Optn (optineurin) - Rat Genome Database

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Gene: Optn (optineurin) Rattus norvegicus
Analyze
Symbol: Optn
Name: optineurin
RGD ID: 628886
Description: Exhibits 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. Localizes to several cellular components, including Golgi apparatus; neuronal cell body; and perinuclear region of cytoplasm. 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
Also 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21773,209,572 - 73,260,251 (+)NCBI
Rnor_6.0 Ensembl1777,167,740 - 77,218,389 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01777,167,700 - 77,218,374 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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)
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)
finasteride  (EXP)
flavonoids  (EXP)
fluvastatin  (ISO)
formaldehyde  (ISO)
hyaluronic acid  (EXP)
hydrogen peroxide  (EXP)
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  (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)
testosterone  (ISO)
tetrachloromethane  (ISO)
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
1. Albagha OM, etal., Nat Genet. 2010 Jun;42(6):520-4. Epub 2010 May 2.
2. Caixeta-Umbelino C, etal., Ophthalmic Genet. 2009 Mar;30(1):13-8. doi: 10.1080/13816810802502970.
3. Chi ZL, etal., Hum Mol Genet. 2010 Jul 1;19(13):2606-15. Epub 2010 Apr 13.
4. Del Bo R, etal., J Neurol Neurosurg Psychiatry. 2011 Nov;82(11):1239-43. Epub 2011 May 25.
5. Deng HX, etal., Arch Neurol. 2011 Aug;68(8):1057-61.
6. Durcan TM and Fon EA, Genes Dev. 2015 May 15;29(10):989-99. doi: 10.1101/gad.262758.115.
7. Fan BJ, etal., Mol Vis. 2005 Aug 29;11:625-31.
8. Funayama T, etal., Invest Ophthalmol Vis Sci. 2004 Dec;45(12):4359-67.
9. Fuse N, etal., J Glaucoma. 2004 Aug;13(4):299-303.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Hortobagyi T, etal., Acta Neuropathol. 2011 Apr;121(4):519-27. Epub 2011 Mar 1.
12. Hu X, etal., Mol Vis. 2017 Jul 19;23:447-456. eCollection 2017.
13. Jansson M, etal., Ophthalmic Genet. 2005 Jun;26(2):85-9.
14. Kim C, etal., J Biol Chem. 2013 Dec 20;288(51):36717-32. doi: 10.1074/jbc.M113.492876. Epub 2013 Nov 14.
15. Kim HJ, etal., J Korean Med Sci. 2005 Dec;20(6):1000-5.
16. Li H, etal., Mol Vis. 2011;17:3314-25. Epub 2011 Dec 17.
17. Liu Y, etal., Mol Vis. 2008;14:2367-72. Epub 2008 Dec 18.
18. Maruyama H, etal., Nature. 2010 May 13;465(7295):223-6. Epub 2010 Apr 28.
19. Melki R, etal., J Med Genet. 2003 Nov;40(11):842-4.
20. Moreland RJ, etal., Nucleic Acids Res. 2000 May 1;28(9):1986-93.
21. Mori F, etal., Acta Neuropathol. 2012 Feb 9.
22. OMIM Disease Annotation Pipeline
23. Oyama M, etal., J Dent Res. 2005 Sep;84(9):842-7.
24. Park BC, etal., Genes Cells. 2007 Aug;12(8):969-79.
25. Pruitt KD and Maglott DR, Nucleic Acids Res. 2001 Jan 1;29(1):137-40.
26. Rezaie T, etal., Science. 2002 Feb 8;295(5557):1077-9.
27. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
28. RGD automated import pipeline for gene-chemical interactions
29. RGD, Sept. 2003
30. Sahlender DA, etal., J Cell Biol. 2005 Apr 25;169(2):285-95. Epub 2005 Apr 18.
31. Senoo K, etal., Odontology. 2017 Aug 3. doi: 10.1007/s10266-017-0314-5.
32. Shen X, etal., J Biol Chem. 2011 Feb 4;286(5):3618-29. doi: 10.1074/jbc.M110.175810. Epub 2010 Nov 8.
33. Sippl C, etal., Cell Tissue Res. 2014 Nov;358(2):567-83. doi: 10.1007/s00441-014-1968-8. Epub 2014 Aug 7.
34. 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. Vittitow J and Borras T, Biochem Biophys Res Commun 2002 Oct 18;298(1):67-74.
36. Wang JT, etal., J Neurosci. 2007 Aug 8;27(32):8593-603.
37. Wise JP and Cannon J, Toxicol Sci. 2016 Oct;153(2):372-81. doi: 10.1093/toxsci/kfw133. Epub 2016 Jul 29.
38. Xu Z, etal., Zhonghua Yan Ke Za Zhi. 2014 Aug;50(8):598-605.
39. 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  


Genomics

Comparative Map Data
Optn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21773,209,572 - 73,260,251 (+)NCBI
Rnor_6.0 Ensembl1777,167,740 - 77,218,389 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01777,167,700 - 77,218,374 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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
GRCh38.p13 Ensembl1013,099,449 - 13,138,308 (+)EnsemblGRCh38hg38GRCh38
GRCh381013,100,082 - 13,138,308 (+)NCBIGRCh38GRCh38hg38GRCh38
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
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
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1913,142,036 - 13,176,996 (+)NCBI
ChlSab1.1 Ensembl913,150,426 - 13,177,021 (+)Ensembl
Optn
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248055,683,095 - 5,717,558 (+)NCBI

Position Markers
BI294994  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21773,259,873 - 73,260,029 (+)MAPPER
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 (+)MAPPER
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 (+)MAPPER
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 (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173205588277922655Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173330362778303627Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173330362785321557Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173628324577922655Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)174117605786176057Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)174117605786176057Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)174173108086731080Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174254187285446768Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174435615789356157Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175347518090690466Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)175387148890843779Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175399194790843779Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175622429686731080Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)176219582286194199Rat
7488963Bp369Blood pressure QTL 3690.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)176549735982019219Rat
1300131Bp193Blood pressure QTL 1933.3arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)176700421277922655Rat
7411577Bw141Body weight QTL 1410.001body mass (VT:0001259)body weight gain (CMO:0000420)176751265790843779Rat
631502Cm26Cardiac mass QTL 263.71heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)176933327285183543Rat
1300129Rf25Renal function QTL 253.03blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)177485263085183543Rat
12904736Cm121Cardiac mass QTL 1210.043heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)177570542786731080Rat

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
Rnor_6.0 Ensembl1777,167,740 - 77,218,389 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000074087   ⟹   ENSRNOP00000066459
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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_006254263   ⟹   XP_006254325
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01777,167,701 - 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_006254325   ⟸   XM_006254263
- Peptide Label: isoform X4
- 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

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 (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/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
BBDP/Wor (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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


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), LEC/Tj (KyushuU), Crl:SD (UDEL), LE/Stm (KyushuU), LE/OrlBarth (UDEL)
17 78882219 78882220 A T snv IS-Tlk/Kyo (KyushuU)


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)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628886 AgrOrtholog
Ensembl Genes ENSRNOG00000017941 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024162 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000045795 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000066459 UniProtKB/TrEMBL
  ENSRNOP00000068551 UniProtKB/TrEMBL
  ENSRNOP00000069034 UniProtKB/TrEMBL
  ENSRNOP00000072832 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024162 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000042881 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000074087 UniProtKB/TrEMBL
  ENSRNOT00000081940 UniProtKB/TrEMBL
  ENSRNOT00000083342 UniProtKB/TrEMBL
  ENSRNOT00000091561 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 A0A0G2JT32_RAT UniProtKB/TrEMBL
  A0A0G2JUB3_RAT UniProtKB/TrEMBL
  A0A0G2K3Z1_RAT UniProtKB/TrEMBL
  F1M9C4_RAT UniProtKB/TrEMBL
  G8JLS4_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