Atp2c1 (ATPase secretory pathway Ca2+ transporting 1) - Rat Genome Database

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Gene: Atp2c1 (ATPase secretory pathway Ca2+ transporting 1) Rattus norvegicus
Analyze
Symbol: Atp2c1
Name: ATPase secretory pathway Ca2+ transporting 1
RGD ID: 621311
Description: Enables P-type calcium transporter activity. Involved in calcium ion transport and cellular calcium ion homeostasis. Located in Golgi apparatus; cytoplasmic vesicle; and plasma membrane. Human ortholog(s) of this gene implicated in Hailey-Hailey disease. Orthologous to human ATP2C1 (ATPase secretory pathway Ca2+ transporting 1); PARTICIPATES IN calcium transport pathway; calcium/calcium-mediated signaling pathway; INTERACTS WITH 17beta-estradiol; 2,4-dinitrotoluene; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: ATP-dependent Ca(2+) pump PMR1; ATPase 2C1; ATPase, Ca++ transporting, type 2C, member 1; ATPase, Ca++-sequestering; Ca(2+)/Mn(2+)-ATPase 2C1; calcium-transporting ATPase 2C1; calcium-transporting ATPase type 2C member 1; LOC103690457; MGC93231; secretory pathway Ca(2+)-ATPase 1; secretory pathway Ca(2+)-transporting ATPase type 1; Spca1; uncharacterized LOC103690457
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
mRatBN7.28106,034,777 - 106,155,854 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl8106,034,636 - 106,156,006 (-)Ensembl
Rnor_6.08113,953,959 - 114,039,965 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8113,955,647 - 114,013,623 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08113,341,077 - 113,426,614 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48110,516,092 - 110,603,620 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18110,562,294 - 110,623,075 (-)NCBI
Celera8105,376,283 - 105,459,249 (-)NCBICelera
Cytogenetic Map8q32NCBI
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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10615129   PMID:11741891   PMID:12477932   PMID:12707275   PMID:12761501   PMID:12804581   PMID:12810057   PMID:14632182   PMID:14632183   PMID:16192278   PMID:16758324   PMID:19946888  
PMID:20981470   PMID:22871113   PMID:23840669   PMID:27133772  


Genomics

Comparative Map Data
Atp2c1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28106,034,777 - 106,155,854 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl8106,034,636 - 106,156,006 (-)Ensembl
Rnor_6.08113,953,959 - 114,039,965 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8113,955,647 - 114,013,623 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08113,341,077 - 113,426,614 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48110,516,092 - 110,603,620 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18110,562,294 - 110,623,075 (-)NCBI
Celera8105,376,283 - 105,459,249 (-)NCBICelera
Cytogenetic Map8q32NCBI
ATP2C1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3130,850,595 - 131,016,712 (+)EnsemblGRCh38hg38GRCh38
GRCh383130,850,595 - 131,016,712 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373130,569,439 - 130,735,556 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363132,096,124 - 132,218,246 (+)NCBINCBI36hg18NCBI36
Build 343132,096,131 - 132,204,690NCBI
Celera3129,038,713 - 129,160,803 (+)NCBI
Cytogenetic Map3q22.1NCBI
HuRef3127,954,018 - 128,119,693 (+)NCBIHuRef
CHM1_13130,532,422 - 130,699,080 (+)NCBICHM1_1
Atp2c1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399105,288,561 - 105,398,456 (-)NCBIGRCm39mm39
GRCm39 Ensembl9105,280,738 - 105,404,518 (-)Ensembl
GRCm389105,411,362 - 105,521,257 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9105,403,539 - 105,527,319 (-)EnsemblGRCm38mm10GRCm38
MGSCv379105,313,692 - 105,397,447 (-)NCBIGRCm37mm9NCBIm37
MGSCv369105,269,462 - 105,353,199 (-)NCBImm8
Celera9105,007,157 - 105,064,980 (-)NCBICelera
Cytogenetic Map9F1NCBI
Atp2c1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555017,383,150 - 7,519,988 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555017,382,657 - 7,519,789 (-)NCBIChiLan1.0ChiLan1.0
ATP2C1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13135,301,721 - 135,423,700 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3135,260,796 - 135,423,700 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03127,937,272 - 128,101,060 (+)NCBIMhudiblu_PPA_v0panPan3
ATP2C1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12328,097,831 - 28,233,675 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2328,066,639 - 28,235,215 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2328,071,244 - 28,206,384 (+)NCBI
ROS_Cfam_1.02328,573,616 - 28,742,803 (+)NCBI
UMICH_Zoey_3.12328,270,690 - 28,439,119 (+)NCBI
UNSW_CanFamBas_1.02328,360,695 - 28,495,909 (+)NCBI
UU_Cfam_GSD_1.02328,610,117 - 28,745,760 (+)NCBI
Atp2c1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560267,579,716 - 67,714,373 (+)NCBI
SpeTri2.0NW_0049365294,340,131 - 4,474,884 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATP2C1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl131,438,615 - 1,612,676 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1131,461,562 - 1,580,035 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2131,118,899 - 1,270,494 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATP2C1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11559,189,075 - 59,348,684 (-)NCBI
ChlSab1.1 Ensembl1559,188,225 - 59,311,709 (-)Ensembl
Vero_WHO_p1.0NW_02366604132,207,172 - 32,372,825 (-)NCBI
Atp2c1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247306,865,197 - 7,001,378 (+)NCBI

Position Markers
D8Got171  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28106,086,869 - 106,087,053 (+)MAPPERmRatBN7.2
Rnor_6.08113,995,621 - 113,995,804NCBIRnor6.0
Rnor_5.08113,382,649 - 113,382,832UniSTSRnor5.0
RGSC_v3.48110,558,156 - 110,558,340RGDRGSC3.4
RGSC_v3.48110,558,157 - 110,558,340UniSTSRGSC3.4
RGSC_v3.18110,577,611 - 110,577,795RGD
Celera8105,414,948 - 105,415,131UniSTS
Cytogenetic Map8q32UniSTS
RH130674  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28106,074,430 - 106,074,635 (+)MAPPERmRatBN7.2
Rnor_6.08113,983,215 - 113,983,419NCBIRnor6.0
Rnor_5.08113,370,200 - 113,370,404UniSTSRnor5.0
RGSC_v3.48110,545,335 - 110,545,539UniSTSRGSC3.4
Celera8105,401,957 - 105,402,161UniSTS
Cytogenetic Map8q32UniSTS
RH131266  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28106,043,610 - 106,043,793 (+)MAPPERmRatBN7.2
Rnor_6.08113,954,013 - 113,954,195NCBIRnor6.0
Rnor_5.08113,341,131 - 113,341,313UniSTSRnor5.0
RGSC_v3.48110,516,146 - 110,516,328UniSTSRGSC3.4
Celera8105,376,337 - 105,376,519UniSTS
RH 3.4 Map81150.5UniSTS
Cytogenetic Map8q32UniSTS
RH133189  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28106,049,199 - 106,049,386 (+)MAPPERmRatBN7.2
Rnor_6.08113,959,607 - 113,959,793NCBIRnor6.0
Rnor_5.08113,346,592 - 113,346,778UniSTSRnor5.0
RGSC_v3.48110,521,963 - 110,522,149UniSTSRGSC3.4
Celera8105,381,926 - 105,382,112UniSTS
Cytogenetic Map8q32UniSTS
BE114010  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28106,069,078 - 106,069,246 (+)MAPPERmRatBN7.2
Rnor_6.08113,977,863 - 113,978,030NCBIRnor6.0
Rnor_5.08113,364,848 - 113,365,015UniSTSRnor5.0
RGSC_v3.48110,539,983 - 110,540,150UniSTSRGSC3.4
Celera8105,396,605 - 105,396,772UniSTS
RH 3.4 Map81151.6UniSTS
Cytogenetic Map8q32UniSTS
BF390084  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28106,034,833 - 106,034,986 (+)MAPPERmRatBN7.2
Rnor_6.08113,945,255 - 113,945,407NCBIRnor6.0
Rnor_5.08113,330,792 - 113,330,944UniSTSRnor5.0
RGSC_v3.48110,506,791 - 110,506,943UniSTSRGSC3.4
Celera8105,367,562 - 105,367,714UniSTS
RH 3.4 Map81152.7UniSTS
Cytogenetic Map8q32UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088624Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)851351728107062046Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)866142385111142385Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)869349194112783834Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)870513503118219066Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)871888757116888757Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)871888757116888757Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)871888757116888757Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)871888757116888757Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)873473045118473045Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)889265192114019816Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8100149864120994388Rat
631217Activ1Activity QTL 115.9voluntary movement trait (VT:0003491)number of photobeam interruptions in an experimental apparatus (CMO:0001517)8102370617108923645Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:250
Count of miRNA genes:176
Interacting mature miRNAs:202
Transcripts:ENSRNOT00000018175, ENSRNOT00000045087
Prediction methods:Microtar, Miranda, Rnahybrid
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 42 57 41 19 41 8 10 74 35 41 11 8
Low 1 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_131907 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080729 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080730 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080731 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080733 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080734 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080735 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080736 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005487741 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC086994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214054 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214433 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M93017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M93018 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000018175   ⟹   ENSRNOP00000018175
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8106,045,245 - 106,105,000 (-)Ensembl
Rnor_6.0 Ensembl8113,955,647 - 114,013,623 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000045087   ⟹   ENSRNOP00000045953
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8106,035,069 - 106,131,314 (-)Ensembl
Rnor_6.0 Ensembl8113,957,279 - 114,010,277 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095638   ⟹   ENSRNOP00000096296
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8106,043,558 - 106,131,314 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000097914   ⟹   ENSRNOP00000088420
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8106,034,636 - 106,131,314 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099084   ⟹   ENSRNOP00000076661
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8106,043,558 - 106,131,407 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102340   ⟹   ENSRNOP00000083761
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8106,043,558 - 106,156,006 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103991   ⟹   ENSRNOP00000085864
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8106,035,062 - 106,156,006 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112729   ⟹   ENSRNOP00000089204
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8106,043,558 - 106,130,413 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000119741   ⟹   ENSRNOP00000097217
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8106,045,245 - 106,131,314 (-)Ensembl
RefSeq Acc Id: NM_131907   ⟹   NP_571982
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28106,043,557 - 106,131,314 (-)NCBI
Rnor_6.08113,953,959 - 114,039,965 (-)NCBI
Rnor_5.08113,341,077 - 113,426,614 (-)NCBI
RGSC_v3.48110,516,092 - 110,603,620 (-)RGD
Celera8105,376,283 - 105,459,249 (-)RGD
Sequence:
RefSeq Acc Id: XM_039080728   ⟹   XP_038936656
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28106,034,777 - 106,155,854 (-)NCBI
RefSeq Acc Id: XM_039080729   ⟹   XP_038936657
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28106,034,777 - 106,155,854 (-)NCBI
RefSeq Acc Id: XM_039080730   ⟹   XP_038936658
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28106,034,777 - 106,131,333 (-)NCBI
RefSeq Acc Id: XM_039080731   ⟹   XP_038936659
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28106,034,777 - 106,131,333 (-)NCBI
RefSeq Acc Id: XM_039080733   ⟹   XP_038936661
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28106,035,147 - 106,155,853 (-)NCBI
RefSeq Acc Id: XM_039080734   ⟹   XP_038936662
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28106,034,777 - 106,131,333 (-)NCBI
RefSeq Acc Id: XM_039080735   ⟹   XP_038936663
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28106,034,777 - 106,131,333 (-)NCBI
RefSeq Acc Id: XM_039080736   ⟹   XP_038936664
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28106,034,777 - 106,131,288 (-)NCBI
RefSeq Acc Id: XR_005487741
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28106,034,777 - 106,155,853 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_571982   ⟸   NM_131907
- UniProtKB: Q5PQW5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018175   ⟸   ENSRNOT00000018175
RefSeq Acc Id: ENSRNOP00000045953   ⟸   ENSRNOT00000045087
RefSeq Acc Id: XP_038936656   ⟸   XM_039080728
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038936657   ⟸   XM_039080729
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038936663   ⟸   XM_039080735
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038936659   ⟸   XM_039080731
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038936662   ⟸   XM_039080734
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038936658   ⟸   XM_039080730
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038936664   ⟸   XM_039080736
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038936661   ⟸   XM_039080733
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000097217   ⟸   ENSRNOT00000119741
RefSeq Acc Id: ENSRNOP00000089204   ⟸   ENSRNOT00000112729
RefSeq Acc Id: ENSRNOP00000096296   ⟸   ENSRNOT00000095638
RefSeq Acc Id: ENSRNOP00000088420   ⟸   ENSRNOT00000097914
RefSeq Acc Id: ENSRNOP00000076661   ⟸   ENSRNOT00000099084
RefSeq Acc Id: ENSRNOP00000085864   ⟸   ENSRNOT00000103991
RefSeq Acc Id: ENSRNOP00000083761   ⟸   ENSRNOT00000102340
Protein Domains
Cation_ATPase_C   Cation_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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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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
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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)
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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)
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)
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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)
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)
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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)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621311 AgrOrtholog
Ensembl Genes ENSRNOG00000013305 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018175 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000045953 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018175 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000045087 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:7106233 IMAGE-MGC_LOAD
InterPro ATP2C1 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_IIA_PMR1 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:170699 UniProtKB/TrEMBL
MGC_CLONE MGC:93231 IMAGE-MGC_LOAD
NCBI Gene 170699 ENTREZGENE
PANTHER PTHR42861:SF2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cation_ATPase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cation_ATPase_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Atp2c1 PhenoGen
PRINTS HATPASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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-IIA2_Ca UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt AT2C1_RAT UniProtKB/Swiss-Prot
  F1M281_RAT UniProtKB/TrEMBL
  F1M9B5_RAT UniProtKB/TrEMBL
  Q5PQW5 ENTREZGENE, UniProtKB/TrEMBL
  Q64566 ENTREZGENE
UniProt Secondary Q64567 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Atp2c1  ATPase secretory pathway Ca2+ transporting 1  LOC103690457  uncharacterized LOC103690457  Data Merged 737654 PROVISIONAL
2016-02-17 Atp2c1  ATPase secretory pathway Ca2+ transporting 1  Atp2c1  ATPase, Ca++ transporting, type 2C, member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 LOC103690457  uncharacterized LOC103690457      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-06-27 Atp2c1  ATPase, Ca++ transporting, type 2C, member 1  Atp2c1  ATPase, Ca++-sequestering  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Atp2c1  ATPase, Ca++-sequestering      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Atp2c1  ATPase, Ca++-sequestering      Symbol and Name status set to provisional 70820 PROVISIONAL