Atp11c (ATPase phospholipid transporting 11C) - Rat Genome Database

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Gene: Atp11c (ATPase phospholipid transporting 11C) Rattus norvegicus
Analyze
Symbol: Atp11c
Name: ATPase phospholipid transporting 11C
RGD ID: 1564481
Description: Predicted to enable phosphatidylethanolamine flippase activity and phosphatidylserine flippase activity. Predicted to be involved in phospholipid translocation; positive regulation of B cell differentiation; and pre-B cell differentiation. Predicted to be integral component of plasma membrane. Predicted to be part of phospholipid-translocating ATPase complex. Predicted to be active in several cellular components, including endoplasmic reticulum; recycling endosome; and trans-Golgi network. Human ortholog(s) of this gene implicated in X-linked congenital hemolytic anemia. Orthologous to human ATP11C (ATPase phospholipid transporting 11C); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: MODEL
Also known as: Atp11c-ps1; ATPase, class VI, type 11C; ATPase, class VI, type 11C, pseudogene 1; LOC317599; phospholipid-transporting ATPase IG; RGD1564481; similar to ATPase, Class VI, type 11C isoform a
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
mRatBN7.2X138,564,459 - 138,752,116 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX138,565,836 - 138,751,204 (-)Ensembl
Rnor_6.0X143,340,712 - 143,525,588 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX143,346,252 - 143,453,612 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X143,369,601 - 143,554,166 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X145,746,536 - 145,861,055 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX134,637,343 - 134,750,541 (-)NCBICelera
Cytogenetic MapXq36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

Additional References at PubMed
PMID:17897319   PMID:21423173   PMID:21914794  


Genomics

Comparative Map Data
Atp11c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X138,564,459 - 138,752,116 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX138,565,836 - 138,751,204 (-)Ensembl
Rnor_6.0X143,340,712 - 143,525,588 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX143,346,252 - 143,453,612 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X143,369,601 - 143,554,166 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X145,746,536 - 145,861,055 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX134,637,343 - 134,750,541 (-)NCBICelera
Cytogenetic MapXq36NCBI
ATP11C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX139,726,346 - 139,945,276 (-)EnsemblGRCh38hg38GRCh38
GRCh38X139,726,346 - 139,933,083 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X138,808,507 - 139,015,212 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X138,636,171 - 138,742,113 (-)NCBINCBI36hg18NCBI36
Build 34X138,534,025 - 138,639,967NCBI
CeleraX139,175,990 - 139,281,918 (-)NCBI
Cytogenetic MapXq27.1NCBI
HuRefX128,075,584 - 128,181,035 (-)NCBIHuRef
CHM1_1X138,719,392 - 138,825,335 (-)NCBICHM1_1
Atp11c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X59,268,643 - 59,450,041 (-)NCBIGRCm39mm39
GRCm39 EnsemblX59,268,650 - 59,636,304 (-)Ensembl
GRCm38X60,223,283 - 60,404,853 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX60,223,290 - 60,592,698 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X57,476,467 - 57,657,156 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X56,570,074 - 56,750,596 (-)NCBImm8
CeleraX46,662,339 - 46,843,830 (-)NCBICelera
Cytogenetic MapXA6NCBI
Atp11c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554895,394,357 - 5,567,405 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554895,394,553 - 5,567,295 (+)NCBIChiLan1.0ChiLan1.0
ATP11C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X139,130,224 - 139,335,751 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX139,132,783 - 139,334,869 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X128,880,747 - 129,085,989 (-)NCBIMhudiblu_PPA_v0panPan3
ATP11C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X109,695,018 - 109,888,284 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX109,697,086 - 109,880,624 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX95,522,302 - 95,715,540 (-)NCBI
ROS_Cfam_1.0X111,683,119 - 111,876,518 (-)NCBI
ROS_Cfam_1.0 EnsemblX111,683,117 - 111,876,801 (-)Ensembl
UMICH_Zoey_3.1X108,815,452 - 109,008,656 (-)NCBI
UNSW_CanFamBas_1.0X110,999,978 - 111,193,126 (-)NCBI
UU_Cfam_GSD_1.0X110,679,492 - 110,872,773 (-)NCBI
Atp11c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X107,724,870 - 107,913,827 (-)NCBI
SpeTri2.0NW_0049365137,701,733 - 7,889,753 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATP11C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX114,394,438 - 114,582,150 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X114,394,436 - 114,575,658 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X130,614,130 - 130,659,634 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATP11C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X114,812,948 - 115,013,557 (-)NCBIChlSab1.1chlSab2
ChlSab1.1X114,812,948 - 115,013,557 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 EnsemblX114,812,930 - 115,013,538 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606552,545,066 - 52,747,624 (-)NCBIVero_WHO_p1.0
Atp11c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248086,778,792 - 6,955,259 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
px-51b11  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X138,630,083 - 138,630,187 (+)MAPPERmRatBN7.2
Rnor_6.0X143,406,721 - 143,406,824NCBIRnor6.0
Rnor_5.0X143,435,674 - 143,435,777UniSTSRnor5.0
RGSC_v3.4X145,811,379 - 145,811,482UniSTSRGSC3.4
CeleraX134,702,830 - 134,702,933UniSTS
Cytogenetic MapXq36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
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
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1548
Count of miRNA genes:347
Interacting mature miRNAs:503
Transcripts:ENSRNOT00000049120, ENSRNOT00000051319
Prediction methods:Microtar, Miranda, Pita
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 4 34 19 16 19 65 26 35 9
Low 3 38 23 22 3 22 8 10 9 9 5 2 8
Below cutoff 1 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_006227566 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257597 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257599 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758571 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588342 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588343 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602408 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602409 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602410 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100443 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100444 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100445 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100446 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100447 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100449 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide FQ209772 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000476 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000051319   ⟹   ENSRNOP00000048676
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX138,566,765 - 138,751,204 (-)Ensembl
Rnor_6.0 EnsemblX143,346,252 - 143,453,612 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098851   ⟹   ENSRNOP00000092019
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX138,566,765 - 138,751,204 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099292   ⟹   ENSRNOP00000083253
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX138,565,836 - 138,751,204 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107692   ⟹   ENSRNOP00000097091
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX138,565,836 - 138,678,841 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109683   ⟹   ENSRNOP00000093385
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX138,565,836 - 138,751,204 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000116612   ⟹   ENSRNOP00000081652
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX138,565,836 - 138,667,430 (-)Ensembl
RefSeq Acc Id: XM_006257597   ⟹   XP_006257659
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X138,564,459 - 138,680,292 (-)NCBI
Rnor_6.0X143,340,712 - 143,454,456 (-)NCBI
Rnor_5.0X143,369,601 - 143,554,166 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006257599   ⟹   XP_006257661
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X138,564,459 - 138,680,292 (-)NCBI
Rnor_6.0X143,340,712 - 143,454,456 (-)NCBI
Rnor_5.0X143,369,601 - 143,554,166 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602409   ⟹   XP_017457898
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X138,564,459 - 138,681,851 (-)NCBI
Rnor_6.0X143,340,712 - 143,454,456 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602410   ⟹   XP_017457899
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X138,564,459 - 138,680,293 (-)NCBI
Rnor_6.0X143,340,712 - 143,454,456 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039100443   ⟹   XP_038956371
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X138,569,995 - 138,752,000 (-)NCBI
RefSeq Acc Id: XM_039100444   ⟹   XP_038956372
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X138,569,995 - 138,752,116 (-)NCBI
RefSeq Acc Id: XM_039100445   ⟹   XP_038956373
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X138,569,995 - 138,752,004 (-)NCBI
RefSeq Acc Id: XM_039100446   ⟹   XP_038956374
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X138,569,995 - 138,752,000 (-)NCBI
RefSeq Acc Id: XM_039100447   ⟹   XP_038956375
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X138,569,995 - 138,752,063 (-)NCBI
RefSeq Acc Id: XM_039100448   ⟹   XP_038956376
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X138,569,992 - 138,681,851 (-)NCBI
RefSeq Acc Id: XM_039100449   ⟹   XP_038956377
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X138,569,993 - 138,680,293 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_006257661   ⟸   XM_006257599
- Peptide Label: isoform X1
- UniProtKB: D3ZFC5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257659   ⟸   XM_006257597
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017457898   ⟸   XM_017602409
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017457899   ⟸   XM_017602410
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000048676   ⟸   ENSRNOT00000051319
RefSeq Acc Id: XP_038956376   ⟸   XM_039100448
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038956377   ⟸   XM_039100449
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038956372   ⟸   XM_039100444
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038956375   ⟸   XM_039100447
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038956373   ⟸   XM_039100445
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038956374   ⟸   XM_039100446
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038956371   ⟸   XM_039100443
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000093385   ⟸   ENSRNOT00000109683
RefSeq Acc Id: ENSRNOP00000083253   ⟸   ENSRNOT00000099292
RefSeq Acc Id: ENSRNOP00000097091   ⟸   ENSRNOT00000107692
RefSeq Acc Id: ENSRNOP00000092019   ⟸   ENSRNOT00000098851
RefSeq Acc Id: ENSRNOP00000081652   ⟸   ENSRNOT00000116612
Protein Domains
PhoLip_ATPase_C   PhoLip_ATPase_N

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)
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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)
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)
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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)
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)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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:1564481 AgrOrtholog
Ensembl Genes ENSRNOG00000003472 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000048676 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000083253 ENTREZGENE
  ENSRNOP00000097091 ENTREZGENE
Ensembl Transcript ENSRNOT00000051319 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000099292 ENTREZGENE
  ENSRNOT00000107692 ENTREZGENE
Gene3D-CATH 3.40.50.1000 UniProtKB/TrEMBL
InterPro ATP11C UniProtKB/TrEMBL
  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_Plipid-transl UniProtKB/TrEMBL
  ATPase_P-typ_TM_dom UniProtKB/TrEMBL
  HAD-like_dom UniProtKB/TrEMBL
  HAD-like_sf UniProtKB/TrEMBL
  P-type_ATPase_N UniProtKB/TrEMBL
  P_typ_ATPase_c UniProtKB/TrEMBL
  P_typ_ATPase_HD_dom UniProtKB/TrEMBL
NCBI Gene 317599 ENTREZGENE
PANTHER PTHR24092 UniProtKB/TrEMBL
  PTHR24092:SF38 UniProtKB/TrEMBL
Pfam PhoLip_ATPase_C UniProtKB/TrEMBL
  PhoLip_ATPase_N UniProtKB/TrEMBL
PhenoGen Atp11c PhenoGen
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-Plipid UniProtKB/TrEMBL
  ATPase_P-type UniProtKB/TrEMBL
UniProt D3ZFC5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Atp11c  ATPase phospholipid transporting 11C  Atp11c  ATPase, class VI, type 11C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-09-04 Atp11c  ATPase, class VI, type 11C  Atp11c-ps1  ATPase, class VI, type 11C, pseudogene 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-20 Atp11c-ps1  ATPase, class VI, type 11C, pseudogene 1  Atp11c  ATPase, class VI, type 11C, pseudogene 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-02-24 Atp11c  ATPase, class VI, type 11C, pseudogene 1  Atp11c-ps1  Atpase, class VI, type 11C, pseudogene 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-01-26 Atp11c-ps1  Atpase, class VI, type 11C, pseudogene 1  Atp11c  Atpase, class VI, type 11C   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Atp11c  Atpase, class VI, type 11C   Atp11c_predicted  Atpase, class VI, type 11C (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Atp11c_predicted  Atpase, class VI, type 11C (predicted)  RGD1564481_predicted  similar to ATPase, Class VI, type 11C isoform a (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1564481_predicted  similar to ATPase, Class VI, type 11C isoform a (predicted)  LOC317599  similar to ATPase, Class VI, type 11C isoform a  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317599  similar to ATPase, Class VI, type 11C isoform a      Symbol and Name status set to provisional 70820 PROVISIONAL