Opa1 (OPA1, mitochondrial dynamin like GTPase) - Rat Genome Database

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Gene: Opa1 (OPA1, mitochondrial dynamin like GTPase) Rattus norvegicus
Analyze
Symbol: Opa1
Name: OPA1, mitochondrial dynamin like GTPase
RGD ID: 708423
Description: Enables kinase binding activity. Involved in several processes, including mitochondrion organization; regulation of dendrite development; and sensory organ development. Located in cytosol. Is extrinsic component of mitochondrial inner membrane. Colocalizes with mitochondrion. Used to study transient cerebral ischemia. Biomarker of several diseases, including artery disease (multiple); chronic kidney disease; fatty liver disease; ocular hypertension; and rhinitis. Human ortholog(s) of this gene implicated in Behr syndrome; dominant optic atrophy plus syndrome; mitochondrial DNA depletion syndrome 14; optic atrophy; and optic atrophy 1. Orthologous to human OPA1 (OPA1 mitochondrial dynamin like GTPase); PARTICIPATES IN mitochondria fusion pathway; INTERACTS WITH 2,6-dinitrotoluene; 4-DAMP(1+); actinomycin D.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: dynamin-like 120 kDa protein, mitochondrial; LOC171116; MGC124921; mitochondrial OPA1; optic atrophy 1; optic atrophy 1 (autosomal dominant); optic atrophy 1 homolog; optic atrophy 1 homolog (human); optic atrophy 1-like protein; optic atrophy protein 1 homolog; RN protein
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
mRatBN7.21171,108,100 - 71,185,170 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1171,109,873 - 71,185,109 (-)Ensembl
Rnor_6.01174,717,600 - 74,793,902 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1174,720,254 - 74,793,803 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01177,761,813 - 77,840,630 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41173,005,470 - 73,058,136 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11173,063,058 - 73,115,780 (-)NCBI
Celera1170,077,956 - 70,151,932 (-)NCBICelera
Cytogenetic Map11q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-dinitrotoluene  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-DAMP(1+)  (EXP)
acrolein  (ISO)
actinomycin D  (EXP)
aflatoxin B1  (ISO)
AICA ribonucleotide  (EXP)
aldehydo-D-glucose  (EXP)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsenous acid  (EXP,ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP)
Brodifacoum  (EXP)
butanal  (ISO)
cadmium dichloride  (ISO)
carnosic acid  (ISO)
CCCP  (ISO)
chlorpyrifos  (ISO)
cisplatin  (EXP,ISO)
curcumin  (EXP)
cycloheximide  (EXP)
D-glucose  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (EXP,ISO)
dibutyl phthalate  (ISO)
diclofenac  (EXP,ISO)
dieldrin  (EXP)
dioxygen  (EXP)
dorsomorphin  (EXP)
doxorubicin  (EXP)
efavirenz  (ISO)
elemental selenium  (ISO)
ethanol  (ISO)
fenofibrate  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fructose  (ISO)
glucose  (EXP)
hexadecanoic acid  (ISO)
hydralazine  (ISO)
hydrogen peroxide  (ISO)
isoprenaline  (EXP)
ivermectin  (ISO)
lamivudine  (ISO)
Licarin A  (ISO)
metformin  (EXP)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
N-acetyl-L-cysteine  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (EXP)
N-nitrosodiethylamine  (EXP)
nitrogen dioxide  (ISO)
okadaic acid  (EXP)
oxidopamine  (EXP,ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
phenethyl caffeate  (EXP)
piroxicam  (ISO)
quercetin 3-O-beta-D-glucofuranoside  (EXP)
quercetin 3-O-beta-D-glucopyranoside  (EXP)
regorafenib  (EXP)
resveratrol  (EXP,ISO)
rimonabant  (ISO)
rotenone  (EXP,ISO)
rutin  (EXP)
Salvianolic acid A  (EXP,ISO)
selenium atom  (ISO)
sevoflurane  (EXP)
sodium arsenite  (EXP)
sodium fluoride  (ISO)
sulfur dioxide  (ISO)
tamoxifen  (ISO)
thapsigargin  (ISO)
trans-cinnamic acid  (EXP)
tungsten  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zidovudine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aging  (IEP)
apoptotic process  (IEA)
calcium import into the mitochondrion  (IMP)
cellular response to glucose stimulus  (IEP)
cellular response to hypoxia  (IEP)
cellular response to L-glutamate  (IEP)
cellular senescence  (ISO,ISS)
cochlea development  (IEP)
GTP metabolic process  (ISO,ISS)
inner mitochondrial membrane organization  (ISO,ISS)
intracellular distribution of mitochondria  (IMP)
membrane tubulation  (ISO,ISS)
mitochondrial fusion  (IBA,ISO,ISS)
mitochondrial genome maintenance  (ISO,ISS)
mitochondrion morphogenesis  (IMP)
mitochondrion organization  (IDA,ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway  (ISO,ISS)
negative regulation of intrinsic apoptotic signaling pathway  (ISO)
negative regulation of release of cytochrome c from mitochondria  (ISO,ISS)
neural tube closure  (ISO)
positive regulation of cellular response to insulin stimulus  (IMP)
positive regulation of dendrite development  (IMP)
positive regulation of dendritic spine morphogenesis  (IMP)
positive regulation of insulin receptor signaling pathway  (IMP)
positive regulation of mitochondrial fusion  (IMP)
positive regulation of neuron maturation  (IMP)
protein complex oligomerization  (ISO)
response to curcumin  (IEP)
response to electrical stimulus  (IEP)
response to muscle activity  (IEP)
response to nutrient levels  (IEP)
retina development in camera-type eye  (IEP)
visual perception  (ISO,ISS)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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2. Aparicio-Trejo OE, etal., Biofactors. 2016 Nov 1. doi: 10.1002/biof.1338.
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7. Borengasser SJ, etal., Physiol Genomics. 2014 Dec 1;46(23):841-50. doi: 10.1152/physiolgenomics.00059.2014. Epub 2014 Oct 21.
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12. Cohn AC, etal., Am J Ophthalmol. 2007 Apr;143(4):656-62. Epub 2007 Feb 15.
13. da Silva AF, etal., Cell Mol Life Sci. 2014 Jun;71(12):2313-24. doi: 10.1007/s00018-014-1557-8. Epub 2014 Jan 18.
14. Dai Y, etal., Invest Ophthalmol Vis Sci. 2011 Apr 16;52(5):2468-76. doi: 10.1167/iovs.10-5873.
15. Davies VJ, etal., Hum Mol Genet. 2007 Jun 1;16(11):1307-18. Epub 2007 Apr 11.
16. del Campo A, etal., Am J Physiol Endocrinol Metab. 2014 Jan 1;306(1):E1-E13. doi: 10.1152/ajpendo.00146.2013. Epub 2013 Oct 1.
17. Fuhrmann N, etal., Mol Neurodegener. 2010 Jun 14;5:25. doi: 10.1186/1750-1326-5-25.
18. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
19. GOA data from the GO Consortium
20. Guo Z, etal., Int J Environ Res Public Health. 2017 Jan 29;14(2). pii: E134. doi: 10.3390/ijerph14020134.
21. Han J, etal., Genet Med. 2006 Apr;8(4):217-25.
22. Hu X, etal., Mol Vis. 2017 Jul 19;23:447-456. eCollection 2017.
23. Ishihara N, etal., EMBO J. 2006 Jul 12;25(13):2966-77. Epub 2006 Jun 15.
24. Javadov S, etal., Basic Res Cardiol. 2011 Jan;106(1):99-109. doi: 10.1007/s00395-010-0122-3. Epub 2010 Oct 1.
25. Ju WK, etal., Invest Ophthalmol Vis Sci. 2009 Feb;50(2):707-16. doi: 10.1167/iovs.08-2499. Epub 2008 Oct 20.
26. Ju WK, etal., Mol Vis. 2008;14:2629-38. Epub 2008 Dec 31.
27. Ju WK, etal., Mol Vis. 2009;15:120-34. Epub 2009 Jan 19.
28. Ju WK, etal., Mol Vis. 2010 Jul 15;16:1331-42.
29. Kamei S, etal., Invest Ophthalmol Vis Sci. 2005 Nov;46(11):4288-94.
30. Kar R, etal., Biochem Biophys Res Commun. 2010 Sep 3;399(4):548-54. doi: 10.1016/j.bbrc.2010.07.108. Epub 2010 Aug 1.
31. Kitaoka Y, etal., Appl Physiol Nutr Metab. 2015 Nov;40(11):1137-42. doi: 10.1139/apnm-2015-0184. Epub 2015 Jul 14.
32. Li R, etal., Chem Res Toxicol. 2015 Mar 16;28(3):408-18. doi: 10.1021/tx5003723. Epub 2015 Jan 16.
33. Li R, etal., J Hazard Mater. 2015 Apr 28;287:392-401. doi: 10.1016/j.jhazmat.2015.02.006. Epub 2015 Feb 4.
34. Li Y, etal., Mol Vis. 2008;14:2451-7. Epub 2008 Dec 29.
35. Lionetti L, etal., PLoS One. 2014 Mar 24;9(3):e92753. doi: 10.1371/journal.pone.0092753. eCollection 2014.
36. Liu W, etal., J Neurosci Res. 2012 Jun;90(6):1183-9. doi: 10.1002/jnr.23016. Epub 2012 Feb 16.
37. Liu Y, etal., Mol Vis. 2007 Nov 26;13:2137-41.
38. Ljubicic V, etal., Mech Ageing Dev. 2010 Feb;131(2):79-88. doi: 10.1016/j.mad.2009.12.004. Epub 2009 Dec 29.
39. Mabuchi F, etal., Am J Ophthalmol. 2007 Jan;143(1):125-130. Epub 2006 Oct 23.
40. Marques-Aleixo I, etal., Cardiovasc Toxicol. 2017 May 23. doi: 10.1007/s12012-017-9412-4.
41. Meng G, etal., Br J Pharmacol. 2017 May 15. doi: 10.1111/bph.13861.
42. MGD data from the GO Consortium
43. Misko AL, etal., J Neurosci. 2012 Mar 21;32(12):4145-55. doi: 10.1523/JNEUROSCI.6338-11.2012.
44. Nakamura M, etal., Ophthalmology. 2006 Mar;113(3):483-488.e1.
45. O'Leary MF, etal., Am J Physiol Cell Physiol. 2013 Mar 1;304(5):C422-30. doi: 10.1152/ajpcell.00240.2012. Epub 2012 Dec 5.
46. OMIM Disease Annotation Pipeline
47. Palmer CS, etal., Cell Signal. 2011 Oct;23(10):1534-45. doi: 10.1016/j.cellsig.2011.05.021. Epub 2011 Jun 13.
48. Pesch UE, etal., Invest Ophthalmol Vis Sci 2004 Nov;45(11):4217-25.
49. Piquereau J, etal., Cardiovasc Res. 2012 Jun 1;94(3):408-17. doi: 10.1093/cvr/cvs117. Epub 2012 Mar 8.
50. Qin M, etal., Mol Vis. 2006 May 12;12:485-91.
51. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
52. RGD automated import pipeline for gene-chemical interactions
53. RGD comprehensive gene curation
54. Rosenfeld M, etal., Biol Psychiatry. 2011 May 15;69(10):980-8. doi: 10.1016/j.biopsych.2011.01.010. Epub 2011 Mar 11.
55. Schlattner U, etal., J Biol Chem. 2013 Jan 4;288(1):111-21. doi: 10.1074/jbc.M112.408633. Epub 2012 Nov 13.
56. Tang Y, etal., Cardiovasc Pathol. 2013 Nov 14. pii: S1054-8807(13)00200-7. doi: 10.1016/j.carpath.2013.11.002.
57. Wang X, etal., J Neurosci. 2009 Jul 15;29(28):9090-103. doi: 10.1523/JNEUROSCI.1357-09.2009.
58. Xue RQ, etal., J Cell Mol Med. 2017 Jan;21(1):58-71. doi: 10.1111/jcmm.12938. Epub 2016 Aug 5.
59. Yao W, etal., Mol Vis. 2006 Jun 12;12:649-54.
60. Yen MY, etal., Ophthalmology. 2010 Feb;117(2):392-6.e1. doi: 10.1016/j.ophtha.2009.07.019. Epub 2009 Dec 6.
61. Yu J, etal., Acta Physiol (Oxf). 2016 Sep 29. doi: 10.1111/apha.12812.
62. Yu J, etal., PeerJ. 2016 Nov 3;4:e2659. eCollection 2016.
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Additional References at PubMed
PMID:11017080   PMID:11847212   PMID:12477932   PMID:12504110   PMID:12509422   PMID:12865426   PMID:14651853   PMID:15489334   PMID:15755804   PMID:15899901   PMID:15912498   PMID:16839884  
PMID:17008324   PMID:17035996   PMID:17545159   PMID:18158317   PMID:18614015   PMID:19046944   PMID:19946888   PMID:20038678   PMID:20185555   PMID:20436456   PMID:21149567   PMID:23220553  
PMID:23453807   PMID:23494933   PMID:24632637   PMID:26316108   PMID:26530815   PMID:27667664   PMID:27890624   PMID:28746876   PMID:29476059   PMID:30988455   PMID:31505169   PMID:31519870  
PMID:32901846   PMID:33119220  


Genomics

Comparative Map Data
Opa1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21171,108,100 - 71,185,170 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1171,109,873 - 71,185,109 (-)Ensembl
Rnor_6.01174,717,600 - 74,793,902 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1174,720,254 - 74,793,803 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01177,761,813 - 77,840,630 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41173,005,470 - 73,058,136 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11173,063,058 - 73,115,780 (-)NCBI
Celera1170,077,956 - 70,151,932 (-)NCBICelera
Cytogenetic Map11q22NCBI
OPA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3193,593,144 - 193,697,811 (+)EnsemblGRCh38hg38GRCh38
GRCh383193,593,149 - 193,697,811 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373193,310,997 - 193,415,600 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363194,793,806 - 194,898,009 (+)NCBINCBI36hg18NCBI36
Build 343194,793,813 - 194,898,017NCBI
Celera3191,726,124 - 191,830,778 (+)NCBI
Cytogenetic Map3q29NCBI
HuRef3190,698,074 - 190,803,338 (+)NCBIHuRef
CHM1_13193,273,732 - 193,378,486 (+)NCBICHM1_1
Opa1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391629,398,099 - 29,481,924 (+)NCBIGRCm39mm39
GRCm39 Ensembl1629,398,152 - 29,473,702 (+)Ensembl
GRCm381629,579,281 - 29,663,127 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1629,579,334 - 29,654,884 (+)EnsemblGRCm38mm10GRCm38
MGSCv371629,579,428 - 29,652,576 (+)NCBIGRCm37mm9NCBIm37
MGSCv361629,499,089 - 29,572,237 (+)NCBImm8
Celera1630,084,446 - 30,156,121 (+)NCBICelera
Cytogenetic Map16B2NCBI
cM Map1620.65NCBI
Opa1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542014,923,575 - 15,007,081 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542014,927,490 - 15,007,082 (-)NCBIChiLan1.0ChiLan1.0
OPA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13201,207,609 - 201,312,358 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3201,207,607 - 201,312,358 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03190,890,242 - 190,995,133 (+)NCBIMhudiblu_PPA_v0panPan3
OPA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12352,068,123 - 52,154,410 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2352,068,118 - 52,151,593 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2351,880,860 - 51,967,154 (+)NCBI
ROS_Cfam_1.02352,711,633 - 52,798,264 (+)NCBI
UMICH_Zoey_3.12352,292,969 - 52,379,474 (+)NCBI
UNSW_CanFamBas_1.02352,346,071 - 52,432,352 (+)NCBI
UU_Cfam_GSD_1.02352,630,584 - 52,717,188 (+)NCBI
Opa1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602123,136,008 - 123,222,290 (+)NCBI
SpeTri2.0NW_0049367111,027,531 - 1,113,796 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OPA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13130,624,823 - 130,719,083 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113130,624,771 - 130,718,345 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213140,148,025 - 140,230,316 (+)NCBISscrofa10.2Sscrofa10.2susScr3
OPA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11587,679,656 - 87,778,767 (+)NCBI
ChlSab1.1 Ensembl1587,679,077 - 87,779,102 (+)Ensembl
Vero_WHO_p1.0NW_02366604161,348,078 - 61,447,152 (+)NCBI
Opa1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473063,911,066 - 63,994,886 (-)NCBI

Position Markers
D11Rat105  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21171,134,896 - 71,135,104 (+)MAPPERmRatBN7.2
Rnor_6.01174,743,188 - 74,743,395NCBIRnor6.0
Rnor_5.01177,789,916 - 77,790,123UniSTSRnor5.0
RGSC_v3.41173,007,964 - 73,008,171UniSTSRGSC3.4
RGSC_v3.41173,007,964 - 73,008,171RGDRGSC3.4
RGSC_v3.11173,065,553 - 73,065,760RGD
Celera1170,101,928 - 70,102,133UniSTS
RH 3.4 Map11572.6UniSTS
RH 3.4 Map11572.6RGD
RH 2.0 Map11123.0RGD
SHRSP x BN Map1134.4799RGD
Cytogenetic Map11q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)115980279482566545Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)115980279482566553Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116611332182169223Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat
1354656Bvd3Brain ventricular dilatation QTL 33.640.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116944607082846715Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:653
Count of miRNA genes:181
Interacting mature miRNAs:210
Transcripts:ENSRNOT00000002338, ENSRNOT00000002343, ENSRNOT00000063999
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_133585 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248497 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248498 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248499 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597865 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597866 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AY333988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY510274 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY660011 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY660012 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY683458 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC111071 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215400 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U93197 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000002338   ⟹   ENSRNOP00000002338
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1171,132,335 - 71,180,355 (-)Ensembl
Rnor_6.0 Ensembl1174,722,819 - 74,793,673 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000002343   ⟹   ENSRNOP00000002343
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1171,109,873 - 71,185,109 (-)Ensembl
Rnor_6.0 Ensembl1174,720,254 - 74,793,803 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104752   ⟹   ENSRNOP00000086026
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1171,109,873 - 71,185,109 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111984   ⟹   ENSRNOP00000079139
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1171,109,873 - 71,185,109 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117359   ⟹   ENSRNOP00000084440
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1171,109,873 - 71,185,109 (-)Ensembl
RefSeq Acc Id: NM_133585   ⟹   NP_598269
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21171,110,751 - 71,185,071 (-)NCBI
Rnor_6.01174,720,246 - 74,793,803 (-)NCBI
Rnor_5.01177,761,813 - 77,840,630 (-)NCBI
RGSC_v3.41173,005,470 - 73,058,136 (-)RGD
Celera1170,077,956 - 70,151,932 (-)RGD
Sequence:
RefSeq Acc Id: XM_006248497   ⟹   XP_006248559
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21171,108,100 - 71,185,170 (-)NCBI
Rnor_6.01174,717,600 - 74,793,902 (-)NCBI
Rnor_5.01177,761,813 - 77,840,630 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248498   ⟹   XP_006248560
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21171,108,100 - 71,185,170 (-)NCBI
Rnor_6.01174,717,600 - 74,793,902 (-)NCBI
Rnor_5.01177,761,813 - 77,840,630 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248499   ⟹   XP_006248561
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21171,108,100 - 71,185,170 (-)NCBI
Rnor_6.01174,717,600 - 74,793,902 (-)NCBI
Rnor_5.01177,761,813 - 77,840,630 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597865   ⟹   XP_017453354
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21171,108,100 - 71,185,170 (-)NCBI
Rnor_6.01174,717,600 - 74,793,902 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597866   ⟹   XP_017453355
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21171,108,100 - 71,185,170 (-)NCBI
Rnor_6.01174,717,600 - 74,793,902 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_598269   ⟸   NM_133585
- Peptide Label: precursor
- UniProtKB: Q2TA68 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006248560   ⟸   XM_006248498
- Peptide Label: isoform X2
- UniProtKB: Q2TA68 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006248561   ⟸   XM_006248499
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006248559   ⟸   XM_006248497
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453355   ⟸   XM_017597866
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017453354   ⟸   XM_017597865
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000002343   ⟸   ENSRNOT00000002343
RefSeq Acc Id: ENSRNOP00000002338   ⟸   ENSRNOT00000002338
RefSeq Acc Id: ENSRNOP00000079139   ⟸   ENSRNOT00000111984
RefSeq Acc Id: ENSRNOP00000084440   ⟸   ENSRNOT00000117359
RefSeq Acc Id: ENSRNOP00000086026   ⟸   ENSRNOT00000104752
Protein Domains
Dynamin-type G

Transcriptome

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

Promoters
RGD ID:13698231
Promoter ID:EPDNEW_R8755
Type:multiple initiation site
Name:Opa1_1
Description:OPA1, mitochondrial dynamin like GTPase
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_6.01174,793,820 - 74,793,880EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
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/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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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/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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
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/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/MavRrrcAek (2020)
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Sequenced By: MCW
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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Sequenced By: MCW
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/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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
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
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 (2020)
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Sequenced By: MCW
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
MR/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
MWF/Hsd (2019)
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Sequenced By: MCW
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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Sequenced By: MCW
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
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)
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
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)
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
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
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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Sequenced By: MCW
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
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 (2020)
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Sequenced By: MCW
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
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 (2019)
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Sequenced By: MCW
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
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)
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
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
WAG/RijCrl (2020)
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Sequenced By: MCW
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/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 (2020)
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Sequenced By: MCW
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/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 (2019)
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Sequenced By: MCW
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/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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 (2020)
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Sequenced By: MCW
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
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:708423 AgrOrtholog
Ensembl Genes ENSRNOG00000001717 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000002338 UniProtKB/Swiss-Prot
  ENSRNOP00000002343 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000002338 UniProtKB/Swiss-Prot
  ENSRNOT00000002343 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7324017 IMAGE-MGC_LOAD
InterPro Dynamin_GTPase UniProtKB/Swiss-Prot
  Dynamin_SF UniProtKB/Swiss-Prot
  G_DYNAMIN_dom UniProtKB/Swiss-Prot
  Opa1 UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot
KEGG Report rno:171116 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124921 IMAGE-MGC_LOAD
NCBI Gene 171116 ENTREZGENE
PANTHER PTHR11566 UniProtKB/Swiss-Prot
  PTHR11566:SF67 UniProtKB/Swiss-Prot
Pfam Dynamin_N UniProtKB/Swiss-Prot
PhenoGen Opa1 PhenoGen
PRINTS DYNAMIN UniProtKB/Swiss-Prot
PROSITE G_DYNAMIN_2 UniProtKB/Swiss-Prot
SMART DYNc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot
UniProt OPA1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O08681 UniProtKB/Swiss-Prot
  Q5MPP1 UniProtKB/Swiss-Prot
  Q5MPP2 UniProtKB/Swiss-Prot
  Q5QJE9 UniProtKB/Swiss-Prot
  Q6B435 UniProtKB/Swiss-Prot
  Q6R611 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-16 Opa1  OPA1, mitochondrial dynamin like GTPase  Opa1  optic atrophy 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-01-22 Opa1  optic atrophy 1  Opa1  optic atrophy 1 homolog (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 Opa1  optic atrophy 1 homolog (human)  LOC171116  RN protein  Symbol and Name updated 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease mutation of the human homolog causes autosomal dominant optic atrophy 1547836
gene_expression expressed in retinal ganglion cells, starburst amacrine cells and horizontal cells of the inner retina 1547836