Atp6v0d1 (ATPase H+ transporting V0 subunit D1) - Rat Genome Database

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Gene: Atp6v0d1 (ATPase H+ transporting V0 subunit D1) Rattus norvegicus
Analyze
Symbol: Atp6v0d1
Name: ATPase H+ transporting V0 subunit D1
RGD ID: 1306159
Description: Predicted to have proton-transporting ATPase activity, rotational mechanism. Involved in brain development. Localizes to several cellular components, including apical plasma membrane; axon terminus; and synaptic vesicle. Predicted to colocalize with centrosome. Orthologous to human ATP6V0D1 (ATPase H+ transporting V0 subunit d1); PARTICIPATES IN oxidative phosphorylation pathway; phagocytosis pathway; rheumatoid arthritis pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,4-dinitrotoluene; aconitine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Ac39; ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1; ATPase, H+ transporting, lysosomal V0 subunit D1; ATPase, H+ transporting, V0 subunit D; ATPase, H+ transporting, V0 subunit D isoform 1; LOC291969; physophilin; V-type proton ATPase subunit d 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21933,403,352 - 33,447,357 (-)NCBI
Rnor_6.0 Ensembl1937,481,782 - 37,525,762 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01937,481,782 - 37,525,762 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01948,347,540 - 48,391,661 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41935,342,041 - 35,386,025 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11935,346,923 - 35,390,906 (-)NCBI
Celera1932,831,706 - 32,875,649 (-)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9670047   PMID:12477932   PMID:12527205   PMID:17897319   PMID:18752060   PMID:19056867   PMID:19199708   PMID:21844891   PMID:23376485   PMID:23533145   PMID:25002582   PMID:28296633  


Genomics

Comparative Map Data
Atp6v0d1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21933,403,352 - 33,447,357 (-)NCBI
Rnor_6.0 Ensembl1937,481,782 - 37,525,762 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01937,481,782 - 37,525,762 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01948,347,540 - 48,391,661 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41935,342,041 - 35,386,025 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11935,346,923 - 35,390,906 (-)NCBI
Celera1932,831,706 - 32,875,649 (-)NCBICelera
Cytogenetic Map19q12NCBI
ATP6V0D1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1667,438,014 - 67,481,181 (-)EnsemblGRCh38hg38GRCh38
GRCh381667,438,019 - 67,481,157 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371667,471,922 - 67,515,060 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361666,029,418 - 66,072,590 (-)NCBINCBI36hg18NCBI36
Build 341666,029,425 - 66,072,589NCBI
Celera1651,980,121 - 52,023,291 (-)NCBI
Cytogenetic Map16q22.1NCBI
HuRef1653,345,066 - 53,388,217 (-)NCBIHuRef
CHM1_11668,879,298 - 68,922,471 (-)NCBICHM1_1
Atp6v0d1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398106,251,093 - 106,292,696 (-)NCBIGRCm39mm39
GRCm39 Ensembl8106,251,097 - 106,292,679 (-)Ensembl
GRCm388105,524,461 - 105,566,064 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8105,524,465 - 105,566,047 (-)EnsemblGRCm38mm10GRCm38
MGSCv378108,048,370 - 108,089,940 (-)NCBIGRCm37mm9NCBIm37
MGSCv368108,413,599 - 108,455,169 (-)NCBImm8
Celera8109,747,720 - 109,789,272 (-)NCBICelera
Cytogenetic Map8D3NCBI
Atp6v0d1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554849,167,439 - 9,206,193 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554849,167,439 - 9,206,193 (+)NCBIChiLan1.0ChiLan1.0
ATP6V0D1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11667,171,883 - 67,214,670 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1667,171,883 - 67,214,670 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01647,783,327 - 47,826,138 (-)NCBIMhudiblu_PPA_v0panPan3
ATP6V0D1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1581,926,589 - 81,965,959 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl581,926,612 - 81,965,526 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha581,916,255 - 81,955,624 (+)NCBI
ROS_Cfam_1.0582,361,885 - 82,401,257 (+)NCBI
UMICH_Zoey_3.1582,188,035 - 82,227,401 (+)NCBI
UNSW_CanFamBas_1.0581,869,135 - 81,908,503 (+)NCBI
UU_Cfam_GSD_1.0582,512,585 - 82,551,949 (+)NCBI
Atp6v0d1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934941,661,672 - 41,700,328 (+)NCBI
SpeTri2.0NW_00493647517,888,788 - 17,927,513 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATP6V0D1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl628,090,181 - 28,131,985 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1628,090,180 - 28,132,080 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2625,357,269 - 25,399,102 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATP6V0D1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1559,976,118 - 60,018,414 (+)NCBI
ChlSab1.1 Ensembl560,002,544 - 60,017,894 (+)Ensembl
Atp6v0d1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474618,828,025 - 18,883,128 (+)NCBI

Position Markers
RH94762  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21933,448,678 - 33,448,781 (+)MAPPER
Rnor_6.01937,527,106 - 37,527,208NCBIRnor6.0
Rnor_5.01948,393,005 - 48,393,107UniSTSRnor5.0
RGSC_v3.41935,387,369 - 35,387,471UniSTSRGSC3.4
Celera1932,877,022 - 32,877,124UniSTS
Cytogenetic Map19q11UniSTS
Atp6e  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21933,403,466 - 33,403,638 (+)MAPPER
Rnor_6.01937,481,894 - 37,482,065NCBIRnor6.0
Rnor_5.01948,347,652 - 48,347,823UniSTSRnor5.0
RGSC_v3.41935,342,153 - 35,342,324UniSTSRGSC3.4
Celera1932,831,818 - 32,831,989UniSTS
Cytogenetic Map19q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19195770746957707Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19807254547318201Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19500757143907843Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191702800352538299Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)193119430141686140Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)193119430141686140Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)193119430141686140Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191593952838798459Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192445572643907843Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19104464846044648Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191130392747879277Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)19370183548701835Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19243296347217667Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19138221845Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)19370183548701835Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19138221845Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19138221845Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19138221845Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:353
Count of miRNA genes:209
Interacting mature miRNAs:238
Transcripts:ENSRNOT00000023606
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 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000023606   ⟹   ENSRNOP00000023606
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1937,481,782 - 37,525,762 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092910   ⟹   ENSRNOP00000076059
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1937,486,670 - 37,525,733 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092990
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1937,487,510 - 37,496,510 (-)Ensembl
RefSeq Acc Id: NM_001011927   ⟹   NP_001011927
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21933,403,355 - 33,447,335 (-)NCBI
Rnor_6.01937,481,782 - 37,525,762 (-)NCBI
Rnor_5.01948,347,540 - 48,391,661 (-)NCBI
RGSC_v3.41935,342,041 - 35,386,025 (-)RGD
Celera1932,831,706 - 32,875,649 (-)RGD
Sequence:
RefSeq Acc Id: XM_039097616   ⟹   XP_038953544
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21933,403,352 - 33,447,357 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001011927 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953544 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88462 (Get FASTA)   NCBI Sequence Viewer  
  EDL92381 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001011927   ⟸   NM_001011927
- UniProtKB: Q5M7T6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000023606   ⟸   ENSRNOT00000023606
RefSeq Acc Id: ENSRNOP00000076059   ⟸   ENSRNOT00000092910
RefSeq Acc Id: XP_038953544   ⟸   XM_039097616
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13701102
Promoter ID:EPDNEW_R11603
Type:initiation region
Name:Atp6v0d1_1
Description:ATPase H+ transporting V0 subunit D1
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_6.01937,525,756 - 37,525,816EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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/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
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 (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
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
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
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
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
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 (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
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)
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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
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)
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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/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
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 (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 (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)
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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
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 (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 (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 (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:1306159 AgrOrtholog
Ensembl Genes ENSRNOG00000017235 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000023606 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000076059 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000023606 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000092910 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1690.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7127604 IMAGE-MGC_LOAD
InterPro ATPase_su_C-like UniProtKB/TrEMBL
  ATPase_V0-cplx_dsu UniProtKB/TrEMBL
  ATPase_V0/A0-cplx_csu/dsu UniProtKB/TrEMBL
  V-type_ATPase_suC UniProtKB/TrEMBL
KEGG Report rno:291969 UniProtKB/TrEMBL
MGC_CLONE MGC:95115 IMAGE-MGC_LOAD
NCBI Gene 291969 ENTREZGENE
PANTHER PTHR11028 UniProtKB/TrEMBL
Pfam vATP-synt_AC39 UniProtKB/TrEMBL
PhenoGen Atp6v0d1 PhenoGen
PIRSF V-ATP_synth_D UniProtKB/TrEMBL
Superfamily-SCOP ATPase_V0/A0_c/d UniProtKB/TrEMBL
UniProt A0A1B0GWX7_RAT UniProtKB/TrEMBL
  Q5M7T6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-18 Atp6v0d1  ATPase H+ transporting V0 subunit D1  Atp6v0d1  ATPase, H+ transporting, lysosomal V0 subunit D1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-04-27 Atp6v0d1  ATPase, H+ transporting, lysosomal V0 subunit D1  Atp6v0d1  ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Atp6v0d1  ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1  Atp6v0d1  ATPase, H+ transporting, lysosomal V0 subunit D1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-03 Atp6v0d1  ATPase, H+ transporting, lysosomal V0 subunit D1  Atp6v0d1  ATPase, H+ transporting, V0 subunit D isoform 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Atp6v0d1  ATPase, H+ transporting, V0 subunit D isoform 1  Atp6v0d1_predicted  ATPase, H+ transporting, V0 subunit D isoform 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Atp6v0d1_predicted  ATPase, H+ transporting, V0 subunit D isoform 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED