Atp6v1a (ATPase H+ transporting V1 subunit A) - Rat Genome Database

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Gene: Atp6v1a (ATPase H+ transporting V1 subunit A) Rattus norvegicus
Analyze
Symbol: Atp6v1a
Name: ATPase H+ transporting V1 subunit A
RGD ID: 1596464
Description: Predicted to enable proton-transporting ATPase activity, rotational mechanism. Predicted to be involved in cellular iron ion homeostasis; cellular response to increased oxygen levels; and proton transmembrane transport. Predicted to be located in several cellular components, including apical plasma membrane; microvillus; and secretory granule. Predicted to be part of vacuolar proton-transporting V-type ATPase, V1 domain. Human ortholog(s) of this gene implicated in autosomal recessive cutis laxa type IID and developmental and epileptic encephalopathy 93. Orthologous to human ATP6V1A (ATPase H+ transporting V1 subunit A); PARTICIPATES IN oxidative phosphorylation pathway; phagocytosis pathway; rheumatoid arthritis pathway; INTERACTS WITH 2,2,2-tetramine; 5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Atp6v1a1; ATPase, H+ transporting, lysosomal V1 subunit A; LOC685232; similar to ATPase, H+ transporting, V1 subunit A, isoform 1; V-type proton ATPase catalytic subunit 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
mRatBN7.21156,561,444 - 56,614,694 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1156,560,974 - 56,614,694 (+)Ensembl
Rnor_6.01161,531,386 - 61,584,634 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1161,531,416 - 61,584,634 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01165,638,315 - 65,691,322 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41158,127,307 - 58,180,225 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1156,114,743 - 56,167,820 (+)NCBICelera
Cytogenetic Map11q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2,2-tetramine  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2,6-di-tert-butyl-4-methylphenol  (ISO)
3-chloropropane-1,2-diol  (ISO)
4-hydroxynon-2-enal  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsenous acid  (ISO)
benzbromarone  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
Brodifacoum  (EXP)
butylated hydroxyanisole  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
cisplatin  (ISO)
clofibrate  (EXP)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
CU-O LINKAGE  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
diethylstilbestrol  (ISO)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
etoposide  (ISO)
finasteride  (EXP)
flutamide  (EXP)
folic acid  (ISO)
genistein  (ISO)
gentamycin  (EXP)
ivermectin  (ISO)
L-ascorbic acid  (ISO)
L-ethionine  (EXP)
lead diacetate  (ISO)
leflunomide  (ISO)
manganese(II) chloride  (EXP)
mercury atom  (ISO)
mercury(0)  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosomorpholine  (EXP)
nefazodone  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
omeprazole  (EXP)
paclitaxel  (ISO)
phenobarbital  (ISO)
pirinixic acid  (EXP,ISO)
progesterone  (ISO)
propiconazole  (ISO)
reactive oxygen species  (ISO)
rotenone  (ISO)
silicon dioxide  (EXP)
sodium arsenite  (EXP)
sulindac  (EXP)
T-2 toxin  (EXP)
tamibarotene  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone enanthate  (ISO)
thioacetamide  (EXP)
trichloroethene  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
uranium atom  (ISO)
valproic acid  (ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

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:14651853   PMID:15632090   PMID:16177003   PMID:17634366   PMID:17897319   PMID:18667600   PMID:19056867   PMID:19199708   PMID:20169059   PMID:20458337   PMID:21700703   PMID:22871113  
PMID:23376485   PMID:23533145   PMID:28296633   PMID:29604406  


Genomics

Comparative Map Data
Atp6v1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21156,561,444 - 56,614,694 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1156,560,974 - 56,614,694 (+)Ensembl
Rnor_6.01161,531,386 - 61,584,634 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1161,531,416 - 61,584,634 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01165,638,315 - 65,691,322 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41158,127,307 - 58,180,225 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1156,114,743 - 56,167,820 (+)NCBICelera
Cytogenetic Map11q21NCBI
ATP6V1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3113,747,033 - 113,812,056 (+)EnsemblGRCh38hg38GRCh38
GRCh383113,747,035 - 113,812,056 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373113,465,882 - 113,530,903 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363114,948,598 - 115,013,593 (+)NCBINCBI36hg18NCBI36
Build 343114,948,597 - 115,013,591NCBI
Celera3111,874,398 - 111,939,560 (+)NCBI
Cytogenetic Map3q13.31NCBI
HuRef3110,840,759 - 110,905,622 (+)NCBIHuRef
CHM1_13113,429,223 - 113,494,222 (+)NCBICHM1_1
Atp6v1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391643,905,765 - 43,960,064 (-)NCBIGRCm39mm39
GRCm39 Ensembl1643,905,765 - 43,960,068 (-)Ensembl
GRCm381644,085,402 - 44,139,702 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1644,085,402 - 44,139,705 (-)EnsemblGRCm38mm10GRCm38
MGSCv371644,085,517 - 44,139,132 (-)NCBIGRCm37mm9NCBIm37
MGSCv361644,006,117 - 44,058,329 (-)NCBImm8
Celera1644,440,632 - 44,496,218 (-)NCBICelera
Cytogenetic Map16B4NCBI
Atp6v1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542713,868,171 - 13,922,028 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542713,868,683 - 13,922,028 (+)NCBIChiLan1.0ChiLan1.0
ATP6V1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13117,808,963 - 117,872,349 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3117,808,963 - 117,872,349 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03110,888,504 - 110,951,750 (+)NCBIMhudiblu_PPA_v0panPan3
ATP6V1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13318,038,143 - 18,103,649 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3318,038,801 - 18,101,435 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3318,140,143 - 18,205,535 (+)NCBI
ROS_Cfam_1.03318,282,343 - 18,349,714 (+)NCBI
UMICH_Zoey_3.13318,086,053 - 18,153,378 (+)NCBI
UNSW_CanFamBas_1.03318,133,128 - 18,198,487 (+)NCBI
UU_Cfam_GSD_1.03318,684,569 - 18,750,022 (+)NCBI
Atp6v1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602136,207,141 - 136,264,040 (-)NCBI
SpeTri2.0NW_0049365361,257,801 - 1,314,770 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATP6V1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13146,121,759 - 146,192,442 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113146,128,664 - 146,165,269 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213155,713,931 - 155,750,535 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATP6V1A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12267,049,745 - 67,112,971 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2267,048,796 - 67,081,962 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604199,356,934 - 99,419,770 (+)NCBIVero_WHO_p1.0
Atp6v1a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473134,721,142 - 34,780,632 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH127473  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22153,926,571 - 153,926,781 (+)MAPPERmRatBN7.2
mRatBN7.21156,614,354 - 56,614,565 (-)MAPPERmRatBN7.2
mRatBN7.21156,614,354 - 56,614,565 (+)MAPPERmRatBN7.2
Rnor_6.01161,584,295 - 61,584,505NCBIRnor6.0
Rnor_6.02166,315,993 - 166,316,202NCBIRnor6.0
Rnor_5.01165,690,983 - 65,691,193UniSTSRnor5.0
Rnor_5.02185,672,845 - 185,673,054UniSTSRnor5.0
RGSC_v3.42159,758,566 - 159,758,775UniSTSRGSC3.4
RGSC_v3.41158,179,886 - 58,180,096UniSTSRGSC3.4
Celera1156,167,481 - 56,167,691UniSTS
Celera2148,272,967 - 148,273,176UniSTS
RH 3.4 Map21005.2UniSTS
Cytogenetic Map2q32UniSTS
Cytogenetic Map11q21UniSTS
RH141877  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21156,612,691 - 56,612,897 (-)MAPPERmRatBN7.2
mRatBN7.21156,612,691 - 56,612,897 (+)MAPPERmRatBN7.2
mRatBN7.22153,928,241 - 153,928,447 (-)MAPPERmRatBN7.2
mRatBN7.22153,928,241 - 153,928,447 (+)MAPPERmRatBN7.2
Rnor_6.02166,317,663 - 166,317,868NCBIRnor6.0
Rnor_6.01161,582,632 - 61,582,837NCBIRnor6.0
Rnor_5.02185,674,515 - 185,674,720UniSTSRnor5.0
Rnor_5.01165,689,320 - 65,689,525UniSTSRnor5.0
RGSC_v3.42159,760,236 - 159,760,441UniSTSRGSC3.4
RGSC_v3.41158,178,223 - 58,178,428UniSTSRGSC3.4
Celera1156,165,895 - 56,166,100UniSTS
Celera2148,274,637 - 148,274,842UniSTS
RH 3.4 Map21004.9UniSTS
Cytogenetic Map2q32UniSTS
Cytogenetic Map11q21UniSTS
Atp6v1a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21156,598,094 - 56,598,324 (+)MAPPERmRatBN7.2
mRatBN7.22153,929,233 - 153,929,380 (+)MAPPERmRatBN7.2
Rnor_6.02166,318,655 - 166,318,801NCBIRnor6.0
Rnor_6.01161,568,037 - 61,568,266NCBIRnor6.0
Rnor_5.01165,674,725 - 65,674,954UniSTSRnor5.0
Rnor_5.02185,675,507 - 185,675,653UniSTSRnor5.0
RGSC_v3.42159,761,228 - 159,761,374UniSTSRGSC3.4
RGSC_v3.41158,163,628 - 58,163,857UniSTSRGSC3.4
Celera1156,151,300 - 56,151,529UniSTS
Celera2148,275,629 - 148,275,775UniSTS
Cytogenetic Map2q32UniSTS
Cytogenetic Map11q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)112952841860324829Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:300
Count of miRNA genes:174
Interacting mature miRNAs:229
Transcripts:ENSRNOT00000002727
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 35 57 41 19 41 2 2 74 35 38 11 2
Low 8 6 9 3 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002727   ⟹   ENSRNOP00000002727
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1156,560,974 - 56,614,691 (+)Ensembl
Rnor_6.0 Ensembl1161,531,578 - 61,584,634 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093263   ⟹   ENSRNOP00000076339
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1161,531,416 - 61,558,785 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093467   ⟹   ENSRNOP00000076121
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1156,584,015 - 56,614,694 (+)Ensembl
Rnor_6.0 Ensembl1161,531,571 - 61,584,634 (+)Ensembl
RefSeq Acc Id: NM_001108318   ⟹   NP_001101788
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21156,561,590 - 56,614,694 (+)NCBI
Rnor_6.01161,531,578 - 61,584,634 (+)NCBI
Rnor_5.01165,638,315 - 65,691,322 (+)NCBI
RGSC_v3.41158,127,307 - 58,180,225 (+)RGD
Celera1156,114,743 - 56,167,820 (+)RGD
Sequence:
RefSeq Acc Id: XM_006248348   ⟹   XP_006248410
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21156,561,457 - 56,614,679 (+)NCBI
Rnor_6.01161,531,559 - 61,584,229 (+)NCBI
Rnor_5.01165,638,315 - 65,691,322 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006248349   ⟹   XP_006248411
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21156,561,457 - 56,614,679 (+)NCBI
Rnor_6.01161,531,386 - 61,584,634 (+)NCBI
Rnor_5.01165,638,315 - 65,691,322 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039088627   ⟹   XP_038944555
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21156,561,445 - 56,614,679 (+)NCBI
RefSeq Acc Id: XM_039088628   ⟹   XP_038944556
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21156,561,444 - 56,614,679 (+)NCBI
RefSeq Acc Id: XM_039088629   ⟹   XP_038944557
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21156,561,444 - 56,614,679 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001101788   ⟸   NM_001108318
- UniProtKB: D4A133 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248410   ⟸   XM_006248348
- Peptide Label: isoform X1
- UniProtKB: D4A133 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248411   ⟸   XM_006248349
- Peptide Label: isoform X1
- UniProtKB: D4A133 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002727   ⟸   ENSRNOT00000002727
RefSeq Acc Id: ENSRNOP00000076121   ⟸   ENSRNOT00000093467
RefSeq Acc Id: ENSRNOP00000076339   ⟸   ENSRNOT00000093263
RefSeq Acc Id: XP_038944556   ⟸   XM_039088628
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038944557   ⟸   XM_039088629
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038944555   ⟸   XM_039088627
- Peptide Label: isoform X2
Protein Domains
ATP-synt_ab   ATP-synt_ab_N   ATP-synt_ab_Xtn

Transcriptome

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

Promoters
RGD ID:13698152
Promoter ID:EPDNEW_R8677
Type:initiation region
Name:Atp6v1a_1
Description:ATPase H+ transporting V1 subunit A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01161,531,611 - 61,531,671EPDNEW

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)
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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)
ACI/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
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)
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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
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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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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
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 65669252 65669253 G T snv BN/SsNSlc (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1596464 AgrOrtholog
Ensembl Genes ENSRNOG00000001992 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002727 UniProtKB/TrEMBL
  ENSRNOP00000076121 UniProtKB/TrEMBL
  ENSRNOP00000076339 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002727 UniProtKB/TrEMBL
  ENSRNOT00000093263 UniProtKB/TrEMBL
  ENSRNOT00000093467 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1140.10 UniProtKB/TrEMBL
  2.40.30.20 UniProtKB/TrEMBL
InterPro ATP-synt_a_Xtn UniProtKB/TrEMBL
  ATP_synth_asu-like_sf UniProtKB/TrEMBL
  ATPase_a/bsu_AS UniProtKB/TrEMBL
  ATPase_a/bsu_nucl-bd UniProtKB/TrEMBL
  ATPase_F1/V1/A1-cplx_a/bsu_N UniProtKB/TrEMBL
  ATPase_F1/V1/A1_a/bsu_N_sf UniProtKB/TrEMBL
  ATPase_F1_bsu/V1_C UniProtKB/TrEMBL
  ATPase_V1-cplx_asu UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  V-ATPase_su_A/alpha UniProtKB/TrEMBL
KEGG Report rno:685232 UniProtKB/TrEMBL
NCBI Gene 685232 ENTREZGENE
PANTHER PTHR43607 UniProtKB/TrEMBL
Pfam ATP-synt_ab UniProtKB/TrEMBL
  ATP-synt_ab_N UniProtKB/TrEMBL
  ATP-synt_ab_Xtn UniProtKB/TrEMBL
PhenoGen Atp6v1a PhenoGen
PROSITE ATPASE_ALPHA_BETA UniProtKB/TrEMBL
Superfamily-SCOP ATPase_a/b_N UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
TIGRFAMs V-ATPase_V1_A UniProtKB/TrEMBL
UniProt A0A1W2Q6N0_RAT UniProtKB/TrEMBL
  D4A133 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-25 Atp6v1a  ATPase H+ transporting V1 subunit A  Atp6v1a  ATPase, H+ transporting, lysosomal V1 subunit A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Atp6v1a  ATPase, H+ transporting, lysosomal V1 subunit A  LOC685232  similar to ATPase, H+ transporting, V1 subunit A, isoform 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC685232  similar to ATPase, H+ transporting, V1 subunit A, isoform 1      Symbol and Name status set to provisional 70820 PROVISIONAL