Atp8a1 (ATPase phospholipid transporting 8A1) - Rat Genome Database

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Gene: Atp8a1 (ATPase phospholipid transporting 8A1) Rattus norvegicus
Analyze
Symbol: Atp8a1
Name: ATPase phospholipid transporting 8A1
RGD ID: 1309619
Description: Predicted to enable phosphatidylserine flippase activity. Predicted to be involved in learning; positive regulation of cell migration; and regulation of membrane lipid distribution. Is integral component of synaptic vesicle membrane. Orthologous to human ATP8A1 (ATPase phospholipid transporting 8A1); INTERACTS WITH 17alpha-ethynylestradiol; 3-chloropropane-1,2-diol; acrylamide.
Type: protein-coding
RefSeq Status: MODEL
Also known as: ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1; LOC289615; phospholipid-transporting ATPase IA; probable phospholipid-transporting ATPase IA
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
mRatBN7.21440,315,013 - 40,557,572 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1440,315,049 - 40,554,611 (+)Ensembl
Rnor_6.01441,972,398 - 42,210,555 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1442,015,347 - 42,206,311 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01441,770,273 - 42,007,304 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41442,923,309 - 43,165,666 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11442,961,030 - 43,105,186 (+)NCBI
Celera1439,507,549 - 39,715,322 (+)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:19946888   PMID:20224745   PMID:20947505   PMID:21700703   PMID:21914794   PMID:22007859   PMID:23269685   PMID:23533145  


Genomics

Comparative Map Data
Atp8a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21440,315,013 - 40,557,572 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1440,315,049 - 40,554,611 (+)Ensembl
Rnor_6.01441,972,398 - 42,210,555 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1442,015,347 - 42,206,311 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01441,770,273 - 42,007,304 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41442,923,309 - 43,165,666 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11442,961,030 - 43,105,186 (+)NCBI
Celera1439,507,549 - 39,715,322 (+)NCBICelera
Cytogenetic Map14p11NCBI
ATP8A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl442,408,373 - 42,657,105 (-)EnsemblGRCh38hg38GRCh38
GRCh38442,408,373 - 42,657,105 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37442,410,390 - 42,659,122 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36442,105,147 - 42,353,879 (-)NCBINCBI36hg18NCBI36
Build 34442,255,562 - 42,499,818NCBI
Celera442,858,235 - 43,107,011 (-)NCBI
Cytogenetic Map4p13NCBI
HuRef441,731,596 - 41,980,330 (-)NCBIHuRef
CHM1_1442,410,660 - 42,659,431 (-)NCBICHM1_1
Atp8a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39567,775,482 - 68,004,822 (-)NCBIGRCm39mm39
GRCm39 Ensembl567,775,483 - 68,004,777 (-)Ensembl
GRCm38567,618,139 - 67,847,484 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl567,618,140 - 67,847,434 (-)EnsemblGRCm38mm10GRCm38
MGSCv37568,009,379 - 68,238,670 (-)NCBIGRCm37mm9NCBIm37
MGSCv36567,897,275 - 68,126,566 (-)NCBImm8
Celera564,913,563 - 65,141,756 (-)NCBICelera
Cytogenetic Map5C3.1NCBI
Atp8a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554435,142,049 - 5,362,147 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554435,142,049 - 5,362,031 (+)NCBIChiLan1.0ChiLan1.0
ATP8A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1442,577,993 - 42,826,610 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl442,582,538 - 42,826,446 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0436,729,820 - 36,978,825 (-)NCBIMhudiblu_PPA_v0panPan3
ATP8A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11339,366,692 - 39,588,879 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1339,368,470 - 39,588,885 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1339,341,834 - 39,565,900 (-)NCBI
ROS_Cfam_1.01339,855,496 - 40,079,905 (-)NCBI
UMICH_Zoey_3.11339,543,722 - 39,767,959 (-)NCBI
UNSW_CanFamBas_1.01339,656,584 - 39,880,750 (-)NCBI
UU_Cfam_GSD_1.01340,121,639 - 40,345,993 (-)NCBI
Atp8a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528536,519,932 - 36,736,026 (+)NCBI
SpeTri2.0NW_0049364829,562,214 - 9,778,494 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATP8A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl833,387,590 - 33,638,841 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1833,384,493 - 33,637,299 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2835,180,910 - 35,309,833 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATP8A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1277,667,704 - 7,933,337 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl277,667,781 - 7,933,325 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604753,957,739 - 54,230,486 (+)NCBIVero_WHO_p1.0
Atp8a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476124,285,317 - 24,508,837 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D14Rat44  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01442,122,557 - 42,122,758NCBIRnor6.0
RGSC_v3.41443,077,432 - 43,077,631UniSTSRGSC3.4
Celera1439,624,995 - 39,625,194UniSTS
RH 2.0 Map14472.8RGD
SHRSP x BN Map1428.34RGD
FHH x ACI Map1439.2099RGD
Cytogenetic Map14p11UniSTS
D14Rat31  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21440,476,240 - 40,476,463 (+)MAPPERmRatBN7.2
Rnor_6.01442,131,950 - 42,132,170NCBIRnor6.0
Rnor_5.01441,928,703 - 41,928,923UniSTSRnor5.0
RGSC_v3.41443,086,821 - 43,087,042RGDRGSC3.4
RGSC_v3.41443,086,822 - 43,087,042UniSTSRGSC3.4
RGSC_v3.11443,089,212 - 43,089,433RGD
Celera1439,634,430 - 39,634,650UniSTS
RH 2.0 Map14478.9RGD
SHRSP x BN Map1430.5RGD
FHH x ACI Map1439.2499RGD
Cytogenetic Map14p11UniSTS
D14Got86  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21440,453,731 - 40,453,868 (+)MAPPERmRatBN7.2
Rnor_6.01442,109,432 - 42,109,568NCBIRnor6.0
Rnor_5.01441,906,724 - 41,906,860UniSTSRnor5.0
RGSC_v3.41443,063,956 - 43,064,093RGDRGSC3.4
RGSC_v3.41443,063,957 - 43,064,093UniSTSRGSC3.4
RGSC_v3.11443,066,347 - 43,066,484RGD
Celera1439,611,656 - 39,611,792UniSTS
Cytogenetic Map14p11UniSTS
RH142480  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21440,319,182 - 40,319,454 (-)MAPPERmRatBN7.2
mRatBN7.21440,319,182 - 40,319,454 (+)MAPPERmRatBN7.2
Rnor_6.01441,026,888 - 41,027,159NCBIRnor6.0
Rnor_6.01441,976,553 - 41,976,824NCBIRnor6.0
Rnor_5.01441,774,420 - 41,774,691UniSTSRnor5.0
Rnor_5.01440,826,619 - 40,826,890UniSTSRnor5.0
RGSC_v3.41442,927,444 - 42,927,715UniSTSRGSC3.4
Celera1439,478,190 - 39,478,461UniSTS
Cytogenetic Map14p11UniSTS
RH143653  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21440,533,656 - 40,533,861 (+)MAPPERmRatBN7.2
Rnor_6.01442,186,630 - 42,186,834NCBIRnor6.0
Rnor_5.01441,983,383 - 41,983,587UniSTSRnor5.0
RGSC_v3.41443,145,499 - 43,145,703UniSTSRGSC3.4
Celera1439,691,398 - 39,691,602UniSTS
Cytogenetic Map14p11UniSTS
BF403317  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21440,410,057 - 40,410,220 (+)MAPPERmRatBN7.2
Rnor_6.01442,067,495 - 42,067,657NCBIRnor6.0
Rnor_5.01441,865,242 - 41,865,404UniSTSRnor5.0
RGSC_v3.41443,018,755 - 43,018,917UniSTSRGSC3.4
Celera1439,568,187 - 39,568,349UniSTS
Cytogenetic Map14p11UniSTS
RH142981  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21440,481,426 - 40,481,597 (+)MAPPERmRatBN7.2
Rnor_6.01442,137,133 - 42,137,303NCBIRnor6.0
Rnor_5.01441,933,886 - 41,934,056UniSTSRnor5.0
Celera1439,639,612 - 39,639,782UniSTS
Cytogenetic Map14p11UniSTS
RH140333  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21440,509,833 - 40,510,081 (+)MAPPERmRatBN7.2
Rnor_6.01442,163,202 - 42,163,449NCBIRnor6.0
Rnor_5.01441,959,955 - 41,960,202UniSTSRnor5.0
RGSC_v3.41443,121,680 - 43,121,927UniSTSRGSC3.4
Celera1439,667,612 - 39,667,859UniSTS
RH 3.4 Map11284.9UniSTS
Cytogenetic Map14p11UniSTS
RH141950  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21440,459,634 - 40,459,833 (+)MAPPERmRatBN7.2
Rnor_6.01442,115,335 - 42,115,533NCBIRnor6.0
Rnor_5.01441,912,627 - 41,912,825UniSTSRnor5.0
RGSC_v3.41443,069,860 - 43,070,058UniSTSRGSC3.4
Celera1439,617,559 - 39,617,757UniSTS
Cytogenetic Map14p11UniSTS
BE119187  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21440,554,345 - 40,554,518 (+)MAPPERmRatBN7.2
Rnor_6.01442,207,329 - 42,207,501NCBIRnor6.0
Rnor_5.01442,004,082 - 42,004,254UniSTSRnor5.0
RGSC_v3.41443,166,198 - 43,166,370UniSTSRGSC3.4
Celera1439,712,096 - 39,712,268UniSTS
Cytogenetic Map14p11UniSTS
AU048779  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21440,476,245 - 40,476,483 (+)MAPPERmRatBN7.2
Rnor_6.01442,131,955 - 42,132,190NCBIRnor6.0
Rnor_5.01441,928,708 - 41,928,943UniSTSRnor5.0
RGSC_v3.41443,086,827 - 43,087,062UniSTSRGSC3.4
Celera1439,634,435 - 39,634,670UniSTS
Cytogenetic Map14p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143999825175582726Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:200
Count of miRNA genes:108
Interacting mature miRNAs:113
Transcripts:ENSRNOT00000041793, ENSRNOT00000044017, ENSRNOT00000063985, ENSRNOT00000065214
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 3 8 33 17 19 17 8 10 66 26 19 11 8
Low 34 24 24 24 1 8 9 22
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000044017   ⟹   ENSRNOP00000039929
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1440,387,872 - 40,554,611 (+)Ensembl
Rnor_6.0 Ensembl1442,015,347 - 42,206,311 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000063985   ⟹   ENSRNOP00000060686
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1440,315,049 - 40,377,942 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000096719   ⟹   ENSRNOP00000097076
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1440,315,049 - 40,554,611 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099913   ⟹   ENSRNOP00000077596
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1440,315,057 - 40,554,611 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113166   ⟹   ENSRNOP00000082854
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1440,315,049 - 40,554,611 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117167   ⟹   ENSRNOP00000078899
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1440,315,147 - 40,554,611 (+)Ensembl
RefSeq Acc Id: XM_006250980   ⟹   XP_006251042
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21440,352,649 - 40,557,572 (+)NCBI
Rnor_6.01442,010,297 - 42,210,555 (+)NCBI
Rnor_5.01441,770,273 - 42,007,304 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039092726   ⟹   XP_038948654
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21440,348,833 - 40,557,572 (+)NCBI
RefSeq Acc Id: XM_039092728   ⟹   XP_038948656
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21440,348,833 - 40,557,572 (+)NCBI
RefSeq Acc Id: XM_039092729   ⟹   XP_038948657
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21440,348,833 - 40,557,572 (+)NCBI
RefSeq Acc Id: XM_039092730   ⟹   XP_038948658
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21440,315,013 - 40,557,572 (+)NCBI
RefSeq Acc Id: XM_039092731   ⟹   XP_038948659
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21440,349,323 - 40,557,572 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_006251042   ⟸   XM_006250980
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: ENSRNOP00000039929   ⟸   ENSRNOT00000044017
RefSeq Acc Id: XP_038948658   ⟸   XM_039092730
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038948654   ⟸   XM_039092726
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948657   ⟸   XM_039092729
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038948656   ⟸   XM_039092728
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038948659   ⟸   XM_039092731
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000077596   ⟸   ENSRNOT00000099913
RefSeq Acc Id: ENSRNOP00000082854   ⟸   ENSRNOT00000113166
RefSeq Acc Id: ENSRNOP00000097076   ⟸   ENSRNOT00000096719
RefSeq Acc Id: ENSRNOP00000060686   ⟸   ENSRNOT00000063985
RefSeq Acc Id: ENSRNOP00000078899   ⟸   ENSRNOT00000117167
Protein Domains
PhoLip_ATPase_C

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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 41805214 41805215 C T snv FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), SBN/Ygl (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309619 AgrOrtholog
Ensembl Genes ENSRNOG00000034200 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000039929 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044017 UniProtKB/TrEMBL
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_P_site UniProtKB/TrEMBL
  ATPase_P-typ_Plipid-transl UniProtKB/TrEMBL
  ATPase_P-typ_TM_dom UniProtKB/TrEMBL
  Cation_transp_P_typ_ATPase UniProtKB/TrEMBL
  HAD-like_dom UniProtKB/TrEMBL
  HAD-like_sf UniProtKB/TrEMBL
  P_typ_ATPase_c UniProtKB/TrEMBL
  P_typ_ATPase_HD_dom UniProtKB/TrEMBL
NCBI Gene 289615 ENTREZGENE
PANTHER PTHR24092 UniProtKB/TrEMBL
Pfam PhoLip_ATPase_C UniProtKB/TrEMBL
PhenoGen Atp8a1 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 F1LUT4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Atp8a1  ATPase phospholipid transporting 8A1  Atp8a1  ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Atp8a1  ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1   Atp8a1_predicted  ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Atp8a1_predicted  ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED