Bace2 (beta-secretase 2) - Rat Genome Database
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Gene: Bace2 (beta-secretase 2) Rattus norvegicus
Analyze
Symbol: Bace2
Name: beta-secretase 2
RGD ID: 1303241
Description: Predicted to have aspartic-type endopeptidase activity. Involved in astrocyte activation. Localizes to dense core granule. Human ortholog(s) of this gene implicated in Alzheimer's disease. Orthologous to human BACE2 (beta-secretase 2); PARTICIPATES IN Alzheimer's disease pathway; INTERACTS WITH 17alpha-ethynylestradiol; 3,3',4,4',5-pentachlorobiphenyl; 3,3',5,5'-tetrabromobisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: beta-site amyloid precursor protein cleaving enzyme 2; beta-site APP cleaving enzyme 2; beta-site APP-cleaving enzyme 2; memapsin-1; membrane-associated aspartic protease 1; theta-secretase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21136,707,473 - 36,789,550 (+)NCBI
Rnor_6.0 Ensembl1137,798,370 - 37,880,821 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01137,798,397 - 37,880,624 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01141,305,984 - 41,389,663 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41137,345,568 - 37,428,155 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11137,403,156 - 37,485,744 (+)NCBI
Celera1136,594,056 - 36,676,118 (+)NCBICelera
Cytogenetic Map11q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5,5'-tetrabromobisphenol A  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
antirheumatic drug  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
carbon nanotube  (ISO)
chloroprene  (EXP)
cisplatin  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
DDE  (EXP)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
entinostat  (ISO)
epoxiconazole  (EXP)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
folic acid  (ISO)
fonofos  (ISO)
formaldehyde  (ISO)
furan  (EXP)
gentamycin  (EXP)
linuron  (EXP)
lovastatin  (EXP,ISO)
mercury dichloride  (ISO)
methapyrilene  (ISO)
methyl methanesulfonate  (ISO)
mitomycin C  (ISO)
mitoxantrone  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
parathion  (ISO)
phenylmercury acetate  (ISO)
potassium dichromate  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
resveratrol  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
terbufos  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
thimerosal  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10591213   PMID:11423558   PMID:12477932   PMID:12801932   PMID:16757811   PMID:21907142   PMID:25342134  


Genomics

Comparative Map Data
Bace2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21136,707,473 - 36,789,550 (+)NCBI
Rnor_6.0 Ensembl1137,798,370 - 37,880,821 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01137,798,397 - 37,880,624 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01141,305,984 - 41,389,663 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41137,345,568 - 37,428,155 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11137,403,156 - 37,485,744 (+)NCBI
Celera1136,594,056 - 36,676,118 (+)NCBICelera
Cytogenetic Map11q12NCBI
BACE2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2141,167,801 - 41,282,530 (+)EnsemblGRCh38hg38GRCh38
GRCh382141,168,160 - 41,282,530 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372142,540,087 - 42,654,457 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh372142,539,728 - 42,654,461 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362141,461,598 - 41,570,394 (+)NCBINCBI36hg18NCBI36
Build 342141,461,597 - 41,570,394NCBI
Celera2127,737,910 - 27,846,710 (+)NCBI
Cytogenetic Map21q22.2-q22.3NCBI
HuRef2128,008,619 - 28,123,292 (+)NCBIHuRef
CHM1_12142,100,065 - 42,215,315 (+)NCBICHM1_1
Bace2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391697,157,928 - 97,244,136 (+)NCBIGRCm39mm39
GRCm381697,356,728 - 97,442,936 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1697,356,742 - 97,442,936 (+)EnsemblGRCm38mm10GRCm38
MGSCv371697,578,335 - 97,660,619 (+)NCBIGRCm37mm9NCBIm37
MGSCv361697,461,672 - 97,543,922 (+)NCBImm8
Celera1698,415,225 - 98,499,352 (+)NCBICelera
Cytogenetic Map16C4NCBI
Bace2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540740,792,887 - 40,874,760 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540740,792,089 - 40,879,872 (+)NCBIChiLan1.0ChiLan1.0
BACE2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12140,831,209 - 40,939,253 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2140,831,203 - 40,938,280 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02127,500,453 - 27,612,795 (+)NCBIMhudiblu_PPA_v0panPan3
BACE2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3135,713,149 - 35,760,681 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13135,714,003 - 35,760,686 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Bace2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365002,362,994 - 2,449,783 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BACE2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13204,600,735 - 204,694,836 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113204,600,740 - 204,720,215 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213214,759,157 - 214,846,140 (+)NCBISscrofa10.2Sscrofa10.2susScr3
BACE2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1285,079,404 - 85,194,908 (+)NCBI
ChlSab1.1 Ensembl285,079,812 - 85,187,944 (+)Ensembl
Bace2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474528,690,045 - 28,765,506 (-)NCBI

Position Markers
D11Got114  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01137,842,323 - 37,842,545NCBIRnor6.0
Rnor_5.01141,349,910 - 41,350,132UniSTSRnor5.0
RGSC_v3.41137,389,771 - 37,389,993UniSTSRGSC3.4
Cytogenetic Map11q12UniSTS
RH133630  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01137,880,506 - 37,880,720NCBIRnor6.0
Rnor_5.01141,388,093 - 41,388,307UniSTSRnor5.0
RGSC_v3.41137,428,037 - 37,428,251UniSTSRGSC3.4
Celera1136,676,000 - 36,676,214UniSTS
RH 3.4 Map11266.6UniSTS
Cytogenetic Map11q12UniSTS
RH134179  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01137,799,382 - 37,799,562NCBIRnor6.0
Rnor_5.01141,306,969 - 41,307,149UniSTSRnor5.0
RGSC_v3.41137,346,553 - 37,346,733UniSTSRGSC3.4
Celera1136,595,041 - 36,595,221UniSTS
RH 3.4 Map11272.3UniSTS
Cytogenetic Map11q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11172720192Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)1132503169342559Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11935127454351274Rat
2290451Scl58Serum cholesterol level QTL 583.48blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)111136730644444347Rat
724517Uae18Urinary albumin excretion QTL 183.7urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)111632197346583360Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111947517979734728Rat
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)112194422966944229Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)112194422966944229Rat
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)112204314944444112Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112540112970401129Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112572003870720038Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112572003870720038Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112831466586994795Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)113043533963186373Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)113043533986714631Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113215552082443118Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113590063480900634Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:34
Count of miRNA genes:27
Interacting mature miRNAs:34
Transcripts:ENSRNOT00000002679
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 3 20 1 12 2 10 11
Low 23 56 41 7 41 8 11 70 35 31 8
Below cutoff 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002679   ⟹   ENSRNOP00000002679
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1137,798,370 - 37,880,821 (+)Ensembl
RefSeq Acc Id: NM_001002802   ⟹   NP_001002802
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21136,707,473 - 36,789,337 (+)NCBI
Rnor_6.01137,798,397 - 37,880,624 (+)NCBI
Rnor_5.01141,305,984 - 41,389,663 (+)NCBI
RGSC_v3.41137,345,568 - 37,428,155 (+)RGD
Celera1136,594,056 - 36,676,118 (+)RGD
Sequence:
RefSeq Acc Id: XM_039088202   ⟹   XP_038944130
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21136,753,746 - 36,789,550 (+)NCBI
RefSeq Acc Id: XM_039088203   ⟹   XP_038944131
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21136,707,669 - 36,789,550 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001002802   ⟸   NM_001002802
- Peptide Label: precursor
- UniProtKB: Q6IE75 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002679   ⟸   ENSRNOT00000002679
RefSeq Acc Id: XP_038944131   ⟸   XM_039088203
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038944130   ⟸   XM_039088202
- Peptide Label: isoform X1
Protein Domains
Peptidase A1

Transcriptome

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

Promoters
RGD ID:13698091
Promoter ID:EPDNEW_R8615
Type:multiple initiation site
Name:Bace2_1
Description:beta-site APP-cleaving enzyme 2
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_6.01137,798,371 - 37,798,431EPDNEW

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)
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 (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)
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
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
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/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
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 (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
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
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/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
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 41375496 41375497 A G snv DOB/Oda (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303241 AgrOrtholog
Ensembl Genes ENSRNOG00000001953 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000002679 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000002679 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.40.70.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7936295 IMAGE-MGC_LOAD
InterPro Aspartic_peptidase_A1 UniProtKB/Swiss-Prot
  Aspartic_peptidase_AS UniProtKB/Swiss-Prot
  BACE UniProtKB/Swiss-Prot
  BACE2 UniProtKB/Swiss-Prot
  Memapsin-like UniProtKB/Swiss-Prot
  PEPTIDASE_A1 UniProtKB/Swiss-Prot
  Peptidase_aspartic_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:288227 UniProtKB/Swiss-Prot
MGC_CLONE MGC:188369 IMAGE-MGC_LOAD
NCBI Gene 288227 ENTREZGENE
PANTHER PTHR47965 UniProtKB/Swiss-Prot
  PTHR47965:SF40 UniProtKB/Swiss-Prot
Pfam Asp UniProtKB/Swiss-Prot
PhenoGen Bace2 PhenoGen
PRINTS BACE2 UniProtKB/Swiss-Prot
  BACEFAMILY UniProtKB/Swiss-Prot
  PEPSIN UniProtKB/Swiss-Prot
PROSITE ASP_PROTEASE UniProtKB/Swiss-Prot
  PEPTIDASE_A1 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50630 UniProtKB/Swiss-Prot
UniProt BACE2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary B2GVB0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-18 Bace2  beta-secretase 2  Bace2  beta-site APP-cleaving enzyme 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Bace2  beta-site APP-cleaving enzyme 2      Symbol and Name status set to approved 1299863 APPROVED
2005-07-14 Bace2  beta-site APP-cleaving enzyme 2      Symbol and Name status set to provisional 70820 PROVISIONAL