Atp2b3 (ATPase plasma membrane Ca2+ transporting 3) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Atp2b3 (ATPase plasma membrane Ca2+ transporting 3) Rattus norvegicus
Analyze
Symbol: Atp2b3
Name: ATPase plasma membrane Ca2+ transporting 3
RGD ID: 621304
Description: Enables PDZ domain binding activity. Involved in brain development and neural retina development. Located in membrane raft; parallel fiber; and parallel fiber to Purkinje cell synapse. Is active in glutamatergic synapse. Is integral component of presynaptic membrane. Human ortholog(s) of this gene implicated in X-linked spinocerebellar ataxia 1. Orthologous to human ATP2B3 (ATPase plasma membrane Ca2+ transporting 3); PARTICIPATES IN calcium transport pathway; calcium/calcium-mediated signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3,4-methylenedioxymethamphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: ATPase, Ca++ transporting, plasma membrane 3; plasma membrane calcium ATPase; plasma membrane calcium pump; plasma membrane calcium-transporting ATPase 3; Pmca3
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
mRatBN7.2X151,216,483 - 151,289,069 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX151,216,507 - 151,286,775 (+)Ensembl
Rnor_6.0X157,236,400 - 157,312,028 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX157,239,306 - 157,312,028 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,988,825 - 153,056,732 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,400,374 - 159,470,665 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X159,473,827 - 159,544,098 (+)NCBI
Celera1136,605,191 - 136,673,058 (-)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Mammalian Phenotype
tremors  (IAGP)
References

Additional References at PubMed
PMID:8428948   PMID:8541282   PMID:12477932   PMID:18029012   PMID:19653992   PMID:21798237   PMID:22871113   PMID:24769233   PMID:25014339   PMID:25276815   PMID:25315779   PMID:28153703  
PMID:29476059   PMID:31032369  


Genomics

Comparative Map Data
Atp2b3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X151,216,483 - 151,289,069 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX151,216,507 - 151,286,775 (+)Ensembl
Rnor_6.0X157,236,400 - 157,312,028 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX157,239,306 - 157,312,028 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,988,825 - 153,056,732 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,400,374 - 159,470,665 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X159,473,827 - 159,544,098 (+)NCBI
Celera1136,605,191 - 136,673,058 (-)NCBICelera
Cytogenetic MapXq37NCBI
ATP2B3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX153,517,642 - 153,582,939 (+)EnsemblGRCh38hg38GRCh38
GRCh38X153,517,642 - 153,582,929 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X152,801,580 - 152,848,387 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X152,454,774 - 152,501,581 (+)NCBINCBI36hg18NCBI36
Build 34X152,322,426 - 152,369,234NCBI
CeleraX153,035,263 - 153,082,068 (+)NCBI
Cytogenetic MapXq28NCBI
HuRefX141,460,036 - 141,506,946 (+)NCBIHuRef
CHM1_1X152,676,076 - 152,722,878 (+)NCBICHM1_1
Atp2b3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X72,546,356 - 72,632,267 (+)NCBIGRCm39mm39
GRCm39 EnsemblX72,546,692 - 72,614,611 (+)Ensembl
GRCm38X73,502,749 - 73,573,275 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX73,503,086 - 73,571,005 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X70,748,425 - 70,816,344 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X69,755,806 - 69,823,725 (+)NCBImm8
CeleraX64,756,927 - 64,824,859 (+)NCBICelera
Cytogenetic MapXA7.3NCBI
Atp2b3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955580269,100 - 333,471 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955580286,092 - 332,657 (+)NCBIChiLan1.0ChiLan1.0
ATP2B3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X152,955,106 - 153,019,445 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX152,955,109 - 153,019,445 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X143,068,171 - 143,133,479 (+)NCBIMhudiblu_PPA_v0panPan3
ATP2B3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X121,355,217 - 121,405,245 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX121,361,239 - 121,403,609 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX106,673,819 - 106,733,766 (+)NCBI
ROS_Cfam_1.0X124,485,607 - 124,545,662 (+)NCBI
UMICH_Zoey_3.1X120,255,434 - 120,315,368 (+)NCBI
UNSW_CanFamBas_1.0X122,770,529 - 122,830,395 (+)NCBI
UU_Cfam_GSD_1.0X122,532,564 - 122,592,473 (+)NCBI
Atp2b3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X118,659,196 - 118,728,749 (+)NCBI
SpeTri2.0NW_004936809396,883 - 466,372 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATP2B3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX124,301,709 - 124,357,642 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X124,318,874 - 124,357,653 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X141,865,126 - 141,921,057 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ATP2B3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X127,966,366 - 128,013,900 (+)NCBI
ChlSab1.1 EnsemblX127,966,492 - 128,013,901 (+)Ensembl
Vero_WHO_p1.0NW_02366606565,809,624 - 65,875,629 (+)NCBI
Atp2b3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624946247,032 - 307,645 (+)NCBI

Position Markers
DXKyo1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,283,904 - 151,284,137 (-)MAPPERmRatBN7.2
Rnor_6.0X157,239,713 - 157,239,945NCBIRnor6.0
Rnor_5.01152,989,232 - 152,989,464UniSTSRnor5.0
RGSC_v3.4X159,470,026 - 159,470,258UniSTSRGSC3.4
Celera1136,605,598 - 136,605,830UniSTS
Cytogenetic MapXq37UniSTS
AW526213  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,271,501 - 151,271,652 (-)MAPPERmRatBN7.2
Rnor_6.0X157,252,198 - 157,252,348NCBIRnor6.0
Rnor_5.01153,001,717 - 153,001,867UniSTSRnor5.0
RGSC_v3.4X159,457,621 - 159,457,771UniSTSRGSC3.4
Celera1136,618,083 - 136,618,233UniSTS
RH 3.4 Map11646.1UniSTS
Cytogenetic MapXq37UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:371
Count of miRNA genes:137
Interacting mature miRNAs:150
Transcripts:ENSRNOT00000023934, ENSRNOT00000029079, ENSRNOT00000029091, ENSRNOT00000049237
Prediction methods:Microtar, 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 8 3 52 5
Low 2 5 1 10 1 8 8 16 35 32 10 8
Below cutoff 1 34 29 25 8 25 6 4 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_133288 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773619 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773620 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773621 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773623 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773625 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601946 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099540 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099541 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099542 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099543 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099544 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099545 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099546 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099547 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099548 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099549 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099550 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AH002774 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH011206 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC089969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J05087 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000491 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M96626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U29397 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000077979   ⟹   ENSRNOP00000071471
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,216,507 - 151,273,590 (+)Ensembl
Rnor_6.0 EnsemblX157,239,306 - 157,312,028 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078100   ⟹   ENSRNOP00000075088
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,216,507 - 151,286,775 (+)Ensembl
Rnor_6.0 EnsemblX157,239,926 - 157,286,936 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098998   ⟹   ENSRNOP00000083651
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,216,507 - 151,286,775 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099418   ⟹   ENSRNOP00000094290
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,216,507 - 151,286,775 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000115963   ⟹   ENSRNOP00000081864
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,216,507 - 151,286,775 (+)Ensembl
RefSeq Acc Id: NM_133288   ⟹   NP_579822
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,216,507 - 151,284,544 (+)NCBI
Rnor_6.0X157,239,306 - 157,312,028 (-)NCBI
Rnor_5.01152,988,825 - 153,056,732 (-)NCBI
RGSC_v3.4X159,400,374 - 159,470,665 (+)RGD
Celera1136,605,191 - 136,673,058 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773620   ⟹   XP_008771842
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,216,487 - 151,289,069 (+)NCBI
Rnor_6.0X157,236,400 - 157,307,197 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099540   ⟹   XP_038955468
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,216,484 - 151,289,069 (+)NCBI
RefSeq Acc Id: XM_039099541   ⟹   XP_038955469
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,216,483 - 151,289,069 (+)NCBI
RefSeq Acc Id: XM_039099542   ⟹   XP_038955470
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,216,484 - 151,289,069 (+)NCBI
RefSeq Acc Id: XM_039099543   ⟹   XP_038955471
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,216,485 - 151,284,488 (+)NCBI
RefSeq Acc Id: XM_039099544   ⟹   XP_038955472
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,236,910 - 151,283,924 (+)NCBI
RefSeq Acc Id: XM_039099545   ⟹   XP_038955473
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,216,484 - 151,271,700 (+)NCBI
RefSeq Acc Id: XM_039099546   ⟹   XP_038955474
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,236,910 - 151,283,924 (+)NCBI
RefSeq Acc Id: XM_039099547   ⟹   XP_038955475
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,216,485 - 151,273,502 (+)NCBI
RefSeq Acc Id: XM_039099548   ⟹   XP_038955476
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,236,910 - 151,283,924 (+)NCBI
RefSeq Acc Id: XM_039099549   ⟹   XP_038955477
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,216,485 - 151,270,361 (+)NCBI
RefSeq Acc Id: XM_039099550   ⟹   XP_038955478
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,236,910 - 151,284,488 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_579822   ⟸   NM_133288
- UniProtKB: Q64568 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008771842   ⟸   XM_008773620
- Peptide Label: isoform X6
- UniProtKB: Q64568 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071471   ⟸   ENSRNOT00000077979
RefSeq Acc Id: ENSRNOP00000075088   ⟸   ENSRNOT00000078100
RefSeq Acc Id: XP_038955469   ⟸   XM_039099541
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955468   ⟸   XM_039099540
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955470   ⟸   XM_039099542
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955473   ⟸   XM_039099545
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038955471   ⟸   XM_039099543
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038955475   ⟸   XM_039099547
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038955477   ⟸   XM_039099549
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038955478   ⟸   XM_039099550
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038955472   ⟸   XM_039099544
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038955474   ⟸   XM_039099546
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038955476   ⟸   XM_039099548
- Peptide Label: isoform X10
RefSeq Acc Id: ENSRNOP00000083651   ⟸   ENSRNOT00000098998
RefSeq Acc Id: ENSRNOP00000094290   ⟸   ENSRNOT00000099418
RefSeq Acc Id: ENSRNOP00000081864   ⟸   ENSRNOT00000115963
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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)
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
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)
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
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)
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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/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
WKY/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
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
WN/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
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621304 AgrOrtholog
Ensembl Genes ENSRNOG00000061304 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000071471 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000075088 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077979 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000078100 UniProtKB/TrEMBL
Gene3D-CATH 3.40.1110.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.1000 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7315385 IMAGE-MGC_LOAD
InterPro ATP_Ca_trans_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-typ_cation-transptr_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-typ_cation-transptr_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-typ_cyto_dom_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-typ_P_site UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-typ_TM_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-typ_transduc_dom_A_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HAD-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HAD_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-type_ATPase_IIB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P_typ_ATPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P_typ_ATPase_HD_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29599 UniProtKB/Swiss-Prot
MGC_CLONE MGC:109344 IMAGE-MGC_LOAD
NCBI Gene 29599 ENTREZGENE
Pfam ATP_Ca_trans_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cation_ATPase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cation_ATPase_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Atp2b3 PhenoGen
PROSITE ATPASE_E1_E2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Cation_ATPase_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56784 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF81653 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF81660 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF81665 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs ATPase-IIB_Ca UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K9Q6_RAT UniProtKB/TrEMBL
  AT2B3_RAT UniProtKB/Swiss-Prot
  Q5EB74_RAT UniProtKB/TrEMBL
  Q64568 ENTREZGENE
UniProt Secondary Q01489 UniProtKB/Swiss-Prot
  Q63444 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Atp2b3  ATPase plasma membrane Ca2+ transporting 3  Atp2b3  ATPase, Ca++ transporting, plasma membrane 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Atp2b3  ATPase, Ca++ transporting, plasma membrane 3      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Atp2b3  ATPase, Ca++ transporting, plasma membrane 3      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_transcript contains alternate splice products, 4.5 kb transcript in skeletal muscle and 7.5 kb transcript in brain 631862