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
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.279,560,604 - 9,565,919 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl79,560,608 - 9,565,929 (-)Ensembl
Rnor_6.0712,426,807 - 12,432,120 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,426,809 - 12,432,130 (-)EnsemblRnor6.0rn6Rnor6.0
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
Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. A combination of resveratrol and quercetin induces browning in white adipose tissue of rats fed an obesogenic diet. Arias N, etal., Obesity (Silver Spring). 2017 Jan;25(1):111-121. doi: 10.1002/oby.21706. Epub 2016 Nov 22.
2. Reduced Mitochondrial Activity is Early and Steady in the Entorhinal Cortex but it is Mainly Unmodified in the Frontal Cortex in Alzheimer's Disease. Armand-Ugon M, etal., Curr Alzheimer Res. 2017;14(12):1327-1334. doi: 10.2174/1567205014666170505095921.
3. Cardioprotection against ischemia/reperfusion injury by QiShenYiQi Pill® via ameliorate of multiple mitochondrial dysfunctions. Chen JR, etal., Drug Des Devel Ther. 2015 Jun 15;9:3051-66. doi: 10.2147/DDDT.S82146. eCollection 2015.
4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. ROCK-dependent ATP5D modulation contributes to the protection of notoginsenoside NR1 against ischemia-reperfusion-induced myocardial injury. 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: Kyoto Encyclopedia of Genes and Genomes KEGG
7. Mitochondrial F(0)F(1) ATP synthase. Subunit regions on the F1 motor shielded by F(0), Functional significance, and evidence for an involvement of the unique F(0) subunit F(6). Ko YH, etal., J Biol Chem. 2000 Oct 20;275(42):32931-9.
8. Protective effects of Notoginsenoside R1 on intestinal ischemia-reperfusion injury in rats. 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. Huang Qi Jian Zhong Pellet Attenuates TNBS-Induced Colitis in Rats via Mechanisms Involving Improvement of Energy Metabolism. Liu DY, etal., Evid Based Complement Alternat Med. 2013;2013:574629. doi: 10.1155/2013/574629. Epub 2013 Jun 6.
10. Astragalus polysaccharide attenuates isoproterenol-induced cardiac hypertrophy by regulating TNF-a/PGC-1a signaling mediated energy biosynthesis. 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. Identification of two proteins associated with mammalian ATP synthase. Meyer B, etal., Mol Cell Proteomics. 2007 Oct;6(10):1690-9. Epub 2007 Jun 17.
12. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
13. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. Delta subunit of rat liver mitochondrial ATP synthase: molecular description and novel insights into the nature of its association with the F1-moiety. Pan W, etal., Biochemistry 1998 May 12;37(19):6911-23.
15. Mitochondrial ATP synthase: dramatic Mg2+-induced alterations in the structure and function of the F1-ATPase moiety. Pedersen PL, etal., Biochemistry. 1987 Dec 29;26(26):8631-7.
16. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
17. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
18. GOA pipeline RGD automated data pipeline
19. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
20. Mechanisms underlying increases in SR Ca2+-ATPase activity after exercise in rat skeletal muscle. Schertzer JD, etal., Am J Physiol Endocrinol Metab 2003 Mar;284(3):E597-610.
21. Calpain-1 Mediated Disorder of Pyrophosphate Metabolism Contributes to Vascular Calcification Induced by oxLDL. Tang F, etal., PLoS One. 2015 Jun 5;10(6):e0129128. doi: 10.1371/journal.pone.0129128. eCollection 2015.
22. Astragaloside IV protects heart from ischemia and reperfusion injury via energy regulation mechanisms. Tu L, etal., Microcirculation. 2013 Nov;20(8):736-47. doi: 10.1111/micc.12074.
23. iTRAQ-Based Proteomic Analysis Reveals Recovery of Impaired Mitochondrial Function in Ischemic Myocardium by Shenmai Formula. Wang Y, etal., J Proteome Res. 2018 Feb 2;17(2):794-803. doi: 10.1021/acs.jproteome.7b00450. Epub 2018 Jan 23.
24. Astragaloside IV protects against isoproterenol-induced cardiac hypertrophy by regulating NF-¿B/PGC-1a signaling mediated energy biosynthesis. 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 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl79,560,608 - 9,565,929 (-)Ensembl
Rnor_6.0712,426,807 - 12,432,120 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,426,809 - 12,432,130 (-)EnsemblRnor6.0rn6Rnor6.0
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
GRCh38191,241,751 - 1,244,825 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl191,241,746 - 1,244,825 (+)EnsemblGRCh38hg38GRCh38
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
T2T-CHM13v2.0191,210,310 - 1,213,384 (+)NCBI
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
ROS_Cfam_1.0 Ensembl2058,290,281 - 58,292,374 (-)Ensembl
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 Ensembl277,216,436 - 77,222,632 (-)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 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl61,010,265 - 1,013,002 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660817,850,087 - 7,853,228 (-)NCBIVero_WHO_p1.0
Atp5f1d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248287,429,915 - 7,432,562 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046248287,429,915 - 7,432,898 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D7Got1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.279,565,207 - 9,565,291 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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 (mRatBN7.2)
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)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat

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
mRatBN7.2 Ensembl79,560,609 - 9,563,839 (-)Ensembl
Rnor_6.0 Ensembl712,426,811 - 12,429,897 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077301   ⟹   ENSRNOP00000073307
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl79,560,608 - 9,565,929 (-)Ensembl
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

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P35434-F1-model_v2 AlphaFold P35434 1-168 view protein structure

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 (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
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
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
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
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
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/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
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
FXLE16/Stm (2020)
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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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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
GK/FarMcwi (2019)
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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
HXB10/IpcvMcwi (2019)
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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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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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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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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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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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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
LEW/Crl (2019)
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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
LEXF10A/StmMcwi (2020)
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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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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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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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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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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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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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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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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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/NRrrcMcwi (2019)
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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
MR/N (2020)
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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
MWF/Hsd (2019)
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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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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
SHR/OlalpcvMcwi (2019)
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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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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
SR/JrHsd (2020)
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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
SS/JrHsdMcwi (2019)
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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
WAG/RijCrl (2020)
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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/N (2020)
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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/NCrl (2019)
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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
WN/N (2020)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621372 AgrOrtholog
BioCyc Gene G2FUF-34918 BioCyc
BioCyc Pathway PWY-7980 [ATP biosynthesis] BioCyc
Ensembl Genes ENSRNOG00000014625 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020670 ENTREZGENE
  ENSRNOP00000020670.2 UniProtKB/TrEMBL
  ENSRNOP00000073307.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020670 ENTREZGENE
  ENSRNOT00000020670.5 UniProtKB/TrEMBL
  ENSRNOT00000077301.2 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