Atp13a2 (ATPase cation transporting 13A2) - Rat Genome Database

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Gene: Atp13a2 (ATPase cation transporting 13A2) Rattus norvegicus
Analyze
Symbol: Atp13a2
Name: ATPase cation transporting 13A2
RGD ID: 1307977
Description: Predicted to enable ABC-type polyamine transporter activity; phosphatidic acid binding activity; and phosphatidylinositol-3,5-bisphosphate binding activity. Involved in regulation of autophagosome size and regulation of mitochondrion organization. Predicted to be located in several cellular components, including cytoplasmic vesicle; neuronal cell body; and vacuole. Predicted to be integral component of lysosomal membrane. Human ortholog(s) of this gene implicated in Kufor-Rakeb syndrome; Parkinson's disease; and hereditary spastic paraplegia. Orthologous to human ATP13A2 (ATPase cation transporting 13A2); PARTICIPATES IN Parkinson's disease pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: ATPase 13A2; ATPase type 13A2; LOC362645; MGC188455; polyamine-transporting ATPase 13A2; probable cation-transporting ATPase 13A2; RGD1307977; similar to RIKEN cDNA 1110012E06
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
mRatBN7.25153,292,722 - 153,312,143 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5153,292,751 - 153,312,139 (+)Ensembl
Rnor_6.05159,512,208 - 159,531,631 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5159,512,285 - 159,531,637 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05163,224,470 - 163,243,886 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45159,847,016 - 159,866,362 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15159,857,176 - 159,876,542 (+)NCBI
Celera5151,657,698 - 151,677,052 (+)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12477932   PMID:16964263   PMID:17897319   PMID:21542062   PMID:21724849   PMID:22198378   PMID:22285144   PMID:23205587   PMID:23499937   PMID:24334770   PMID:24603074   PMID:25392495  
PMID:26134396   PMID:26818499   PMID:27057733   PMID:27278822   PMID:30538141   PMID:31132336   PMID:31996848  


Genomics

Comparative Map Data
Atp13a2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25153,292,722 - 153,312,143 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5153,292,751 - 153,312,139 (+)Ensembl
Rnor_6.05159,512,208 - 159,531,631 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5159,512,285 - 159,531,637 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05163,224,470 - 163,243,886 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45159,847,016 - 159,866,362 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15159,857,176 - 159,876,542 (+)NCBI
Celera5151,657,698 - 151,677,052 (+)NCBICelera
Cytogenetic Map5q36NCBI
ATP13A2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl116,985,958 - 17,011,928 (-)EnsemblGRCh38hg38GRCh38
GRCh38116,985,958 - 17,011,972 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37117,312,453 - 17,338,423 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36117,185,040 - 17,210,854 (-)NCBINCBI36hg18NCBI36
Build 34117,057,758 - 17,083,573NCBI
Celera115,634,791 - 15,660,760 (-)NCBI
Cytogenetic Map1p36.13NCBI
HuRef115,556,532 - 15,582,505 (-)NCBIHuRef
CHM1_1117,420,791 - 17,446,761 (-)NCBICHM1_1
Atp13a2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394140,711,812 - 140,734,641 (+)NCBIGRCm39mm39
GRCm39 Ensembl4140,714,184 - 140,734,641 (+)Ensembl
GRCm384140,986,216 - 141,007,330 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4140,986,873 - 141,007,330 (+)EnsemblGRCm38mm10GRCm38
MGSCv374140,542,788 - 140,563,616 (+)NCBIGRCm37mm9NCBIm37
MGSCv364140,259,004 - 140,279,406 (+)NCBImm8
Celera4142,787,644 - 142,807,639 (+)NCBICelera
Cytogenetic Map4D3NCBI
Atp13a2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555271,806,009 - 1,823,344 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555271,805,854 - 1,823,623 (+)NCBIChiLan1.0ChiLan1.0
ATP13A2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1116,975,538 - 17,006,022 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl116,986,385 - 17,006,033 (-)Ensemblpanpan1.1panPan2
PanPan1.1 Ensembl116,975,544 - 17,006,022 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0115,929,613 - 15,955,631 (-)NCBIMhudiblu_PPA_v0panPan3
ATP13A2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1281,196,355 - 81,215,736 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl281,196,463 - 81,215,689 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha277,733,475 - 77,752,482 (+)NCBI
ROS_Cfam_1.0281,842,888 - 81,861,861 (+)NCBI
ROS_Cfam_1.0 Ensembl281,842,987 - 81,861,861 (+)Ensembl
UMICH_Zoey_3.1278,595,908 - 78,614,871 (+)NCBI
UNSW_CanFamBas_1.0279,612,457 - 79,631,767 (+)NCBI
UU_Cfam_GSD_1.0280,680,908 - 80,699,865 (+)NCBI
Atp13a2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505838,143,432 - 38,156,097 (-)NCBI
SpeTri2.0NW_0049364743,968,216 - 3,980,821 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATP13A2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl675,618,416 - 75,638,591 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1675,618,317 - 75,638,591 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2669,931,621 - 69,951,929 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATP13A2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120115,578,185 - 115,605,416 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl20115,578,261 - 115,605,647 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666033515,071 - 542,556 (-)NCBIVero_WHO_p1.0
Atp13a2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247642,614,541 - 2,631,972 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH134640  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25153,311,825 - 153,312,020 (+)MAPPERmRatBN7.2
Rnor_6.05159,531,317 - 159,531,511NCBIRnor6.0
Rnor_5.05163,243,569 - 163,243,763UniSTSRnor5.0
RGSC_v3.45159,866,048 - 159,866,242UniSTSRGSC3.4
Celera5151,676,738 - 151,676,932UniSTS
RH 3.4 Map51052.4UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5143608201161165651Rat
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5143799107158428037Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5144358090157869054Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5144377876161317411Rat
1298090Bp155Blood pressure QTL 1553.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)5151006154161165494Rat
1354631Swd2Spike wave discharge measurement QTL 23.640.0002brain electrophysiology trait (VT:0010557)brain total spike-and-wave discharge duration (CMO:0001740)5151113452164465185Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5151113452166875058Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:46
Count of miRNA genes:41
Interacting mature miRNAs:46
Transcripts:ENSRNOT00000010884
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 2 26 10 6 15 6 2 74 23 37 11
Low 1 17 47 35 4 35 8 9 12 4 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010884   ⟹   ENSRNOP00000010884
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5153,292,793 - 153,312,139 (+)Ensembl
Rnor_6.0 Ensembl5159,512,285 - 159,531,630 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088082   ⟹   ENSRNOP00000070096
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5153,292,751 - 153,312,128 (+)Ensembl
Rnor_6.0 Ensembl5159,512,380 - 159,531,637 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114069   ⟹   ENSRNOP00000082003
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5153,292,873 - 153,312,139 (+)Ensembl
RefSeq Acc Id: NM_001173432   ⟹   NP_001166903
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25153,292,793 - 153,312,140 (+)NCBI
Rnor_6.05159,512,285 - 159,531,631 (+)NCBI
Rnor_5.05163,224,470 - 163,243,886 (+)NCBI
Celera5151,657,698 - 151,677,052 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006239246   ⟹   XP_006239308
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25153,292,722 - 153,312,143 (+)NCBI
Rnor_6.05159,512,209 - 159,531,631 (+)NCBI
Rnor_5.05163,224,470 - 163,243,886 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006239247   ⟹   XP_006239309
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25153,292,722 - 153,312,143 (+)NCBI
Rnor_6.05159,512,208 - 159,531,631 (+)NCBI
Rnor_5.05163,224,470 - 163,243,886 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006239250   ⟹   XP_006239312
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25153,292,722 - 153,312,143 (+)NCBI
Rnor_6.05159,512,209 - 159,531,631 (+)NCBI
Rnor_5.05163,224,470 - 163,243,886 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006239251   ⟹   XP_006239313
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25153,292,751 - 153,311,968 (+)NCBI
Rnor_6.05159,512,208 - 159,531,631 (+)NCBI
Rnor_5.05163,224,470 - 163,243,886 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001166903   ⟸   NM_001173432
- UniProtKB: B5DEH6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239308   ⟸   XM_006239246
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006239312   ⟸   XM_006239250
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006239309   ⟸   XM_006239247
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006239313   ⟸   XM_006239251
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000010884   ⟸   ENSRNOT00000010884
RefSeq Acc Id: ENSRNOP00000070096   ⟸   ENSRNOT00000088082
RefSeq Acc Id: ENSRNOP00000082003   ⟸   ENSRNOT00000114069

Transcriptome

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

Promoters
RGD ID:13694215
Promoter ID:EPDNEW_R4740
Type:multiple initiation site
Name:Atp13a2_1
Description:ATPase 13A2
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_6.05159,512,229 - 159,512,289EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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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)
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)
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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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 163237572 163237573 G T snv ACI/EurMcwi (MCW), ZF (KyushuU), GH/OmrMcwi (MCW), SR/JrHsd (MCW), WN/N (KNAW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MHS/Gib (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHL/EurMcwi (KNAW), M520/N (KNAW), MNS/Gib (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), SDLEF7/Barth (UDEL), IS/Kyo (KyushuU), F344/DuCrlCrlj (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), FHL/EurMcwi (MCW)
5 163242713 163242714 C T snv IS-Tlk/Kyo (KyushuU), IS/Kyo (KyushuU)
5 163242849 163242850 C T snv DOB/Oda (KyushuU)
5 163243371 163243372 G C snv MR/N (KNAW), SS/JrHsdMcwi (KNAW), BUF/N (KNAW), DA/BklArbNsi (KNAW), GK/Ox (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), SDLEF7/Barth (UDEL), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), LE/Stm (KyushuU), HWY/Slc (KyushuU), DOB/Oda (KyushuU), ZFDM (KyushuU), SS/JrHsdMcwi (MCW), SBN/Ygl (MCW), COP/CrCrl (MCW & UW), SBH/Ygl (MCW)
5 163243557 163243558 G A snv FHL/EurMcwi (MCW), WN/N (KNAW), FHL/EurMcwi (KNAW)
5 163243634 163243635 G A snv ACI/EurMcwi (MCW), ZF (KyushuU), SR/JrHsd (MCW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MHS/Gib (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), M520/N (KNAW), MNS/Gib (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), SDLEF7/Barth (UDEL), F344/DuCrlCrlj (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), F344/Stm (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), GH/OmrMcwi (MCW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 153305829 153305830 G T snv ACI/EurMcwi (2019), ACI/N (2020), WN/N (2020), WKY/N (2020), WKY/NCrl (2019), WAG/RijCrl (2020), SR/JrHsd (2020), SHR/OlalpcvMcwi (2019), SHRSP/A3NCrl (2019), PVG/Seac (2019), MR/N (2020), M520/N (2020), BXH3/CubMcwi (2020), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB31/IpcvMcwi (2019), HXB4/IpcvMcwi (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LH/MavRrrcAek (2020), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), M520/NRrrcMcwi (2019)
5 153311628 153311629 G C snv DA/OlaHsd (2019), BUF/N (2020), MWF/Hsd (2019), LEXF10A/StmMcwi (2020), LE/Stm (2019), SS/JrHsdMcwi (2019), LEXF3/Stm (2020), LEXF11/Stm (2020), LEW/Crl (2019), GK/FarMcwi (2019), LEXF4/Stm (2020)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 159525320 159525321 G T snv ACI/EurMcwi (MCW), WN/N (2020), GH/OmrMcwi (MCW), SR/JrHsd (MCW), ACI/N (MCW), F344/NRrrc (MCW), WN/N (MCW), ACI/EurMcwi (RGD), BBDP/Wor (RGD), F344/NCrl (RGD), FHL/EurMcwi (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), LL/MavRrrc (RGD), MHS/Gib (RGD), MNS/Gib (RGD), SHR/NHsd (RGD), SR/JrHsd (RGD), SS/Jr (RGD), WAG/Rij (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), WKY/NHsd (RGD), ACI/EurMcwi (2019), ACI/N (2020), BXH3/CubMcwi (2020), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB31/IpcvMcwi (2019), HXB4/IpcvMcwi (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LH/MavRrrcAek (2020), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), PVG/Seac (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), SR/JrHsd (2020), WAG/RijCrl (2020), WKY/NCrl (2019), WKY/N (2020), FHL/EurMcwi (MCW)
5 159531119 159531120 G C snv CDR, CDS, COP/CrCrl (MCW & UW), SBH/Ygl (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), MR/N (MCW), GK/Ox (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), SS/JrHsdMcwi (RGD), BUF/N (2020), DA/OlaHsd (2019), GK/FarMcwi (2019), LEW/Crl (2019), LEXF11/Stm (2020), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), MWF/Hsd (2019), SS/JrHsdMcwi (2019)
5 159531305 159531306 G A snv FHL/EurMcwi (RGD), WN/N (MCW), FHL/EurMcwi (MCW), WN/N (2020)
5 159531382 159531383 G A snv F344/NRrrc (MCW), M520/N (MCW), WKY/N (MCW), ACI/EurMcwi (RGD), BBDP/Wor (RGD), F344/NCrl (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), LL/MavRrrc (RGD), MHS/Gib (RGD), MNS/Gib (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), SR/JrHsd (RGD), SS/Jr (RGD), WAG/Rij (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), WKY/NHsd (RGD), WKY/N (2020), ACI/N (2020), BXH3/CubMcwi (2020), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB31/IpcvMcwi (2019), HXB4/IpcvMcwi (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LH/MavRrrcAek (2020), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), PVG/Seac (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), SR/JrHsd (2020), WAG/RijCrl (2020), WKY/NCrl (2019), ACI/N (MCW), SR/JrHsd (MCW), GH/OmrMcwi (MCW), ACI/EurMcwi (MCW), ACI/EurMcwi (2019)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307977 AgrOrtholog
Ensembl Genes ENSRNOG00000008052 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000010884 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070096 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000082003 ENTREZGENE
Ensembl Transcript ENSRNOT00000010884 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000088082 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000114069 ENTREZGENE
Gene3D-CATH 3.40.1110.10 UniProtKB/TrEMBL
  3.40.50.1000 UniProtKB/TrEMBL
InterPro ATPase_P-typ_ATPase-assoc-dom UniProtKB/TrEMBL
  ATPase_P-typ_cyto_domN UniProtKB/TrEMBL
  ATPase_P-typ_ion-transptr UniProtKB/TrEMBL
  ATPase_P-typ_P_site UniProtKB/TrEMBL
  ATPase_P-typ_TM_dom UniProtKB/TrEMBL
  ATPase_P-typ_unknown-pump-sp UniProtKB/TrEMBL
  HAD-like_sf UniProtKB/TrEMBL
  HAD_sf UniProtKB/TrEMBL
  P_typ_ATPase_HD_dom UniProtKB/TrEMBL
KEGG Report rno:362645 UniProtKB/TrEMBL
NCBI Gene 362645 ENTREZGENE
Pfam P5-ATPase UniProtKB/TrEMBL
PhenoGen Atp13a2 PhenoGen
PRINTS HATPASE UniProtKB/TrEMBL
PROSITE ATPASE_E1_E2 UniProtKB/TrEMBL
Superfamily-SCOP ATPase_cation_domN UniProtKB/TrEMBL
  HAD-like_dom UniProtKB/TrEMBL
  SSF81653 UniProtKB/TrEMBL
  SSF81665 UniProtKB/TrEMBL
TIGRFAMs ATPase_P-type UniProtKB/TrEMBL
  P-ATPase-V UniProtKB/TrEMBL
UniProt A0A0G2JX15_RAT UniProtKB/TrEMBL
  B5DEH6 ENTREZGENE, UniProtKB/TrEMBL
  F1MAA4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-03-13 Atp13a2  ATPase cation transporting 13A2  Atp13a2  ATPase 13A2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-17 Atp13a2  ATPase 13A2  Atp13a2  ATPase type 13A2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Atp13a2  ATPase type 13A2   Atp13a2_predicted  ATPase type 13A2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Atp13a2_predicted  ATPase type 13A2 (predicted)  RGD1307977_predicted  similar to RIKEN cDNA 1110012E06 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1307977_predicted  similar to RIKEN cDNA 1110012E06 (predicted)  LOC362645_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC362645_predicted  similar to RIKEN cDNA 1110012E06 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL