Atp5f1d (ATP synthase F1 subunit delta) - Rat Genome Database

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Gene: Atp5f1d (ATP synthase F1 subunit delta) Rattus norvegicus
Analyze
Symbol: Atp5f1d
Name: ATP synthase F1 subunit delta
RGD ID: 621372
Description: Contributes to ATP hydrolysis activity. Involved in ATP metabolic process and response to resveratrol. Located in mitochondrial inner membrane. Part of mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1). Used to study obesity. Biomarker of colitis and myocardial infarction. Human ortholog(s) of this gene implicated in mitochondrial complex V (ATP synthase) deficiency. Orthologous to human ATP5F1D (ATP synthase F1 subunit delta); PARTICIPATES IN electron transport chain pathway; Alzheimer's disease pathway; Huntington's disease pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; aldehydo-D-glucose.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: ATP synthase subunit delta, mitochondrial; ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit; Atp5d; F-ATPase delta subunit; hypothetical protein LOC690935; LOC690935
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
mRatBN7.279,560,604 - 9,565,919 (-)NCBI
Rnor_6.0 Ensembl712,426,809 - 12,432,130 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0712,426,807 - 12,432,120 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0712,596,910 - 12,602,225 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4711,072,820 - 11,075,906 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1711,072,819 - 11,075,906 (-)NCBI
Celera77,736,636 - 7,739,719 (-)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Arias N, etal., Obesity (Silver Spring). 2017 Jan;25(1):111-121. doi: 10.1002/oby.21706. Epub 2016 Nov 22.
2. Armand-Ugon M, etal., Curr Alzheimer Res. 2017;14(12):1327-1334. doi: 10.2174/1567205014666170505095921.
3. Chen JR, etal., Drug Des Devel Ther. 2015 Jun 15;9:3051-66. doi: 10.2147/DDDT.S82146. eCollection 2015.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. He K, etal., Am J Physiol Heart Circ Physiol. 2014 Dec 15;307(12):H1764-76. doi: 10.1152/ajpheart.00259.2014. Epub 2014 Oct 10.
6. KEGG
7. Ko YH, etal., J Biol Chem. 2000 Oct 20;275(42):32931-9.
8. Li C, etal., Am J Physiol Gastrointest Liver Physiol. 2014 Jan;306(2):G111-22. doi: 10.1152/ajpgi.00123.2013. Epub 2013 Nov 14.
9. Liu DY, etal., Evid Based Complement Alternat Med. 2013;2013:574629. doi: 10.1155/2013/574629. Epub 2013 Jun 6.
10. Luan A, etal., Environ Toxicol Pharmacol. 2015 May;39(3):1081-90. doi: 10.1016/j.etap.2015.03.014. Epub 2015 Mar 31.
11. Meyer B, etal., Mol Cell Proteomics. 2007 Oct;6(10):1690-9. Epub 2007 Jun 17.
12. MGD data from the GO Consortium
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. Pan W, etal., Biochemistry 1998 May 12;37(19):6911-23.
15. Pedersen PL, etal., Biochemistry. 1987 Dec 29;26(26):8631-7.
16. Pipeline to import KEGG annotations from KEGG into RGD
17. Pipeline to import SMPDB annotations from SMPDB into RGD
18. RGD automated data pipeline
19. RGD automated import pipeline for gene-chemical interactions
20. Schertzer JD, etal., Am J Physiol Endocrinol Metab 2003 Mar;284(3):E597-610.
21. Tang F, etal., PLoS One. 2015 Jun 5;10(6):e0129128. doi: 10.1371/journal.pone.0129128. eCollection 2015.
22. Tu L, etal., Microcirculation. 2013 Nov;20(8):736-47. doi: 10.1111/micc.12074.
23. Wang Y, etal., J Proteome Res. 2018 Feb 2;17(2):794-803. doi: 10.1021/acs.jproteome.7b00450. Epub 2018 Jan 23.
24. Zhang S, etal., PLoS One. 2015 Mar 4;10(3):e0118759. doi: 10.1371/journal.pone.0118759. eCollection 2015.
Additional References at PubMed
PMID:12110673   PMID:12477932   PMID:12865426   PMID:18614015   PMID:25002582   PMID:29476059   PMID:29478781  


Genomics

Comparative Map Data
Atp5f1d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.279,560,604 - 9,565,919 (-)NCBI
Rnor_6.0 Ensembl712,426,809 - 12,432,130 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0712,426,807 - 12,432,120 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0712,596,910 - 12,602,225 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4711,072,820 - 11,075,906 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1711,072,819 - 11,075,906 (-)NCBI
Celera77,736,636 - 7,739,719 (-)NCBICelera
Cytogenetic Map7q11NCBI
ATP5F1D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl191,241,746 - 1,244,825 (+)EnsemblGRCh38hg38GRCh38
GRCh38191,241,751 - 1,244,825 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37191,241,750 - 1,244,824 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36191,192,749 - 1,195,824 (+)NCBINCBI36hg18NCBI36
Build 34191,192,748 - 1,195,823NCBI
Celera191,175,982 - 1,179,057 (+)NCBI
Cytogenetic Map19p13.3NCBI
HuRef191,016,668 - 1,019,743 (+)NCBIHuRef
CHM1_1191,241,977 - 1,245,052 (+)NCBICHM1_1
Atp5d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391079,974,451 - 79,981,662 (+)NCBIGRCm39mm39
GRCm39 Ensembl1079,974,466 - 79,981,652 (+)Ensembl
GRCm381080,138,698 - 80,145,828 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1080,138,632 - 80,145,818 (+)EnsemblGRCm38mm10GRCm38
MGSCv371079,605,060 - 79,608,563 (+)NCBIGRCm37mm9NCBIm37
MGSCv361079,545,494 - 79,548,940 (+)NCBImm8
Celera1081,157,147 - 81,160,650 (+)NCBICelera
Cytogenetic Map10C1NCBI
Atp5f1d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554956,664,394 - 6,666,693 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554956,664,394 - 6,666,693 (-)NCBIChiLan1.0ChiLan1.0
ATP5F1D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1191,224,055 - 1,228,283 (+)NCBIpanpan1.1PanPan1.1panPan2
ATP5F1D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12057,547,575 - 57,550,110 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2057,547,371 - 57,549,722 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2057,350,373 - 57,352,904 (-)NCBI
ROS_Cfam_1.02058,290,280 - 58,292,813 (-)NCBI
UMICH_Zoey_3.12057,346,093 - 57,348,625 (-)NCBI
UNSW_CanFamBas_1.02057,825,374 - 57,827,905 (-)NCBI
UU_Cfam_GSD_1.02058,028,376 - 58,030,908 (-)NCBI
Atp5f1d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118217,220,035 - 217,222,515 (-)NCBI
SpeTri2.0NW_004936588612,255 - 614,894 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATP5F1D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl277,216,433 - 77,222,749 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1277,216,430 - 77,219,301 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2277,781,975 - 77,784,843 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ATP5F1D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.161,010,210 - 1,013,360 (+)NCBI
ChlSab1.1 Ensembl61,010,265 - 1,013,002 (+)Ensembl
Vero_WHO_p1.0NW_0236660817,850,087 - 7,853,228 (-)NCBI
Atp5f1d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248287,429,915 - 7,432,898 (-)NCBI

Position Markers
D7Got1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.279,565,207 - 9,565,291 (+)MAPPER
Rnor_6.0712,431,409 - 12,431,492NCBIRnor6.0
Rnor_5.0712,601,514 - 12,601,597UniSTSRnor5.0
RGSC_v3.4711,077,417 - 11,077,501RGDRGSC3.4
RGSC_v3.4711,077,418 - 11,077,501UniSTSRGSC3.4
RGSC_v3.1711,077,418 - 11,077,501RGD
Celera77,741,231 - 7,741,314UniSTS
RH 3.4 Map734.6UniSTS
RH 3.4 Map734.6RGD
RH 2.0 Map70.0RGD
Cytogenetic Map7q11UniSTS
RH134373  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.279,560,837 - 9,561,162 (+)MAPPER
Rnor_6.0712,427,039 - 12,427,363NCBIRnor6.0
Rnor_5.0712,597,144 - 12,597,468UniSTSRnor5.0
RGSC_v3.4711,073,048 - 11,073,372UniSTSRGSC3.4
Celera77,736,864 - 7,737,188UniSTS
RH 3.4 Map726.1UniSTS
Cytogenetic Map7q11UniSTS
BI275930  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.279,560,837 - 9,561,155 (+)MAPPER
Rnor_6.0712,427,039 - 12,427,356NCBIRnor6.0
Rnor_5.0712,597,144 - 12,597,461UniSTSRnor5.0
RGSC_v3.4711,073,048 - 11,073,365UniSTSRGSC3.4
Celera77,736,864 - 7,737,181UniSTS
RH 3.4 Map739.4UniSTS
Cytogenetic Map7q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7134147172Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7134828535Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7134828535Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7137009673Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7138119654Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7265313832258115Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7591147750911477Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7595196950951969Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7975804554758045Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)71164710256647102Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71232846767193263Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)712328467106995532Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:57
Count of miRNA genes:53
Interacting mature miRNAs:56
Transcripts:ENSRNOT00000020670
Prediction methods: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 51 35 17 35 8 11 74 35 38 11 8
Low 6 6 2 6 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020670   ⟹   ENSRNOP00000020670
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl712,426,811 - 12,429,897 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077301   ⟹   ENSRNOP00000073307
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl712,426,809 - 12,432,130 (-)Ensembl
RefSeq Acc Id: NM_139106   ⟹   NP_620806
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.279,560,610 - 9,563,696 (-)NCBI
Rnor_6.0712,426,811 - 12,429,897 (-)NCBI
Rnor_5.0712,596,910 - 12,602,225 (-)NCBI
RGSC_v3.4711,072,820 - 11,075,906 (-)RGD
Celera77,736,636 - 7,739,719 (-)RGD
Sequence:
RefSeq Acc Id: XM_006240845   ⟹   XP_006240907
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.279,560,604 - 9,565,919 (-)NCBI
Rnor_6.0712,426,807 - 12,432,120 (-)NCBI
Rnor_5.0712,596,910 - 12,602,225 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_620806   ⟸   NM_139106
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_006240907   ⟸   XM_006240845
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000073307   ⟸   ENSRNOT00000077301
RefSeq Acc Id: ENSRNOP00000020670   ⟸   ENSRNOT00000020670
Protein Domains
ATP-synt_DE_N

Transcriptome

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

Promoters
RGD ID:13695033
Promoter ID:EPDNEW_R5557
Type:initiation region
Name:Atp5f1d_1
Description:ATP synthase F1 subunit delta
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_6.0712,429,959 - 12,430,019EPDNEW

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)
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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/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/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
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
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 (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:621372 AgrOrtholog
Ensembl Genes ENSRNOG00000014625 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020670 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073307 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020670 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000077301 UniProtKB/TrEMBL
Gene3D-CATH 2.60.15.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro ATP_F1_dsu/esu_C_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATP_synth_F1_dsu/esu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATP_synth_F1_dsu/esu_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPsynth_dsu/esu_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:245965 UniProtKB/Swiss-Prot
NCBI Gene 245965 ENTREZGENE
PANTHER PTHR13822 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam ATP-synt_DE_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Atp5f1d PhenoGen
Superfamily-SCOP SSF46604 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF51344 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs ATP_synt_epsi UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt ATPD_RAT UniProtKB/Swiss-Prot
  B1WBP7_RAT UniProtKB/TrEMBL
  G3V7Y3_RAT UniProtKB/TrEMBL
  P35434 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-11-30 Atp5f1d  ATP synthase F1 subunit delta  Atp5d  ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-29 Atp5d  ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit  LOC690935  hypothetical protein LOC690935  Data Merged 737654 PROVISIONAL
2006-11-20 LOC690935  hypothetical protein LOC690935      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-09-10 Atp5d  ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Atp5d  ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_protein 168 amino acids; 14.7 kDa 724594