Atp5f1b (ATP synthase F1 subunit beta) - Rat Genome Database
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Gene: Atp5f1b (ATP synthase F1 subunit beta) Rattus norvegicus
Analyze
Symbol: Atp5f1b
Name: ATP synthase F1 subunit beta
RGD ID: 621368
Description: Exhibits several functions, including adenyl ribonucleotide binding activity; calcium ion binding activity; and lipoprotein particle receptor activity. Predicted to contribute to proton-transporting ATP synthase activity, rotational mechanism. Involved in several processes, including cold acclimation; response to 3,3',5-triiodo-L-thyronine; and response to curcumin. Localizes to cell surface; membrane raft; and mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1). Used to study obesity. Biomarker of cardiomyopathy; polycystic ovary syndrome; transient cerebral ischemia; and type 2 diabetes mellitus. Orthologous to human ATP5F1B (ATP synthase F1 subunit beta); PARTICIPATES IN electron transport chain pathway; Alzheimer's disease pathway; Huntington's disease pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1,3-dinitrobenzene; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: ATP synthase subunit beta, mitochondrial; ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit; ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide; Atp5b; mitochondrial ATP synthase beta subunit
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
mRatBN7.27515,454 - 521,858 (+)NCBI
Rnor_6.0 Ensembl72,504,695 - 2,511,749 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.072,504,708 - 2,511,748 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.072,484,095 - 2,490,338 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.471,376,552 - 1,383,228 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.171,377,178 - 1,383,228 (+)NCBI
Celera7394,648 - 401,125 (+)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-dexrazoxane  (ISO)
(Z)-3-butylidenephthalide  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2,2-tetramine  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-methyl-2-[4-(1,2,3,4-tetrahydronaphthalen-1-yl)phenoxy]propanoic acid  (EXP)
5-aza-2'-deoxycytidine  (ISO)
7,12-dimethyltetraphene  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
aniline  (EXP)
Aroclor 1254  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (ISO)
beta-naphthoflavone  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (EXP)
cadmium dichloride  (EXP)
captan  (ISO)
carbon nanotube  (ISO)
chloropicrin  (ISO)
choline  (ISO)
chromium trinitrate  (ISO)
clobetasol  (ISO)
clofibrate  (EXP)
clozapine  (EXP)
cocaine  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
diclofenac  (EXP)
diethyl maleate  (EXP)
dioxygen  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
folpet  (ISO)
fulvestrant  (ISO)
furan  (EXP)
glyphosate  (EXP)
gold atom  (ISO)
gold(0)  (ISO)
hyaluronic acid  (EXP)
hydrogen peroxide  (EXP,ISO)
isoflavones  (EXP)
isoniazide  (ISO)
josamycin  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
lithium atom  (EXP)
lithium hydride  (EXP)
methamphetamine  (EXP)
methapyrilene  (EXP)
methoxychlor  (EXP)
N,N-diethyl-m-toluamide  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosomorpholine  (EXP)
nafenopin  (EXP)
naphthalene  (ISO)
nicotinic acid  (ISO)
nitric oxide  (ISO)
Nonylphenol  (EXP)
ochratoxin A  (ISO)
oxybenzone  (EXP)
paracetamol  (ISO)
paraoxon  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (EXP)
phenethyl isothiocyanate  (ISO)
PhIP  (EXP)
pioglitazone  (ISO)
piperonyl butoxide  (EXP)
potassium chromate  (ISO)
potassium dichromate  (ISO)
progesterone  (EXP)
promethazine  (EXP)
Pyridostigmine bromide  (EXP)
quercetin  (ISO)
rotenone  (EXP)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
sodium nitrate  (ISO)
streptozocin  (EXP)
sulforaphane  (ISO)
T-2 toxin  (EXP)
tamoxifen  (EXP,ISO)
tanespimycin  (ISO)
testosterone  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
tolcapone  (EXP)
toluene  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
vitamin E  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Andersson U, etal., Biochem J. 1997 Apr 15;323 ( Pt 2):379-85.
2. Bianchet M, etal., J Biol Chem. 1991 Nov 5;266(31):21197-201.
3. Datta A, etal., J Proteome Res. 2011 Nov 4;10(11):5199-213. doi: 10.1021/pr200673y. Epub 2011 Oct 20.
4. Garboczi DN, etal., Biochemistry 1988 Jan 26;27(2):553-60.
5. Garboczi DN, etal., J Biol Chem. 1988 Oct 25;263(30):15694-8.
6. Garboczi DN, etal., J Biol Chem. 1990 Aug 25;265(24):14632-7.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Han D, etal., J Proteome Res. 2011 Feb 4;10(2):564-77. doi: 10.1021/pr100759a. Epub 2010 Dec 20.
9. Hubbard MJ and McHugh NJ, FEBS Lett. 1996 Aug 12;391(3):323-9.
10. KEGG
11. Ko YH, etal., J Biol Chem. 2000 Oct 20;275(42):32931-9.
12. Ledesma MD, etal., Brain Res. 2003 Oct 10;987(1):107-16.
13. Li W, etal., J Huazhong Univ Sci Technolog Med Sci. 2017 Apr;37(2):210-216. doi: 10.1007/s11596-017-1717-9. Epub 2017 Apr 11.
14. Li Y, etal., Zhonghua Er Ke Za Zhi. 2006 Oct;44(10):787-91.
15. Luis AM, etal., J Biol Chem. 1993 Jan 25;268(3):1868-75.
16. Martinez LO, etal., Nature 2003 Jan 2;421(6918):75-9.
17. Meyer B, etal., Mol Cell Proteomics. 2007 Oct;6(10):1690-9. Epub 2007 Jun 17.
18. Mukherjee R and Yun JW, Life Sci. 2016 Mar 1;148:112-7. doi: 10.1016/j.lfs.2016.02.018. Epub 2016 Feb 13.
19. NCBI rat LocusLink and RefSeq merged data July 26, 2002
20. Osanai T, etal., Cardiovasc Res. 2009 Mar 1;81(4):780-7. doi: 10.1093/cvr/cvn356. Epub 2008 Dec 22.
21. Pedersen PL, etal., Biochemistry. 1987 Dec 29;26(26):8631-7.
22. Pipeline to import KEGG annotations from KEGG into RGD
23. Pipeline to import SMPDB annotations from SMPDB into RGD
24. Qiu P, etal., J Agric Food Chem. 2016 Apr 6;64(13):2765-71. doi: 10.1021/acs.jafc.6b00053. Epub 2016 Mar 25.
25. Ramm S, etal., Toxicology. 2015 May 4;331:100-11. doi: 10.1016/j.tox.2015.03.004. Epub 2015 Mar 13.
26. RGD automated data pipeline
27. RGD automated import pipeline for gene-chemical interactions
28. Severino V, etal., J Proteome Res. 2011 Jul 1;10(7):3212-24. Epub 2011 Jun 1.
29. You YA, etal., Mol Cell Proteomics. 2015 Nov;14(11):2901-9. doi: 10.1074/mcp.M114.046888. Epub 2015 Sep 4.
30. Yu JH, etal., Proteomics. 2003 Dec;3(12):2446-53. doi: 10.1002/pmic.200300545.
31. Zhang Q, etal., J Mol Endocrinol. 2012 Jun 26;49(1):35-46. doi: 10.1530/JME-12-0020. Print 2012 Aug.
32. Zhang S, etal., Toxicol Appl Pharmacol. 2005 Jan 1;202(1):13-7.
Additional References at PubMed
PMID:2522775   PMID:2531579   PMID:2870059   PMID:2907347   PMID:8006588   PMID:9736690   PMID:10077593   PMID:12110673   PMID:12477932   PMID:12865426   PMID:14651853   PMID:14673794  
PMID:15489334   PMID:15572201   PMID:16210410   PMID:16751257   PMID:16854843   PMID:17303654   PMID:17510399   PMID:17612527   PMID:17634366   PMID:17643490   PMID:17675573   PMID:17709438  
PMID:18063578   PMID:18510804   PMID:18614015   PMID:19056867   PMID:19199708   PMID:19808025   PMID:19946888   PMID:20458337   PMID:20833797   PMID:21106936   PMID:21630459   PMID:21926988  
PMID:22082260   PMID:23106098   PMID:23376485   PMID:23533145   PMID:23979707   PMID:24042457   PMID:24625528   PMID:25931508   PMID:26316108   PMID:26767982   PMID:26769832   PMID:29476059  
PMID:29581031   PMID:29867124   PMID:30552345  


Genomics

Comparative Map Data
Atp5f1b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27515,454 - 521,858 (+)NCBI
Rnor_6.0 Ensembl72,504,695 - 2,511,749 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.072,504,708 - 2,511,748 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.072,484,095 - 2,490,338 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.471,376,552 - 1,383,228 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.171,377,178 - 1,383,228 (+)NCBI
Celera7394,648 - 401,125 (+)NCBICelera
Cytogenetic Map7q11NCBI
ATP5F1B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1256,638,175 - 56,645,984 (-)EnsemblGRCh38hg38GRCh38
GRCh381256,638,175 - 56,645,984 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371257,031,959 - 57,039,768 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh371257,031,959 - 57,039,852 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361255,318,226 - 55,326,119 (-)NCBINCBI36hg18NCBI36
Build 341255,318,227 - 55,326,119NCBI
Celera1256,683,671 - 56,691,564 (-)NCBI
Cytogenetic Map12q13.3NCBI
HuRef1254,071,237 - 54,079,130 (-)NCBIHuRef
CHM1_11256,999,492 - 57,007,379 (-)NCBICHM1_1
Atp5b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910127,919,176 - 127,926,257 (+)NCBIGRCm39mm39
GRCm3810128,083,307 - 128,090,388 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10128,083,273 - 128,090,391 (+)EnsemblGRCm38mm10GRCm38
MGSCv3710127,520,363 - 127,527,444 (+)NCBIGRCm37mm9NCBIm37
MGSCv3610127,486,256 - 127,493,337 (+)NCBImm8
Celera10130,478,043 - 130,485,124 (+)NCBICelera
Cytogenetic Map10D3NCBI
Atp5f1b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554584,186,461 - 4,195,494 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554584,188,167 - 4,195,575 (-)NCBIChiLan1.0ChiLan1.0
ATP5F1B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11232,519,749 - 32,527,753 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1232,519,749 - 32,527,753 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01232,264,570 - 32,272,419 (+)NCBIMhudiblu_PPA_v0panPan3
ATP5F1B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl10870,392 - 909,161 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.110870,405 - 876,937 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Atp5f1b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936646951,236 - 958,907 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATP5F1B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl521,984,580 - 21,992,407 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1521,984,750 - 21,992,393 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2523,659,081 - 23,666,726 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATP5F1B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11152,587,608 - 52,600,057 (-)NCBI
ChlSab1.1 Ensembl1152,587,143 - 52,600,756 (-)Ensembl
Atp5f1b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462480211,400,288 - 11,408,785 (+)NCBI

Position Markers
ATP5B  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.072,505,735 - 2,505,871NCBIRnor6.0
Rnor_6.0225,599,724 - 25,599,860NCBIRnor6.0
Rnor_5.072,485,122 - 2,485,258UniSTSRnor5.0
Rnor_5.0244,754,009 - 44,754,145UniSTSRnor5.0
RGSC_v3.471,377,579 - 1,377,715UniSTSRGSC3.4
RGSC_v3.4228,334,600 - 28,334,736UniSTSRGSC3.4
Celera7395,675 - 395,811UniSTS
Celera225,173,156 - 25,173,292UniSTS
Cytogenetic Map2q12UniSTS
Cytogenetic Map7q11UniSTS
RH127966  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.072,510,875 - 2,511,643NCBIRnor6.0
Rnor_6.0225,601,210 - 25,601,425NCBIRnor6.0
Rnor_5.072,489,465 - 2,490,233UniSTSRnor5.0
Rnor_5.0244,755,495 - 44,755,710UniSTSRnor5.0
RGSC_v3.471,382,355 - 1,383,123UniSTSRGSC3.4
RGSC_v3.4228,336,799 - 28,337,015UniSTSRGSC3.4
Celera7400,252 - 401,020UniSTS
Celera225,174,642 - 25,174,857UniSTS
Cytogenetic Map2q12UniSTS
Cytogenetic Map7q11UniSTS
AW549786  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.072,510,907 - 2,511,545NCBIRnor6.0
Rnor_5.072,489,497 - 2,490,135UniSTSRnor5.0
RGSC_v3.471,382,387 - 1,383,025UniSTSRGSC3.4
Celera7400,284 - 400,922UniSTS
Cytogenetic Map7q11UniSTS
MARC_26134-26135:1030377217:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.072,506,602 - 2,507,177NCBIRnor6.0
Rnor_5.072,485,989 - 2,486,564UniSTSRnor5.0
RGSC_v3.471,378,446 - 1,379,021UniSTSRGSC3.4
Celera7396,542 - 397,117UniSTS
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

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:37
Count of miRNA genes:35
Interacting mature miRNAs:37
Transcripts:ENSRNOT00000003965
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 3 43 53 41 4 41 8 11 70 35 27 8
Medium 4 15 4 14 11
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003965   ⟹   ENSRNOP00000003965
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl72,504,695 - 2,511,749 (+)Ensembl
RefSeq Acc Id: NM_134364   ⟹   NP_599191
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27515,454 - 521,858 (+)NCBI
Rnor_6.072,504,708 - 2,511,748 (+)NCBI
Rnor_5.072,484,095 - 2,490,338 (+)NCBI
RGSC_v3.471,376,552 - 1,383,228 (+)RGD
Celera7394,648 - 401,125 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_599191   ⟸   NM_134364
- Peptide Label: precursor
- UniProtKB: P10719 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003965   ⟸   ENSRNOT00000003965
Protein Domains
AAA

Transcriptome

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

Promoters
RGD ID:13694922
Promoter ID:EPDNEW_R5447
Type:multiple initiation site
Name:Atp5f1b_1
Description:ATP synthase F1 subunit beta
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_6.072,504,709 - 2,504,769EPDNEW

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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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:621368 AgrOrtholog
Ensembl Genes ENSRNOG00000002840 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003965 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003965 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.1140.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7937989 IMAGE-MGC_LOAD
InterPro AAA+_ATPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATP_synth_F1_bsu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_a/bsu_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_F1/V1/A1_a/bsu_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_F1/V1/A1_a/bsu_N_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_F1/V1/A1_a/bsu_nucl-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_F1/V1_b/a_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:171374 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124522 IMAGE-MGC_LOAD
NCBI Gene 171374 ENTREZGENE
Pfam ATP-synt_ab UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATP-synt_ab_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Atp5f1b PhenoGen
PROSITE ATPASE_ALPHA_BETA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART AAA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50615 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs atpD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt ATPB_RAT UniProtKB/Swiss-Prot
  G3V6D3_RAT UniProtKB/TrEMBL
  P10719 ENTREZGENE
UniProt Secondary Q499W0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-11-30 Atp5f1b  ATP synthase F1 subunit beta  Atp5b  ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Atp5b  ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide  Atp5b  ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-22 Atp5b  ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit  Atp5b  ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Atp5b  ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Atp5b  ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide      Symbol and Name status set to provisional 70820 PROVISIONAL