Atp5f1d (ATP synthase F1 subunit delta)

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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 ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	ATP5F1D (ATP synthase F1 subunit delta)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Atp5d (ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Atp5f1d (ATP synthase F1 subunit delta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	ATP5F1D (ATP synthase F1 subunit delta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	ATP5F1D (ATP synthase F1 subunit delta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Atp5f1d (ATP synthase F1 subunit delta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	ATP5F1D (ATP synthase F1 subunit delta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	ATP5F1D (ATP synthase F1 subunit delta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Atp5f1d (ATP synthase F1 subunit delta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Atp5d (ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	ATP5F1D (ATP synthase F1 subunit delta)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	atp5f1d	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	ATP16	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	ATPsyndelta	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	F58F12.1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	7	9,560,604 - 9,565,919 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	7	9,560,608 - 9,565,929 (-)	Ensembl
Rnor_6.0	7	12,426,807 - 12,432,120 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	12,426,809 - 12,432,130 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	7	12,596,910 - 12,602,225 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	11,072,820 - 11,075,906 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	7	11,072,819 - 11,075,906 (-)	NCBI
Celera	7	7,736,636 - 7,739,719 (-)	NCBI		Celera
Cytogenetic Map	7	q11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Alzheimer's disease (ISO)

Aortic Calcification (IEP)

Cardiomegaly (IEP)

cerebral creatine deficiency syndrome (ISO)

colitis (IEP)

Intestinal Reperfusion Injury (IEP)

Left Ventricular Hypertrophy (IEP)

mitochondrial complex V (ATP synthase) deficiency (ISS)

mitochondrial complex V (ATP synthase) deficiency nuclear type 3 (ISO)

Mitochondrial Complex V (ATP Synthase) Deficiency, Nuclear Type 5 (ISO)

mitochondrial metabolism disease (ISO)

myocardial infarction (IEP)

Myocardial Reperfusion Injury (IEP)

obesity (IDA)

urinary bladder cancer (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

14-Deoxy-11,12-didehydroandrographolide (ISO)

17alpha-ethynylestradiol (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,4-dinitrotoluene (EXP)

3,4-methylenedioxymethamphetamine (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

5-fluorouracil (ISO)

acrolein (ISO)

aldehydo-D-glucose (EXP)

alpha-pinene (ISO)

ammonium chloride (EXP)

amphetamine (ISO)

aristolochic acid (ISO)

benzo[a]pyrene (ISO)

bexarotene (EXP)

bisphenol A (EXP,ISO)

cadmium atom (ISO)

carmustine (ISO)

choline (ISO)

cisplatin (ISO)

clofibrate (ISO)

cyclosporin A (ISO)

D-glucose (EXP)

dexamethasone (ISO)

dibutyl phthalate (ISO)

dioxygen (EXP,ISO)

doxorubicin (ISO)

ethyl methanesulfonate (ISO)

fenthion (ISO)

flutamide (EXP)

folic acid (ISO)

gamma-hexachlorocyclohexane (EXP)

gentamycin (EXP)

glucose (EXP)

glyphosate (EXP)

indometacin (ISO)

isoprenaline (EXP)

ivermectin (ISO)

L-methionine (ISO)

lipopolysaccharide (ISO)

lithium atom (EXP)

lithium hydride (EXP)

methidathion (ISO)

methotrexate (ISO)

methyl methanesulfonate (ISO)

nefazodone (EXP)

niclosamide (ISO)

notoginsenoside R1 (EXP)

ochratoxin A (EXP,ISO)

okadaic acid (ISO)

ozone (ISO)

paracetamol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

picrotoxin (EXP)

rotenone (ISO)

sodium arsenite (EXP,ISO)

sunitinib (ISO)

tetrachloroethene (ISO)

thimerosal (ISO)

titanium dioxide (ISO)

triptonide (ISO)

valproic acid (ISO)

Y-27632 (EXP)

zidovudine (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

aerobic respiration (ISO,ISS)

ATP biosynthetic process (TAS)

ATP metabolic process (IDA)

ion transport (IEA)

mitochondrial proton-transporting ATP synthase complex assembly (IEA,ISO,ISS)

proton motive force-driven ATP synthesis (IBA,IEA,TAS)

proton motive force-driven mitochondrial ATP synthesis (IEA,ISO)

proton transmembrane transport (IEA)

response to resveratrol (IEP)

Cellular Component

mitochondrial inner membrane (IDA,IEA)

mitochondrial proton-transporting ATP synthase complex (IDA,IEA,ISO)

mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) (IBA,IDA)

proton-transporting ATP synthase complex (TAS)

proton-transporting ATP synthase complex, catalytic core F(1) (IDA,IEA)

Molecular Function

ATP hydrolysis activity (IDA)

protein binding (ISO)

protein-containing complex binding (IDA)

proton-transporting ATP synthase activity, rotational mechanism (IEA,ISO,TAS)

Molecular Pathway Annotations Click to see Annotation Detail View

Alzheimer's disease pathway (IEA)

electron transport chain pathway (ISO)

Huntington's disease pathway (IEA)

oxidative phosphorylation pathway (IEA)

Parkinson's disease pathway (IEA)

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	7	9,560,604 - 9,565,919 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	7	9,560,608 - 9,565,929 (-)	Ensembl
Rnor_6.0	7	12,426,807 - 12,432,120 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	12,426,809 - 12,432,130 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	7	12,596,910 - 12,602,225 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	11,072,820 - 11,075,906 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	7	11,072,819 - 11,075,906 (-)	NCBI
Celera	7	7,736,636 - 7,739,719 (-)	NCBI		Celera
Cytogenetic Map	7	q11	NCBI

ATP5F1D
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	19	1,241,751 - 1,244,825 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	19	1,241,746 - 1,244,825 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	19	1,241,750 - 1,244,824 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	19	1,192,749 - 1,195,824 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	19	1,192,748 - 1,195,823	NCBI
Celera	19	1,175,982 - 1,179,057 (+)	NCBI
Cytogenetic Map	19	p13.3	NCBI
HuRef	19	1,016,668 - 1,019,743 (+)	NCBI		HuRef
CHM1_1	19	1,241,977 - 1,245,052 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	19	1,210,310 - 1,213,384 (+)	NCBI

Atp5d
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	79,974,451 - 79,981,662 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	10	79,974,466 - 79,981,652 (+)	Ensembl
GRCm38	10	80,138,698 - 80,145,828 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	80,138,632 - 80,145,818 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	79,605,060 - 79,608,563 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	10	79,545,494 - 79,548,940 (+)	NCBI			mm8
Celera	10	81,157,147 - 81,160,650 (+)	NCBI		Celera
Cytogenetic Map	10	C1	NCBI

Atp5f1d
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955495	6,664,394 - 6,666,693 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955495	6,664,394 - 6,666,693 (-)	NCBI	ChiLan1.0	ChiLan1.0

ATP5F1D
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	19	1,224,055 - 1,228,283 (+)	NCBI	panpan1.1	PanPan1.1	panPan2

ATP5F1D
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	20	57,547,575 - 57,550,110 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	20	57,547,371 - 57,549,722 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	20	57,350,373 - 57,352,904 (-)	NCBI
ROS_Cfam_1.0	20	58,290,280 - 58,292,813 (-)	NCBI
ROS_Cfam_1.0 Ensembl	20	58,290,281 - 58,292,374 (-)	Ensembl
UMICH_Zoey_3.1	20	57,346,093 - 57,348,625 (-)	NCBI
UNSW_CanFamBas_1.0	20	57,825,374 - 57,827,905 (-)	NCBI
UU_Cfam_GSD_1.0	20	58,028,376 - 58,030,908 (-)	NCBI

Atp5f1d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405118	217,220,035 - 217,222,515 (-)	NCBI
SpeTri2.0	NW_004936588	612,255 - 614,894 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ATP5F1D
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	77,216,436 - 77,222,632 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	77,216,430 - 77,219,301 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	77,781,975 - 77,784,843 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

ATP5F1D
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	6	1,010,210 - 1,013,360 (+)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	6	1,010,265 - 1,013,002 (+)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666081	7,850,087 - 7,853,228 (-)	NCBI	Vero_WHO_p1.0

Atp5f1d
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624828	7,429,915 - 7,432,562 (-)	Ensembl	HetGla_female_1.0		hetGla2
HetGla 1.0	NW_004624828	7,429,915 - 7,432,898 (-)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

D7Got1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	7	9,565,207 - 9,565,291 (+)	MAPPER	mRatBN7.2
Rnor_6.0	7	12,431,409 - 12,431,492	NCBI	Rnor6.0
Rnor_5.0	7	12,601,514 - 12,601,597	UniSTS	Rnor5.0
RGSC_v3.4	7	11,077,417 - 11,077,501	RGD	RGSC3.4
RGSC_v3.4	7	11,077,418 - 11,077,501	UniSTS	RGSC3.4
RGSC_v3.1	7	11,077,418 - 11,077,501	RGD
Celera	7	7,741,231 - 7,741,314	UniSTS
RH 3.4 Map	7	34.6	UniSTS
RH 3.4 Map	7	34.6	RGD
RH 2.0 Map	7	0.0	RGD
Cytogenetic Map	7	q11	UniSTS

RH134373

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	7	9,560,837 - 9,561,162 (+)	MAPPER	mRatBN7.2
Rnor_6.0	7	12,427,039 - 12,427,363	NCBI	Rnor6.0
Rnor_5.0	7	12,597,144 - 12,597,468	UniSTS	Rnor5.0
RGSC_v3.4	7	11,073,048 - 11,073,372	UniSTS	RGSC3.4
Celera	7	7,736,864 - 7,737,188	UniSTS
RH 3.4 Map	7	26.1	UniSTS
Cytogenetic Map	7	q11	UniSTS

BI275930

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	7	9,560,837 - 9,561,155 (+)	MAPPER	mRatBN7.2
Rnor_6.0	7	12,427,039 - 12,427,356	NCBI	Rnor6.0
Rnor_5.0	7	12,597,144 - 12,597,461	UniSTS	Rnor5.0
RGSC_v3.4	7	11,073,048 - 11,073,365	UniSTS	RGSC3.4
Celera	7	7,736,864 - 7,737,181	UniSTS
RH 3.4 Map	7	39.4	UniSTS
Cytogenetic Map	7	q11	UniSTS

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2298550	Neuinf6	Neuroinflammation QTL 6	3.3		nervous system integrity trait (VT:0010566)	spinal cord RT1-B protein level (CMO:0002132)	7	1	27829089	Rat
7411566	Bw136	Body weight QTL 136	10.4	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	7	1	31962314	Rat
9590142	Scort5	Serum corticosterone level QTL 5	24.4	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	7	1	31962314	Rat
724560	Plsm3	Polydactyly-luxate syndrome (PLS) morphotypes QTL 3		0.0003	tibia length (VT:0004357)	tibia length (CMO:0000450)	7	1	34000259	Rat
2317047	Wbc4	White blood cell count QTL 4		0.01	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	7	1	35342956	Rat
61410	Bw19	Body weight QTL 19	6.2	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	7	1	44782185	Rat
631503	Bp102	Blood pressure QTL 102	1.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	7	1	44822433	Rat
1300176	Hrtrt10	Heart rate QTL 10	3.19		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	7	664270	26029351	Rat
634336	Anxrr17	Anxiety related response QTL 17	3.66		locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	7	924703	115097879	Rat
10755438	Coatc9	Coat color QTL 9		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	3529280	48529280	Rat
9590102	Sffal5	Serum free fatty acids level QTL 5	8.62	0.001	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	7	5329019	50329019	Rat
10755440	Coatc10	Coat color QTL 10		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	7496499	52496499	Rat
10059592	Kidm45	Kidney mass QTL 45	3.95	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	7	7573985	52573985	Rat
2298547	Neuinf5	Neuroinflammation QTL 5	3.7		nervous system integrity trait (VT:0010566)	spinal cord Cd74 protein level (CMO:0002131)	7	9462246	58265113	Rat
1643004	Pain2	Pain QTL 2	1		mechanical nociception trait (VT:0002734)	self mutilation severity score (CMO:0002145)	7	9462246	98011544	Rat

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

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_139106	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006240845	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC141331	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC161836	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474029	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ214102	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ223899	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000177	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U00926	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000020670 ⟹ ENSRNOP00000020670

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	7	9,560,609 - 9,563,839 (-)	Ensembl
Rnor_6.0 Ensembl	7	12,426,811 - 12,429,897 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000077301 ⟹ ENSRNOP00000073307

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	7	9,560,608 - 9,565,929 (-)	Ensembl
Rnor_6.0 Ensembl	7	12,426,809 - 12,432,130 (-)	Ensembl

RefSeq Acc Id:

NM_139106 ⟹ NP_620806

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	7	9,560,610 - 9,563,696 (-)	NCBI
Rnor_6.0	7	12,426,811 - 12,429,897 (-)	NCBI
Rnor_5.0	7	12,596,910 - 12,602,225 (-)	NCBI
RGSC_v3.4	7	11,072,820 - 11,075,906 (-)	RGD
Celera	7	7,736,636 - 7,739,719 (-)	RGD

Sequence:

show sequence

GGAATTCCGCTGCTGTCGCTAAGCTAAAGTCACTGACGTTTCCGCCACCATGCTGCCCGCCGCA
TTGCTTCGTCACCCAGGTCTGCGCCGTCTGGTGCTCCAGGCGCGTACGTACGCCCAGGCCGCCG
CCTCACCTGCCCCCGCCGCTGGGCCTGGACAGATGTCCTTCACCTTCGCCTCCCCGACGCAGGT
GTTCTTTGATGGTGCCAATGTCCGGCAAGTGGATGTGCCTACGCTGACTGGAGCCTTTGGCATC
CTGGCATCCCATGTCCCCACACTACAGGTCCTACGGCCTGGGCTGGTAATGGTTCATGCGGAAG
ATGGCACCACAACTAAGTATTTTGTGAGCAGCGGCTCCGTCACTGTGAATGCGGACTCCTCTGT
GCAATTACTAGCTGAAGAAGTCGTGACACTGGACATGCTGGACCTCGGGGCAGCCCGGGCAAAC
CTGGAGAAGGCGCAGTCAGAGCTGTCAGGGGCAGCAGATGAGGCAGCACGGGCTGAGATCCAAA
TCCGGATCGAGGCCAATGAAGCCCTGGTGAAGGCCCTGGAGTAGGCGTACTTTGTCTGTCACCC
ACAGGGTAACAGAGGCAGGTCCTGGGGGGCTGAAGTCGCCACCAGGGGGCAGCAGTGCTCCGGT
TACTGGCTTAAAGCTTCCCTGGTGCTGCCTGCCAGGTCATGGAGGGCTTCCCCAGGCTTCCAGA
GTCTGGGATCCCCAGGATGCCTCTGGAGAGCTGGCCTTGATTGCCCCTCAAAGCCACCCGGACA
GTCAGCTGGCCCAGCCTATCTGCATTAAATACCACGGAATTCC

hide sequence

RefSeq Acc Id:

XM_006240845 ⟹ XP_006240907

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	7	9,560,604 - 9,565,919 (-)	NCBI
Rnor_6.0	7	12,426,807 - 12,432,120 (-)	NCBI
Rnor_5.0	7	12,596,910 - 12,602,225 (-)	NCBI

Sequence:

show sequence

TCTCTTTCTGTTGGTGCTTGGGTTCGAACCCCGGGACTGTCCTTTTATAAGAGCCTAAGCTTCC
AGGCCCTTCTTCCCGGCTTCGCCATAGTCAAGACAAGTGTCATCATGAAGGTTTGCTTCTTTTG
GGCCTGAATGCGCGCTAAGTGCCTCTCTCCAATGGTTGGGACCTGACATCAAACCGGCATCTTT
TCAGCTCAAACGTACTCTCCGGAGGGAAGGTGTCCGTTTGCAGAACACGGTCCTATGGACCCAG
GGCACCGTTTGCTGTTAGAAGGCGAAGAAAACTACAGTTCCCAGAATGATTCACGAGGCATAGG
AGGGTCCCACTTCTAGGCAGCACTGCAAGGGGTGTGGCTAAGGCAAAGTATACCTCCCAGTATG
CTCAGCGCGTTCTGCACCGCGCAGCCTTCGGAGCATCGCAGTGCGCGCGTGCGTTCTTGTGGGA
ACTGCGCCTCCCAGAAGACACCGCGCGTCGTCCTCCTCGCCCTCCCTGAAGGCCGCCTCGCTAT
CCCTGTGTGTCTGCTGTCCGCTAAGCTAAAGTCCACTGACGTTTCCGCCACCATGCTGCCCGCC
GCATTGCTTCGTCACCCAGGTCTGCGCCGTCTGGTGCTCCAGGCGCGTACGTACGCCCAGGCCG
CCGCCTCACCTGCCCCCGCCGCTGGGCCTGGACAGATGTCCTTCACCTTCGCCTCCCCGACGCA
GGTGTTCTTTGATGGTGCCAATGTCCGGCAAGTGGATGTGCCTACGCTGACTGGAGCCTTTGGC
ATCCTGGCATCCCATGTCCCCACACTACAGGTCCTACGGCCTGGGCTGGTAGTGGTTCATGCGG
AAGATGGCACCACAACTAAGTATTTTGTGAGCAGCGGCTCCGTCACTGTGAATGCGGACTCCTC
TGTGCAATTACTAGCTGAAGAAGTCGTGACACTGGACATGCTGGACCTCGGGGCAGCCCGGGCA
AACCTGGAGAAGGCGCAGTCAGAGCTGTCAGGGGCAGCAGATGAGGCAGCACGGGCTGAGATCC
AAATCCGGATCGAGGCCAATGAAGCCCTGGTGAAGGCCCTGGAGTAGGCGTACTTTGTCTGTCA
CCCACAGGGTAACAGAGGCAGGTCCTGGGGGGCTGAAGTCGCCACCAGGGGGCAGCAGTGCTCC
GGTTACTGGCTTAAAGCTTCCCTGGTGCTGCCTGCCAGGTCATGGAGGGCTTCCCCAGGCTTCC
AGAGTCTGGGATCCCCAGGATGCCTCTGGAGAGCTGGCCTTGATTGCCCCTCAAAGCCACCCGG
ACAGTCAGCTGGCCCAGCCTATCTGCATTAAATACCAGGAACCAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_620806	(Get FASTA)	NCBI Sequence Viewer
	XP_006240907	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAC28872	(Get FASTA)	NCBI Sequence Viewer
	AAI61836	(Get FASTA)	NCBI Sequence Viewer
	EDL89323	(Get FASTA)	NCBI Sequence Viewer
	EDL89324	(Get FASTA)	NCBI Sequence Viewer
	EDL89325	(Get FASTA)	NCBI Sequence Viewer
	EDL89326	(Get FASTA)	NCBI Sequence Viewer
	P35434	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_620806 ⟸ NM_139106
- Peptide Label:	precursor
- Sequence:	show sequence MLPAALLRHPGLRRLVLQARTYAQAAASPAPAAGPGQMSFTFASPTQVFFDGANVRQVDVPTLT GAFGILASHVPTLQVLRPGLVMVHAEDGTTTKYFVSSGSVTVNADSSVQLLAEEVVTLDMLDLG AARANLEKAQSELSGAADEAARAEIQIRIEANEALVKALE hide sequence

RefSeq Acc Id:

XP_006240907 ⟸ XM_006240845

- Peptide Label:

isoform X1

- Sequence:

show sequence

MLSAFCTAQPSEHRSARVRSCGNCASQKTPRVVLLALPEGRLAIPVCLLSAKLKSTDVSATMLP
AALLRHPGLRRLVLQARTYAQAAASPAPAAGPGQMSFTFASPTQVFFDGANVRQVDVPTLTGAF
GILASHVPTLQVLRPGLVVVHAEDGTTTKYFVSSGSVTVNADSSVQLLAEEVVTLDMLDLGAAR
ANLEKAQSELSGAADEAARAEIQIRIEANEALVKALE

hide 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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	7	12,429,959 - 12,430,019	EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)

ACI/EurMcwi (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

ACI/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

BN-Lx/CubMcwi (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

BN/NHsdMcwi (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

BN/NHsdMcwi (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

BN/SsN (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

BUF/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

BXH2/CubMcwi (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

BXH3/CubMcwi (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

DA/OlaHsd (2019)

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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

F344/DuCrl (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

F344/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

F344/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

F344/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

FHH/EurMcwi (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

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

External Database Links

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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)