Sep 15;197(1-2):383-7.
23. Tanahashi H and Tabira T, Biochim Biophys Acta 1998 Mar 13;1396(3):259-62.
24. To MD, etal., Oncogene. 2006 Jun 15;25(25):3557-64. Epub 2006 Feb 13.
25. Wolozin B, etal., Science 1996 Dec 6;274(5293):1710-3.
Additional References at PubMed
PMID:8940094   PMID:9203550   PMID:9298903   PMID:9353287   PMID:9535056   PMID:9632714   PMID:9950750   PMID:10557208   PMID:10846187   PMID:11943765   PMID:12460542   PMID:12646573  
PMID:12684521   PMID:15066262   PMID:15122901   PMID:15148382   PMID:15280425   PMID:15489334   PMID:15525534   PMID:15886206   PMID:16169548   PMID:16204356   PMID:16257512   PMID:16603547  
PMID:17097608   PMID:17418105   PMID:17556541   PMID:17614943   PMID:17626841   PMID:17698590   PMID:17920016   PMID:19376115   PMID:19779553   PMID:19946888   PMID:20208556   PMID:21285369  
PMID:21703454   PMID:25429133   PMID:26721367   PMID:27804997  


Genomics

Comparative Map Data
Psen2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01398,513,600 - 98,539,347 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1398,513,570 - 98,530,724 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013103,521,460 - 103,547,174 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41395,934,674 - 95,951,836 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11396,123,177 - 96,145,989 (-)NCBI
Celera1391,515,731 - 91,532,398 (-)NCBICelera
Cytogenetic Map13q26NCBI
PSEN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1226,870,184 - 226,896,105 (+)EnsemblGRCh38hg38GRCh38
GRCh381226,870,594 - 226,903,829 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371227,057,885 - 227,083,804 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361225,124,896 - 225,150,427 (+)NCBINCBI36hg18NCBI36
Build 341223,365,694 - 223,390,532NCBI
Celera1200,249,068 - 200,274,610 (+)NCBI
Cytogenetic Map1q42.13NCBI
HuRef1197,575,178 - 197,600,711 (+)NCBIHuRef
CHM1_11228,331,030 - 228,356,564 (+)NCBICHM1_1
Psen2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391180,054,569 - 180,091,030 (-)NCBI
GRCm381180,227,004 - 180,263,467 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1180,227,004 - 180,263,438 (-)EnsemblGRCm38mm10GRCm38
MGSCv371182,157,135 - 182,186,431 (-)NCBIGRCm37mm9NCBIm37
MGSCv361182,063,681 - 182,082,576 (-)NCBImm8
Celera1187,291,668 - 187,320,266 (-)NCBICelera
Cytogenetic Map1H4NCBI
cM Map184.19NCBI
Psen2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554065,727,367 - 5,752,234 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554065,727,367 - 5,748,798 (+)NCBIChiLan1.0ChiLan1.0
PSEN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11207,320,937 - 207,346,295 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1207,320,937 - 207,346,295 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01202,328,987 - 202,354,440 (+)NCBIMhudiblu_PPA_v0panPan3
PSEN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl738,147,173 - 38,166,722 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1738,147,157 - 38,163,023 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Psen2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365263,584,194 - 3,611,719 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PSEN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1014,532,550 - 14,561,858 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11014,532,556 - 14,561,862 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21016,862,708 - 16,891,775 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap10p16-p11NCBI
PSEN2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl252,862,251 - 2,877,386 (-)Ensembl
ChlSab1.1252,862,354 - 2,888,735 (-)NCBI
Psen2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477117,183,538 - 17,205,460 (-)NCBI

Position Markers
RH142771  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01398,532,666 - 98,532,820NCBIRnor6.0
Rnor_5.013103,540,526 - 103,540,680UniSTSRnor5.0
RGSC_v3.41395,953,778 - 95,953,932UniSTSRGSC3.4
Celera1391,534,340 - 91,534,494UniSTS
Cytogenetic Map13q26UniSTS
RH 3.4 Map13617.2UniSTS
RH140726  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01398,513,880 - 98,514,007NCBIRnor6.0
Rnor_5.013103,521,740 - 103,521,867UniSTSRnor5.0
RGSC_v3.41395,934,520 - 95,934,647UniSTSRGSC3.4
Celera1391,515,577 - 91,515,704UniSTS
Cytogenetic Map13q26UniSTS
RH 3.4 Map13630.9UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1357903612102903612Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1362975663107975663Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1366971778111971778Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1379567081103613733Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1380403559108770687Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1386833393114033958Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:40
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000040203
Prediction methods:Miranda, Rnahybrid
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 2 39 49 41 13 41 53 28 31 11
Low 1 4 8 6 8 11 21 7 10 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_031087 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250405 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250407 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250408 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250410 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769877 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598939 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAHX01077025 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01077026 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB004454 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC139413 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC078805 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D83700 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X99267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000040203   ⟹   ENSRNOP00000049605
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1398,514,034 - 98,530,724 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091715   ⟹   ENSRNOP00000070964
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1398,513,570 - 98,529,040 (-)Ensembl
RefSeq Acc Id: NM_031087   ⟹   NP_112349
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01398,514,034 - 98,530,724 (-)NCBI
Rnor_5.013103,521,460 - 103,547,174 (-)NCBI
RGSC_v3.41395,934,674 - 95,951,836 (-)RGD
Celera1391,515,731 - 91,532,398 (-)RGD
Sequence:
RefSeq Acc Id: XM_006250405   ⟹   XP_006250467
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01398,513,600 - 98,539,331 (-)NCBI
Rnor_5.013103,521,460 - 103,547,174 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006250407   ⟹   XP_006250469
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01398,513,600 - 98,539,313 (-)NCBI
Rnor_5.013103,521,460 - 103,547,174 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006250408   ⟹   XP_006250470
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01398,513,600 - 98,539,347 (-)NCBI
Rnor_5.013103,521,460 - 103,547,174 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006250410   ⟹   XP_006250472
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01398,513,600 - 98,531,794 (-)NCBI
Rnor_5.013103,521,460 - 103,547,174 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008769877   ⟹   XP_008768099
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01398,513,600 - 98,536,024 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598939   ⟹   XP_017454428
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01398,513,600 - 98,539,297 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_112349   ⟸   NM_031087
- UniProtKB: O88777 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006250470   ⟸   XM_006250408
- Peptide Label: isoform X1
- UniProtKB: O88777 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006250467   ⟸   XM_006250405
- Peptide Label: isoform X1
- UniProtKB: O88777 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006250469   ⟸   XM_006250407
- Peptide Label: isoform X1
- UniProtKB: O88777 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006250472   ⟸   XM_006250410
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008768099   ⟸   XM_008769877
- Peptide Label: isoform X1
- UniProtKB: O88777 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017454428   ⟸   XM_017598939
- Peptide Label: isoform X1
- UniProtKB: O88777 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000049605   ⟸   ENSRNOT00000040203
RefSeq Acc Id: ENSRNOP00000070964   ⟸   ENSRNOT00000091715

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 (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 (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/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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/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
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 (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
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
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
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
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
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 (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
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)
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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/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
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 (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 (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
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 (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 (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/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 (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621060 AgrOrtholog
Ensembl Genes ENSRNOG00000002879 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000049605 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000070964 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000040203 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000091715 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.472.100 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7109917 IMAGE-MGC_LOAD
InterPro Pept_A22A_PS2 UniProtKB/Swiss-Prot
  Peptidase_A22A UniProtKB/Swiss-Prot
  Preselin/SPP UniProtKB/Swiss-Prot
  Presenilin_C UniProtKB/Swiss-Prot
KEGG Report rno:81751 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93382 IMAGE-MGC_LOAD
NCBI Gene 81751 ENTREZGENE
PANTHER PTHR10202 UniProtKB/Swiss-Prot
Pfam Presenilin UniProtKB/Swiss-Prot
PhenoGen Psen2 PhenoGen
PRINTS PRESENILIN UniProtKB/Swiss-Prot
  PRESENILIN2 UniProtKB/Swiss-Prot
SMART PSN UniProtKB/Swiss-Prot
UniGene Rn.11045 ENTREZGENE
UniProt O88777 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary O08947 UniProtKB/Swiss-Prot
  O35546 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Psen2  presenilin 2    presenilin-2  Name updated 1299863 APPROVED
2002-08-07 Psen2  presenilin-2      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_homology 95% amino acid identity to human homolog 729647
gene_protein 448 amino acids 729647