Optn (optineurin) - Rat Genome Database

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Gene: Optn (optineurin) Rattus norvegicus
Analyze
Symbol: Optn
Name: optineurin
RGD ID: 628886
Description: Enables TFIIIA-class transcription factor binding activity; identical protein binding activity; and ubiquitin binding activity. Involved in several processes, including cellular response to L-glutamate; cellular response to tumor necrosis factor; and regulation of neuron apoptotic process. Located in several cellular components, including axon; neuronal cell body; and perinuclear region of cytoplasm. Colocalizes with Golgi apparatus. Biomarker of Parkinson's disease; bladder neck obstruction; proteinuria; and transient cerebral ischemia. Human ortholog(s) of this gene implicated in Paget's disease of bone; amyotrophic lateral sclerosis (multiple); and glaucoma (multiple). Orthologous to human OPTN (optineurin); PARTICIPATES IN mitochondrial autophagy pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 14.7K-interacting protein 2; FIP-2-like protein; Fip2
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
mRatBN7.21773,209,572 - 73,260,251 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1773,209,575 - 73,260,251 (+)Ensembl
Rnor_6.01777,167,700 - 77,218,374 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1777,167,740 - 77,218,389 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01778,833,443 - 78,884,464 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41784,298,122 - 84,348,330 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11784,317,800 - 84,359,163 (+)NCBI
Celera1772,649,264 - 72,699,727 (+)NCBICelera
Cytogenetic Map17q12.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP,ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
carbon nanotube  (ISO)
chloroquine  (ISO)
chromium(6+)  (ISO)
ciglitazone  (ISO)
cisplatin  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
dioxygen  (ISO)
elemental selenium  (ISO)
Enterolactone  (ISO)
entinostat  (ISO)
epoxomicin  (EXP,ISO)
ethyl methanesulfonate  (ISO)
fenthion  (ISO)
finasteride  (EXP)
flavonoids  (EXP)
fluvastatin  (ISO)
formaldehyde  (ISO)
gentamycin  (EXP)
hyaluronic acid  (EXP)
hydrogen peroxide  (EXP)
ivermectin  (ISO)
lactacystin  (EXP,ISO)
leflunomide  (EXP,ISO)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
methylparaben  (ISO)
methylseleninic acid  (ISO)
N-nitrosodiethylamine  (EXP)
nickel dichloride  (ISO)
nocodazole  (ISO)
oxaliplatin  (EXP)
paracetamol  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (EXP)
pirinixic acid  (ISO)
piroxicam  (ISO)
propiconazole  (ISO)
puromycin  (ISO)
rotenone  (EXP)
selenium atom  (ISO)
sirolimus  (ISO)
sodium arsenite  (EXP,ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
toluene  (EXP)
topotecan  (EXP,ISO)
triclosan  (ISO)
troglitazone  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
autophagosome  (IEA)
axon  (IDA)
cytoplasm  (IBA,IDA)
cytoplasmic vesicle  (IDA)
cytosol  (IEA,ISO)
Golgi apparatus  (IBA,IDA,IEA,ISO)
neuronal cell body  (IDA)
nucleus  (IBA,IDA)
perinuclear region of cytoplasm  (IDA,IEA,ISO)
recycling endosome  (IEA)
trans-Golgi network  (IEA,ISO,ISS)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Genome-wide association study identifies variants at CSF1, OPTN and TNFRSF11A as genetic risk factors for Paget's disease of bone. Albagha OM, etal., Nat Genet. 2010 Jun;42(6):520-4. Epub 2010 May 2.
2. Lack of association between optineurin gene variants T34T, E50K, M98K, 691_692insAG and R545Q and primary open angle glaucoma in Brazilian patients. Caixeta-Umbelino C, etal., Ophthalmic Genet. 2009 Mar;30(1):13-8. doi: 10.1080/13816810802502970.
3. Overexpression of optineurin E50K disrupts Rab8 interaction and leads to a progressive retinal degeneration in mice. Chi ZL, etal., Hum Mol Genet. 2010 Jul 1;19(13):2606-15. Epub 2010 Apr 13.
4. Novel optineurin mutations in patients with familial and sporadic amyotrophic lateral sclerosis. Del Bo R, etal., J Neurol Neurosurg Psychiatry. 2011 Nov;82(11):1239-43. Epub 2011 May 25.
5. Differential involvement of optineurin in amyotrophic lateral sclerosis with or without SOD1 mutations. Deng HX, etal., Arch Neurol. 2011 Aug;68(8):1057-61.
6. The three 'P's of mitophagy: PARKIN, PINK1, and post-translational modifications. Durcan TM and Fon EA, Genes Dev. 2015 May 15;29(10):989-99. doi: 10.1101/gad.262758.115.
7. SNPs and interaction analyses of myocilin, optineurin, and apolipoprotein E in primary open angle glaucoma patients. Fan BJ, etal., Mol Vis. 2005 Aug 29;11:625-31.
8. Variants in optineurin gene and their association with tumor necrosis factor-alpha polymorphisms in Japanese patients with glaucoma. Funayama T, etal., Invest Ophthalmol Vis Sci. 2004 Dec;45(12):4359-67.
9. Molecular genetic analysis of optineurin gene for primary open-angle and normal tension glaucoma in the Japanese population. Fuse N, etal., J Glaucoma. 2004 Aug;13(4):299-303.
10. 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.
11. Optineurin inclusions occur in a minority of TDP-43 positive ALS and FTLD-TDP cases and are rarely observed in other neurodegenerative disorders. Hortobagyi T, etal., Acta Neuropathol. 2011 Apr;121(4):519-27. Epub 2011 Mar 1.
12. Parkin overexpression protects retinal ganglion cells against glutamate excitotoxicity. Hu X, etal., Mol Vis. 2017 Jul 19;23:447-456. eCollection 2017.
13. Analysis of rare variants and common haplotypes in the optineurin gene in Swedish glaucoma cases. Jansson M, etal., Ophthalmic Genet. 2005 Jun;26(2):85-9.
14. Gel-based protease proteomics for identifying the novel calpain substrates in dopaminergic neuronal cell. Kim C, etal., J Biol Chem. 2013 Dec 20;288(51):36717-32. doi: 10.1074/jbc.M113.492876. Epub 2013 Nov 14.
15. Investigation of early protein changes in the urinary bladder following partial bladder outlet obstruction by proteomic approach. Kim HJ, etal., J Korean Med Sci. 2005 Dec;20(6):1000-5.
16. Effects of optineurin siRNA on apoptotic genes and apoptosis in RGC-5 cells. Li H, etal., Mol Vis. 2011;17:3314-25. Epub 2011 Dec 17.
17. Optineurin coding variants in Ghanaian patients with primary open-angle glaucoma. Liu Y, etal., Mol Vis. 2008;14:2367-72. Epub 2008 Dec 18.
18. Mutations of optineurin in amyotrophic lateral sclerosis. Maruyama H, etal., Nature. 2010 May 13;465(7295):223-6. Epub 2010 Apr 28.
19. The M98K variant of the OPTINEURIN (OPTN) gene modifies initial intraocular pressure in patients with primary open angle glaucoma. Melki R, etal., J Med Genet. 2003 Nov;40(11):842-4.
20. Identification of a transcription factor IIIA-interacting protein. Moreland RJ, etal., Nucleic Acids Res. 2000 May 1;28(9):1986-93.
21. Optineurin immunoreactivity in neuronal nuclear inclusions of polyglutamine diseases (Huntington's, DRPLA, SCA2, SCA3) and intranuclear inclusion body disease. Mori F, etal., Acta Neuropathol. 2012 Feb 9.
22. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
23. Isolation and expression of FIP-2 in wounded pulp of the rat. Oyama M, etal., J Dent Res. 2005 Sep;84(9):842-7.
24. Interaction between two glaucoma genes, optineurin and myocilin. Park BC, etal., Genes Cells. 2007 Aug;12(8):969-79.
25. RefSeq and LocusLink: NCBI gene-centered resources Pruitt KD and Maglott DR, Nucleic Acids Res. 2001 Jan 1;29(1):137-40.
26. Adult-onset primary open-angle glaucoma caused by mutations in optineurin. Rezaie T, etal., Science. 2002 Feb 8;295(5557):1077-9.
27. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
28. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
29. Information Derived from GenBank Report RGD, Sept. 2003
30. Optineurin links myosin VI to the Golgi complex and is involved in Golgi organization and exocytosis. Sahlender DA, etal., J Cell Biol. 2005 Apr 25;169(2):285-95. Epub 2005 Apr 18.
31. Expression of optineurin isolated from rat-injured dental pulp and the effects on inflammatory signals in normal rat kidney cells. Senoo K, etal., Odontology. 2017 Aug 3. doi: 10.1007/s10266-017-0314-5.
32. Processing of optineurin in neuronal cells. Shen X, etal., J Biol Chem. 2011 Feb 4;286(5):3618-29. doi: 10.1074/jbc.M110.175810. Epub 2010 Nov 8.
33. Optineurin associates with the podocyte Golgi complex to maintain its structure. Sippl C, etal., Cell Tissue Res. 2014 Nov;358(2):567-83. doi: 10.1007/s00441-014-1968-8. Epub 2014 Aug 7.
34. Depletion of optineurin in RGC-5 cells derived from retinal neurons causes apoptosis and reduces the secretion of neurotrophins. Sippl C, etal., Exp Eye Res. 2011 Nov;93(5):669-80. doi: 10.1016/j.exer.2011.08.011. Epub 2011 Aug 27.
35. Expression of optineurin, a glaucoma-linked gene, is influenced by elevated intraocular pressure. Vittitow J and Borras T, Biochem Biophys Res Commun 2002 Oct 18;298(1):67-74.
36. Disease gene candidates revealed by expression profiling of retinal ganglion cell development. Wang JT, etal., J Neurosci. 2007 Aug 8;27(32):8593-603.
37. From the Cover: Alterations in Optineurin Expression and Localization in Pre-clinical Parkinson's Disease Models. Wise JP and Cannon J, Toxicol Sci. 2016 Oct;153(2):372-81. doi: 10.1093/toxsci/kfw133. Epub 2016 Jul 29.
38. [Effects of decreased OPTN expression on the survival of the rat retinal ganglion cell line RGC5]. Xu Z, etal., Zhonghua Yan Ke Za Zhi. 2014 Aug;50(8):598-605.
39. Posttranslational modifications, localization, and protein interactions of optineurin, the product of a glaucoma gene. Ying H, etal., PLoS One. 2010 Feb 11;5(2):e9168.
Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:15607428   PMID:16091361   PMID:17646400   PMID:17702576   PMID:19959812   PMID:20174559   PMID:21617041   PMID:22854040   PMID:22871113   PMID:23414517  
PMID:24983867   PMID:25294927   PMID:25416956   PMID:25803835   PMID:25910212   PMID:26871637   PMID:27534431   PMID:30100066   PMID:31934852  


Genomics

Comparative Map Data
Optn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21773,209,572 - 73,260,251 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1773,209,575 - 73,260,251 (+)Ensembl
Rnor_6.01777,167,700 - 77,218,374 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1777,167,740 - 77,218,389 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01778,833,443 - 78,884,464 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41784,298,122 - 84,348,330 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11784,317,800 - 84,359,163 (+)NCBI
Celera1772,649,264 - 72,699,727 (+)NCBICelera
Cytogenetic Map17q12.3NCBI
OPTN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381013,100,082 - 13,138,308 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1013,099,449 - 13,138,308 (+)EnsemblGRCh38hg38GRCh38
GRCh371013,142,082 - 13,180,308 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361013,182,088 - 13,220,282 (+)NCBINCBI36hg18NCBI36
Build 341013,182,087 - 13,220,282NCBI
Celera1013,068,965 - 13,107,102 (+)NCBI
Cytogenetic Map10p13NCBI
HuRef1013,055,075 - 13,092,916 (+)NCBIHuRef
CHM1_11013,142,092 - 13,180,464 (+)NCBICHM1_1
T2T-CHM13v2.01013,114,413 - 13,152,929 (+)NCBI
Optn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3925,023,902 - 5,069,210 (-)NCBIGRCm39mm39
GRCm39 Ensembl25,025,453 - 5,068,862 (-)Ensembl
GRCm3825,020,521 - 5,064,399 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl25,020,642 - 5,064,051 (-)EnsemblGRCm38mm10GRCm38
MGSCv3724,941,688 - 4,984,984 (-)NCBIGRCm37mm9NCBIm37
MGSCv3624,937,914 - 4,981,210 (-)NCBImm8
Celera24,975,403 - 5,009,506 (-)NCBICelera
Cytogenetic Map2A1NCBI
cM Map23.15NCBI
Optn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554621,107,510 - 1,151,269 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554621,098,118 - 1,150,291 (+)NCBIChiLan1.0ChiLan1.0
OPTN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11013,077,345 - 13,115,773 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1013,077,345 - 13,115,773 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01013,104,335 - 13,142,725 (+)NCBIMhudiblu_PPA_v0panPan3
OPTN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1223,356,471 - 23,390,569 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl223,357,237 - 23,392,511 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha220,366,503 - 20,408,197 (-)NCBI
ROS_Cfam_1.0223,726,267 - 23,767,964 (-)NCBI
ROS_Cfam_1.0 Ensembl223,724,291 - 23,767,912 (-)Ensembl
UMICH_Zoey_3.1220,852,635 - 20,894,292 (-)NCBI
UNSW_CanFamBas_1.0221,695,361 - 21,737,080 (-)NCBI
UU_Cfam_GSD_1.0222,411,832 - 22,453,523 (-)NCBI
LOC101956249
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244093442,868,730 - 2,952,140 (-)NCBI
SpeTri2.0NW_004936862488,591 - 516,819 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OPTN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1048,530,844 - 48,582,910 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11048,532,029 - 48,582,952 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21077,689,153 - 77,740,521 (-)NCBISscrofa10.2Sscrofa10.2susScr3
OPTN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1913,142,036 - 13,176,996 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl913,150,426 - 13,177,021 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605118,674,614 - 18,710,695 (+)NCBIVero_WHO_p1.0
Optn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248055,683,021 - 5,721,336 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046248055,683,095 - 5,717,558 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
BI294994  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21773,259,873 - 73,260,029 (+)MAPPERmRatBN7.2
Rnor_6.01777,217,997 - 77,218,152NCBIRnor6.0
Rnor_5.01778,884,089 - 78,884,244UniSTSRnor5.0
RGSC_v3.41784,348,260 - 84,348,415UniSTSRGSC3.4
Celera1772,699,657 - 72,699,812UniSTS
RH 3.4 Map17725.8UniSTS
Cytogenetic Map17q12.3UniSTS
RH136760  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21773,259,970 - 73,260,113 (+)MAPPERmRatBN7.2
Rnor_6.01777,218,094 - 77,218,236NCBIRnor6.0
Rnor_5.01778,884,186 - 78,884,328UniSTSRnor5.0
RGSC_v3.41784,348,357 - 84,348,499UniSTSRGSC3.4
Celera1772,699,754 - 72,699,896UniSTS
Cytogenetic Map17q12.3UniSTS
BM387785  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21773,229,026 - 73,229,241 (+)MAPPERmRatBN7.2
Rnor_6.01777,187,154 - 77,187,368NCBIRnor6.0
Rnor_5.01778,853,241 - 78,853,455UniSTSRnor5.0
RGSC_v3.41784,317,417 - 84,317,631UniSTSRGSC3.4
Celera1772,668,531 - 72,668,745UniSTS
RH 3.4 Map17729.6UniSTS
Cytogenetic Map17q12.3UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)172840914773409147Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)172840914773409147Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173136839173951021Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173199078476990784Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173199078481292925Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173455084373951021Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)173747984782479847Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)173828150983281509Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)173828150983281509Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174054004180387013Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174099000585990005Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)174992015486533673Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175004027186533673Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175090909986022412Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175349882882479847Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)175724684382046127Rat
7488963Bp369Blood pressure QTL 3690.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)175900564977910000Rat
2317045Aia11Adjuvant induced arthritis QTL 114.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)176078142686533673Rat
7411577Bw141Body weight QTL 1410.001body mass (VT:0001259)body weight gain (CMO:0000420)176261951686533673Rat
1300131Bp193Blood pressure QTL 1933.3arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)176364000973951021Rat
631502Cm26Cardiac mass QTL 263.71heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)176570358081153923Rat
1300129Rf25Renal function QTL 253.03blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)177100332581153923Rat
12904736Cm121Cardiac mass QTL 1210.043heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)177177462182479847Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1884
Count of miRNA genes:318
Interacting mature miRNAs:429
Transcripts:ENSRNOT00000024162, ENSRNOT00000042881, ENSRNOT00000074087
Prediction methods:Microtar, Miranda, Pita, 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 29 53 37 19 37 8 11 54 31 33 11 8
Low 14 4 4 4 20 4 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_145081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006254262 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006254263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006254264 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600454 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600455 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095343 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095344 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095345 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095346 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095347 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095348 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095349 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB050777 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB069907 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB194259 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB194260 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB222073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB222074 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC105577 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC086976 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473990 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223875 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000294 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000024162   ⟹   ENSRNOP00000024162
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1777,176,716 - 77,216,243 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000042881   ⟹   ENSRNOP00000045795
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1773,209,575 - 73,260,251 (+)Ensembl
Rnor_6.0 Ensembl1777,167,740 - 77,218,389 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000074087   ⟹   ENSRNOP00000066459
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1773,209,575 - 73,260,251 (+)Ensembl
Rnor_6.0 Ensembl1777,195,715 - 77,218,374 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000081940   ⟹   ENSRNOP00000068551
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1777,195,247 - 77,216,240 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000083342   ⟹   ENSRNOP00000069034
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1777,176,716 - 77,216,243 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091561   ⟹   ENSRNOP00000072832
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1773,209,575 - 73,260,251 (+)Ensembl
Rnor_6.0 Ensembl1777,185,053 - 77,218,061 (+)Ensembl
RefSeq Acc Id: NM_145081   ⟹   NP_659549
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21773,209,573 - 73,260,251 (+)NCBI
Rnor_6.01777,167,860 - 77,218,067 (+)NCBI
Rnor_5.01778,833,443 - 78,884,464 (+)NCBI
RGSC_v3.41784,298,122 - 84,348,330 (+)RGD
Celera1772,649,264 - 72,699,727 (+)RGD
Sequence:
RefSeq Acc Id: XM_006254262   ⟹   XP_006254324
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21773,209,574 - 73,260,251 (+)NCBI
Rnor_6.01777,167,700 - 77,218,374 (+)NCBI
Rnor_5.01778,833,443 - 78,884,464 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006254264   ⟹   XP_006254326
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21773,209,575 - 73,260,251 (+)NCBI
Rnor_6.01777,167,701 - 77,218,374 (+)NCBI
Rnor_5.01778,833,443 - 78,884,464 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600454   ⟹   XP_017455943
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21773,209,573 - 73,260,251 (+)NCBI
Rnor_6.01777,167,700 - 77,218,374 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600455   ⟹   XP_017455944
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21773,209,573 - 73,260,251 (+)NCBI
Rnor_6.01777,167,700 - 77,218,374 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039095343   ⟹   XP_038951271
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21773,209,574 - 73,260,251 (+)NCBI
RefSeq Acc Id: XM_039095344   ⟹   XP_038951272
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21773,209,572 - 73,260,251 (+)NCBI
RefSeq Acc Id: XM_039095345   ⟹   XP_038951273
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21773,209,574 - 73,260,251 (+)NCBI
RefSeq Acc Id: XM_039095346   ⟹   XP_038951274
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21773,209,575 - 73,253,194 (+)NCBI
RefSeq Acc Id: XM_039095347   ⟹   XP_038951275
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21773,209,574 - 73,260,251 (+)NCBI
RefSeq Acc Id: XM_039095348   ⟹   XP_038951276
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21773,225,641 - 73,260,251 (+)NCBI
RefSeq Acc Id: XM_039095349   ⟹   XP_038951277
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21773,209,573 - 73,260,251 (+)NCBI
RefSeq Acc Id: XM_039095350   ⟹   XP_038951278
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21773,240,286 - 73,260,251 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_659549   ⟸   NM_145081
- Sequence:
RefSeq Acc Id: XP_006254324   ⟸   XM_006254262
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006254326   ⟸   XM_006254264
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017455943   ⟸   XM_017600454
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017455944   ⟸   XM_017600455
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000024162   ⟸   ENSRNOT00000024162
RefSeq Acc Id: ENSRNOP00000072832   ⟸   ENSRNOT00000091561
RefSeq Acc Id: ENSRNOP00000068551   ⟸   ENSRNOT00000081940
RefSeq Acc Id: ENSRNOP00000069034   ⟸   ENSRNOT00000083342
RefSeq Acc Id: ENSRNOP00000045795   ⟸   ENSRNOT00000042881
RefSeq Acc Id: ENSRNOP00000066459   ⟸   ENSRNOT00000074087
RefSeq Acc Id: XP_038951272   ⟸   XM_039095344
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038951277   ⟸   XM_039095349
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038951271   ⟸   XM_039095343
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038951273   ⟸   XM_039095345
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038951275   ⟸   XM_039095347
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038951274   ⟸   XM_039095346
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038951276   ⟸   XM_039095348
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038951278   ⟸   XM_039095350
- Peptide Label: isoform X12
Protein Domains
CCHC NOA-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8R5M4-F1-model_v2 AlphaFold Q8R5M4 1-585 view protein structure

Transcriptome

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

Promoters
RGD ID:13700577
Promoter ID:EPDNEW_R11095
Type:initiation region
Name:Optn_1
Description:optineurin
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_6.01777,167,718 - 77,167,778EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 77196899 77196900 G A snv M520/N (MCW), LEXF11/Stm (2020), LEXF2B/Stm (2019), M520/N (2020), LEXF4/Stm (2020), LE/Stm (2019), M520/NRrrcMcwi (2019), LEXF3/Stm (2020)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 78862986 78862987 G A snv LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), M520/N (KNAW), LE/OrlBarth (UDEL), Crl:SD (UDEL), LE/Stm (KyushuU), LEC/Tj (KyushuU)
17 78882219 78882220 A T snv IS-Tlk/Kyo (KyushuU)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 73238776 73238777 G A snv LEXF11/Stm (2020), LEXF2B/Stm (2019), LEXF3/Stm (2020), M520/N (2020), LE/Stm (2019), M520/NRrrcMcwi (2019), LEXF4/Stm (2020)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628886 AgrOrtholog
BioCyc Gene G2FUF-8690 BioCyc
Ensembl Genes ENSRNOG00000017941 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000045795 ENTREZGENE
  ENSRNOP00000045795.4 UniProtKB/TrEMBL
  ENSRNOP00000066459 ENTREZGENE
  ENSRNOP00000066459.3 UniProtKB/TrEMBL
  ENSRNOP00000072832.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000042881 ENTREZGENE
  ENSRNOT00000042881.7 UniProtKB/TrEMBL
  ENSRNOT00000074087 ENTREZGENE
  ENSRNOT00000074087.3 UniProtKB/TrEMBL
  ENSRNOT00000091561.2 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7111026 IMAGE-MGC_LOAD
InterPro CC2-LZ_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NEMO_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NEMO_ZF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Optineurin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:246294 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93070 IMAGE-MGC_LOAD
NCBI Gene 246294 ENTREZGENE
PANTHER PTHR31553:SF2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CC2-LZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NEMO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Optn PhenoGen
PROSITE ZF_CCHC_NOA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K3Z1_RAT UniProtKB/TrEMBL
  F1M9C4_RAT UniProtKB/TrEMBL
  M0RAB4_RAT UniProtKB/TrEMBL
  OPTN_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q5PQX8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Optn  optineurin      Symbol and Name status set to approved 625702 APPROVED
2003-02-27 Optn  optineurin      Symbol and Name status set to provisional 70820 PROVISIONAL