Apbb2 (amyloid beta precursor protein binding family B member 2) - Rat Genome Database

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Gene: Apbb2 (amyloid beta precursor protein binding family B member 2) Rattus norvegicus
Analyze
Symbol: Apbb2
Name: amyloid beta precursor protein binding family B member 2
RGD ID: 1562438
Description: Predicted to enable amyloid-beta binding activity. Predicted to be involved in several processes, including maintenance of lens transparency; negative regulation of cell cycle phase transition; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within extracellular matrix organization; generation of neurons; and regulation of apoptotic process. Predicted to be located in Golgi apparatus; early endosome; and endoplasmic reticulum. Predicted to be active in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in Alzheimer's disease and cognitive disorder. Orthologous to human APBB2 (amyloid beta precursor protein binding family B member 2); INTERACTS WITH 2,3,4,7,8-Pentachlorodibenzofuran; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: MODEL
Also known as: amyloid beta (A4) precursor protein-binding, family B, member 2; amyloid beta A4 precursor protein-binding family B member 2; amyloid-beta A4 precursor protein-binding family B member 2; LOC305338; RGD1562438; similar to amyloid beta (A4) precursor protein-binding, family B, member 2
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
mRatBN7.21441,557,918 - 41,878,622 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1441,557,972 - 41,877,495 (+)Ensembl
Rnor_6.01443,205,047 - 43,526,968 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1443,512,901 - 43,523,080 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01443,126,873 - 43,315,801 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41444,197,568 - 44,526,047 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1440,786,859 - 41,031,083 (+)NCBICelera
Cytogenetic Map14p11NCBI
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
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,4,7,8-Pentachlorodibenzofuran  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP,ISO)
2-hydroxypropanoic acid  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
carbamazepine  (ISO)
chloroprene  (EXP)
chromium(6+)  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP,ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
dieldrin  (EXP)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
Enterolactone  (ISO)
entinostat  (ISO)
geraniol  (ISO)
menadione  (ISO)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
nickel dichloride  (EXP)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
picoxystrobin  (ISO)
potassium chromate  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
quinolin-8-ol  (ISO)
rac-lactic acid  (ISO)
resorcinol  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
torcetrapib  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)

References

Additional References at PubMed
PMID:12089154   PMID:15629131   PMID:16407979  


Genomics

Comparative Map Data
Apbb2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21441,557,918 - 41,878,622 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1441,557,972 - 41,877,495 (+)Ensembl
Rnor_6.01443,205,047 - 43,526,968 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1443,512,901 - 43,523,080 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01443,126,873 - 43,315,801 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41444,197,568 - 44,526,047 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1440,786,859 - 41,031,083 (+)NCBICelera
Cytogenetic Map14p11NCBI
APBB2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl440,810,027 - 41,216,714 (-)EnsemblGRCh38hg38GRCh38
GRCh38440,810,027 - 41,216,714 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37440,812,044 - 41,216,559 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36440,510,996 - 40,911,245 (-)NCBINCBI36hg18NCBI36
Build 34440,657,166 - 41,057,416NCBI
Celera441,255,358 - 41,659,952 (-)NCBI
Cytogenetic Map4p14-p13NCBI
HuRef440,134,003 - 40,538,593 (-)NCBIHuRef
CHM1_1440,811,768 - 41,216,779 (-)NCBICHM1_1
Apbb2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39566,456,068 - 66,779,189 (-)NCBIGRCm39mm39
GRCm39 Ensembl566,456,046 - 66,776,127 (-)Ensembl
GRCm38566,298,725 - 66,619,064 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl566,298,703 - 66,618,784 (-)EnsemblGRCm38mm10GRCm38
MGSCv37566,693,127 - 67,009,910 (-)NCBIGRCm37mm9NCBIm37
MGSCv36566,581,023 - 66,897,806 (-)NCBImm8
Celera563,600,514 - 63,917,425 (-)NCBICelera
Cytogenetic Map5C3.1NCBI
Apbb2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554436,513,980 - 6,783,014 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554436,513,762 - 6,786,247 (+)NCBIChiLan1.0ChiLan1.0
APBB2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1440,984,632 - 41,386,264 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl440,988,428 - 41,189,064 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0435,133,490 - 35,538,443 (-)NCBIMhudiblu_PPA_v0panPan3
APBB2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1371,454,814 - 71,830,482 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl371,454,585 - 71,826,749 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha374,004,793 - 74,379,285 (+)NCBI
ROS_Cfam_1.0372,215,300 - 72,590,507 (+)NCBI
ROS_Cfam_1.0 Ensembl372,215,204 - 72,588,489 (+)Ensembl
UMICH_Zoey_3.1371,492,277 - 71,866,478 (+)NCBI
UNSW_CanFamBas_1.0371,647,497 - 72,022,440 (+)NCBI
UU_Cfam_GSD_1.0372,031,249 - 72,406,523 (+)NCBI
Apbb2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528537,746,664 - 38,134,814 (+)NCBI
SpeTri2.0NW_0049364828,166,380 - 8,489,489 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APBB2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl831,921,587 - 32,301,975 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1831,921,587 - 32,302,237 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2833,221,452 - 33,426,852 (+)NCBISscrofa10.2Sscrofa10.2susScr3
APBB2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1279,130,947 - 9,530,897 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl279,311,146 - 9,534,105 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604755,463,239 - 55,867,809 (+)NCBIVero_WHO_p1.0
Apbb2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476125,924,747 - 26,265,763 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D14Mit9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,873,444 - 41,873,686 (+)MAPPERmRatBN7.2
Rnor_6.01443,521,791 - 43,522,032NCBIRnor6.0
Rnor_5.01443,311,872 - 43,312,113UniSTSRnor5.0
RGSC_v3.41444,521,426 - 44,521,668RGDRGSC3.4
RGSC_v3.41444,521,427 - 44,521,668UniSTSRGSC3.4
RGSC_v3.11444,523,774 - 44,524,072RGD
Celera1441,025,904 - 41,026,147UniSTS
RH 2.0 Map14459.3RGD
Cytogenetic Map14p11UniSTS
D14Mgh5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,871,022 - 41,871,196 (+)MAPPERmRatBN7.2
Rnor_6.01443,519,364 - 43,519,537NCBIRnor6.0
Rnor_5.01443,309,667 - 43,309,840UniSTSRnor5.0
RGSC_v3.41444,508,397 - 44,508,570UniSTSRGSC3.4
RGSC_v3.41444,519,090 - 44,519,264RGDRGSC3.4
RGSC_v3.41444,508,396 - 44,508,570RGDRGSC3.4
RGSC_v3.41444,519,091 - 44,519,264UniSTSRGSC3.4
RGSC_v3.11444,521,481 - 44,521,655RGD
Celera1441,023,490 - 41,023,663UniSTS
Cytogenetic Map14p11UniSTS
D14Mgh6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,658,190 - 41,658,327 (+)MAPPERmRatBN7.2
Rnor_6.01443,305,859 - 43,305,995NCBIRnor6.0
Rnor_5.01443,097,692 - 43,097,828UniSTSRnor5.0
RGSC_v3.41444,291,075 - 44,291,212RGDRGSC3.4
RGSC_v3.41444,291,076 - 44,291,212UniSTSRGSC3.4
RGSC_v3.11444,293,466 - 44,293,603RGD
Celera1440,811,690 - 40,811,826UniSTS
Cytogenetic Map14p11UniSTS
D14Rat56  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,625,003 - 41,625,190 (+)MAPPERmRatBN7.2
Rnor_6.01443,272,603 - 43,272,789NCBIRnor6.0
Rnor_5.01443,064,714 - 43,064,900UniSTSRnor5.0
RGSC_v3.41444,257,619 - 44,257,806RGDRGSC3.4
RGSC_v3.41444,257,620 - 44,257,806UniSTSRGSC3.4
RGSC_v3.11444,260,010 - 44,260,197RGD
Celera1440,778,345 - 40,778,531UniSTS
RH 2.0 Map14439.5RGD
SHRSP x BN Map1428.2599RGD
FHH x ACI Map1439.47RGD
Cytogenetic Map14p11UniSTS
D14Rat63  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,806,290 - 41,806,385 (+)MAPPERmRatBN7.2
Rnor_6.01443,454,225 - 43,454,319NCBIRnor6.0
Rnor_5.01443,244,698 - 43,244,792UniSTSRnor5.0
RGSC_v3.41444,443,343 - 44,443,438RGDRGSC3.4
RGSC_v3.41444,443,344 - 44,443,438UniSTSRGSC3.4
RGSC_v3.11444,445,734 - 44,445,829RGD
Celera1440,958,541 - 40,958,635UniSTS
RH 2.0 Map14460.1RGD
SHRSP x BN Map1428.34RGD
FHH x ACI Map1439.47RGD
Cytogenetic Map14p11UniSTS
D14Got53  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,588,838 - 41,589,076 (+)MAPPERmRatBN7.2
Rnor_6.01443,236,538 - 43,236,775NCBIRnor6.0
Rnor_5.01443,028,642 - 43,028,879UniSTSRnor5.0
RGSC_v3.41444,220,787 - 44,221,025RGDRGSC3.4
RGSC_v3.41444,220,788 - 44,221,025UniSTSRGSC3.4
RGSC_v3.11444,223,178 - 44,223,416RGD
Celera1440,742,201 - 40,742,438UniSTS
RH 2.0 Map14449.1RGD
Cytogenetic Map14p11UniSTS
BI277850  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,877,776 - 41,877,949 (+)MAPPERmRatBN7.2
Rnor_6.01443,526,123 - 43,526,295NCBIRnor6.0
Rnor_5.01443,316,204 - 43,316,376UniSTSRnor5.0
RGSC_v3.41444,525,759 - 44,525,931UniSTSRGSC3.4
Celera1441,030,238 - 41,030,410UniSTS
Cytogenetic Map14p11UniSTS
RH141190  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,877,158 - 41,877,363 (+)MAPPERmRatBN7.2
Rnor_6.01443,525,505 - 43,525,709NCBIRnor6.0
Rnor_5.01443,315,586 - 43,315,790UniSTSRnor5.0
RGSC_v3.41444,525,141 - 44,525,345UniSTSRGSC3.4
Celera1441,029,620 - 41,029,824UniSTS
Cytogenetic Map14p11UniSTS
stSG602612  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,834,909 - 41,836,169 (+)MAPPERmRatBN7.2
mRatBN7.21441,834,961 - 41,836,169 (+)MAPPERmRatBN7.2
Rnor_6.01443,482,833 - 43,484,040NCBIRnor6.0
Rnor_6.01443,482,781 - 43,484,040NCBIRnor6.0
Rnor_5.01443,273,084 - 43,274,343UniSTSRnor5.0
Rnor_5.01443,273,136 - 43,274,343UniSTSRnor5.0
RGSC_v3.41444,472,396 - 44,473,603UniSTSRGSC3.4
RGSC_v3.41444,472,344 - 44,473,603UniSTSRGSC3.4
Celera1440,987,207 - 40,988,414UniSTS
Celera1440,987,155 - 40,988,414UniSTS
Cytogenetic Map14p11UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1736
Count of miRNA genes:306
Interacting mature miRNAs:424
Transcripts:ENSRNOT00000029018, ENSRNOT00000049214, ENSRNOT00000050664
Prediction methods:Microtar, Miranda, 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 43 24 8 19 8 8 11 74 35 35 11 8
Low 33 33 33 6
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_006221745 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765354 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765358 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599456 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599457 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599458 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604784 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604785 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604786 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604787 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604788 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604789 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604790 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604791 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604792 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604793 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604794 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092524 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092525 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092526 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092527 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092528 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092529 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092530 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092531 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092532 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092533 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000050664   ⟹   ENSRNOP00000041399
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1443,512,901 - 43,523,080 (+)Ensembl
RefSeq Acc Id: XM_017599456   ⟹   XP_017454945
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,557,946 - 41,878,622 (+)NCBI
Rnor_6.01443,205,047 - 43,526,335 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599457   ⟹   XP_017454946
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,834,981 - 41,878,622 (+)NCBI
Rnor_6.01443,488,336 - 43,526,968 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039092524   ⟹   XP_038948452
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,557,946 - 41,878,622 (+)NCBI
RefSeq Acc Id: XM_039092525   ⟹   XP_038948453
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,557,931 - 41,877,374 (+)NCBI
RefSeq Acc Id: XM_039092526   ⟹   XP_038948454
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,557,941 - 41,877,374 (+)NCBI
RefSeq Acc Id: XM_039092527   ⟹   XP_038948455
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,557,931 - 41,877,374 (+)NCBI
RefSeq Acc Id: XM_039092528   ⟹   XP_038948456
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,557,931 - 41,877,374 (+)NCBI
RefSeq Acc Id: XM_039092529   ⟹   XP_038948457
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,557,946 - 41,878,622 (+)NCBI
RefSeq Acc Id: XM_039092530   ⟹   XP_038948458
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,557,931 - 41,877,374 (+)NCBI
RefSeq Acc Id: XM_039092531   ⟹   XP_038948459
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,557,931 - 41,877,374 (+)NCBI
RefSeq Acc Id: XM_039092532   ⟹   XP_038948460
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,557,928 - 41,877,374 (+)NCBI
RefSeq Acc Id: XM_039092533   ⟹   XP_038948461
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,557,918 - 41,825,214 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_017454945   ⟸   XM_017599456
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017454946   ⟸   XM_017599457
- Peptide Label: isoform X11
- UniProtKB: F1LZU7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000041399   ⟸   ENSRNOT00000050664
RefSeq Acc Id: XP_038948461   ⟸   XM_039092533
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038948460   ⟸   XM_039092532
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038948455   ⟸   XM_039092527
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038948458   ⟸   XM_039092530
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038948453   ⟸   XM_039092525
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038948456   ⟸   XM_039092528
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038948459   ⟸   XM_039092531
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038948454   ⟸   XM_039092526
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038948452   ⟸   XM_039092524
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948457   ⟸   XM_039092529
- Peptide Label: isoform X6
Protein Domains
PID

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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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
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)
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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
BBDP/Wor (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
BN-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
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 (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
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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
M520/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
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
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)
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
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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: 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)
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/OlalpcvMcwi (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
SHRSP/A3NCrl (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
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/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)
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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 (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)
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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:1562438 AgrOrtholog
Ensembl Genes ENSRNOG00000025509 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000063717 Ensembl, ENTREZGENE
Ensembl Protein ENSRNOP00000041399 UniProtKB/TrEMBL
  ENSRNOP00000082727 ENTREZGENE
  ENSRNOP00000084452 ENTREZGENE
  ENSRNOP00000084619 ENTREZGENE
  ENSRNOP00000088203 ENTREZGENE
Ensembl Transcript ENSRNOT00000050664 UniProtKB/TrEMBL
  ENSRNOT00000100119 ENTREZGENE
  ENSRNOT00000106751 ENTREZGENE
  ENSRNOT00000115068 ENTREZGENE
  ENSRNOT00000119030 ENTREZGENE
Gene3D-CATH 2.30.29.30 UniProtKB/TrEMBL
InterPro Fe65 UniProtKB/TrEMBL
  PH_type UniProtKB/TrEMBL
  PTyr_interaction_dom UniProtKB/TrEMBL
NCBI Gene 305338 ENTREZGENE
PANTHER PTHR14058 UniProtKB/TrEMBL
Pfam PID UniProtKB/TrEMBL
PhenoGen Apbb2 PhenoGen
PROSITE PID UniProtKB/TrEMBL
SMART PTB UniProtKB/TrEMBL
UniProt F1LZU7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-27 Apbb2  amyloid beta precursor protein binding family B member 2  Apbb2  amyloid beta (A4) precursor protein-binding, family B, member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-29 Apbb2  amyloid beta (A4) precursor protein-binding, family B, member 2  RGD1562438_predicted  similar to amyloid beta (A4) precursor protein-binding, family B, member 2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1562438_predicted  similar to amyloid beta (A4) precursor protein-binding, family B, member 2 (predicted)  LOC305338  similar to amyloid beta (A4) precursor protein-binding, family B, member 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC305338  similar to amyloid beta (A4) precursor protein-binding, family B, member 2      Symbol and Name status set to provisional 70820 PROVISIONAL