Ocln (occludin) - Rat Genome Database

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Gene: Ocln (occludin) Rattus norvegicus
Analyze
Symbol: Ocln
Name: occludin
RGD ID: 620089
Description: Predicted to enable protein domain specific binding activity. Involved in cellular response to tumor necrosis factor and response to interleukin-18. Located in apical plasma membrane and lateral plasma membrane. Biomarker of diabetic retinopathy. Human ortholog(s) of this gene implicated in Crohn's disease and pseudo-TORCH syndrome 1. Orthologous to human OCLN (occludin); PARTICIPATES IN transforming growth factor-beta Smad dependent signaling pathway; hepatitis C pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 17-glucosiduronic acid; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
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
mRatBN7.2231,657,217 - 31,707,466 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl231,657,220 - 31,764,150 (-)Ensembl
Rnor_6.0230,527,327 - 30,577,218 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl230,527,715 - 30,577,218 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0249,686,707 - 49,737,380 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4231,317,090 - 31,367,485 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1231,237,461 - 31,287,854 (-)NCBI
Celera227,670,881 - 27,719,967 (-)NCBICelera
Cytogenetic Map2q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-amphetamine  (ISO)
(S)-colchicine  (ISO)
1,10-phenanthroline  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 17-glucosiduronic acid  (EXP)
17beta-estradiol 3-benzoate  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP,ISO)
2,3',4,4',5-Pentachlorobiphenyl  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-D  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,3',5-triiodo-L-thyronine  (EXP)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-tert-Octylphenol  (EXP)
5-azacytidine  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acadesine  (ISO)
acetaldehyde  (ISO)
acrylonitrile  (ISO)
actinidine  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
alpha,alpha-trehalose  (ISO)
alpha-D-galactose  (ISO)
ammonium chloride  (EXP)
arsane  (EXP,ISO)
arsenic atom  (EXP,ISO)
arsenous acid  (ISO)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butyric acid  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
carbon nanotube  (ISO)
chlorogenic acid  (EXP)
chloroquine  (ISO)
chlorpyrifos  (EXP)
choline  (ISO)
chromium(6+)  (EXP)
cisplatin  (ISO)
clopidogrel  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
corticosterone  (ISO)
cortisol  (ISO)
cyclophosphamide  (ISO)
D-glucose  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
diclofenac  (EXP,ISO)
Dictamnine  (ISO)
diiodine  (ISO)
dimethyl sulfoxide  (ISO)
dioxygen  (EXP,ISO)
dizocilpine maleate  (ISO)
dorsomorphin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
excitatory amino acid agonist  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fulvestrant  (EXP,ISO)
fumonisin B1  (ISO)
furan  (ISO)
galactose  (ISO)
gamma-linolenic acid  (ISO)
genistein  (ISO)
Ginkgolide A  (ISO)
ginsenoside Re  (ISO)
glucose  (ISO)
glycine  (ISO)
glyphosate  (ISO)
hydrogen peroxide  (ISO)
hydrogen sulfide  (ISO)
hydroquinone  (EXP)
hydroxychloroquine  (ISO)
indometacin  (EXP,ISO)
iron atom  (EXP)
iron(0)  (EXP)
isoprene  (ISO)
kaempferol  (ISO)
ketamine  (ISO)
L-ascorbic acid  (EXP)
L-methionine  (ISO)
lead diacetate  (ISO)
lead(0)  (EXP)
lead(2+)  (EXP)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (ISO)
LY294002  (EXP,ISO)
malaoxon  (EXP)
malathion  (EXP)
methotrexate  (EXP,ISO)
microcystin-LR  (EXP,ISO)
minocycline  (EXP)
mono(2-ethylhexyl) phthalate  (EXP)
Monobutylphthalate  (EXP,ISO)
myricetin  (EXP)
N(6),N(6)-dimethyladenine  (EXP)
N-acetyl-L-cysteine  (ISO)
nickel atom  (ISO)
nitric oxide  (EXP)
nitrofen  (EXP)
Nor-9-carboxy-delta9-THC  (ISO)
ochratoxin A  (ISO)
okadaic acid  (ISO)
p-tert-Amylphenol  (EXP)
papaverine  (EXP)
paraquat  (ISO)
patulin  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (ISO)
phenobarbital  (ISO)
phoxim  (EXP)
pirinixic acid  (ISO)
poly(vinylpyrrolidone)  (ISO)
potassium dichromate  (EXP)
potassium iodide  (EXP)
pregnenolone 16alpha-carbonitrile  (EXP)
probenecid  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
Pyridostigmine bromide  (ISO)
quercetin  (EXP,ISO)
quercitrin  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
rifampicin  (ISO)
rotenone  (ISO)
rottlerin  (ISO)
Salidroside  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
serpentine asbestos  (ISO)
simvastatin  (EXP)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
sodium sulfide (anhydrous)  (ISO)
Soman  (EXP)
streptozocin  (ISO)
sunitinib  (ISO)
T-2 toxin  (ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (ISO)
thalidomide  (ISO)
thioacetamide  (EXP)
tioguanine  (ISO)
titanium dioxide  (ISO)
toluene  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
Triptolide  (ISO)
troglitazone  (ISO)
uranium atom  (EXP)
valproic acid  (ISO)
vitamin E  (EXP)
zafirlukast  (ISO)
zileuton  (ISO)
zinc sulfate  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Chehade JM, etal., Neurochem Res 2002 Mar;27(3):249-52.
2. GOA data from the GO Consortium
3. Hori S, etal., J Neurochem 2004 Apr;89(2):503-13.
4. Hussar P, etal., Chem Senses 2002 Jan;27(1):7-11.
5. Lee DH and Kim DH, Xenobiotica 1999 Sep;29(9):909-16.
6. Li X, etal., Biochim Biophys Acta. 2012 Feb;1822(2):196-203. doi: 10.1016/j.bbadis.2011.09.019. Epub 2011 Oct 7.
7. NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. OMIM Disease Annotation Pipeline
9. Pipeline to import KEGG annotations from KEGG into RGD
10. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
11. Poritz LS, etal., Dig Dis Sci. 2011 Oct;56(10):2802-9. doi: 10.1007/s10620-011-1688-9. Epub 2011 Jul 12.
12. RGD automated data pipeline
13. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14. RGD automated import pipeline for gene-chemical interactions
15. Siu ER, etal., Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9298-303. doi: 10.1073/pnas.0813113106. Epub 2009 May 21.
16. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
17. Su L, etal., Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):19623-8. doi: 10.1073/pnas.1111414108. Epub 2011 Nov 21.
18. Takakuwa Y, etal., Cell Tissue Res 2002 Feb;307(2):181-9.
19. Yang Y, etal., Neurobiol Dis. 2018 Jun;114:95-110. doi: 10.1016/j.nbd.2018.02.012. Epub 2018 Feb 24.
20. Yu Z, etal., J Diabetes Res. 2015;2015:518317. doi: 10.1155/2015/518317. Epub 2015 Jan 1.
Additional References at PubMed
PMID:9647647   PMID:11025210   PMID:11090614   PMID:11782481   PMID:11810420   PMID:12060405   PMID:12498716   PMID:12507281   PMID:12734665   PMID:14685273   PMID:15052661   PMID:15489334  
PMID:15528189   PMID:15605377   PMID:15775979   PMID:16365161   PMID:16510873   PMID:16520537   PMID:16651389   PMID:17000770   PMID:17065217   PMID:17130295   PMID:17245419   PMID:17666436  
PMID:17825302   PMID:18183615   PMID:18279593   PMID:18647175   PMID:18706176   PMID:18855986   PMID:19017651   PMID:19129494   PMID:19213829   PMID:19319148   PMID:19332538   PMID:19457074  
PMID:19507189   PMID:19555995   PMID:20028514   PMID:20089884   PMID:20152177   PMID:20164257   PMID:20170644   PMID:20180397   PMID:20473716   PMID:20970449   PMID:21192956   PMID:21257729  
PMID:21318404   PMID:21334421   PMID:21336719   PMID:21415414   PMID:22378877   PMID:22559818   PMID:22946046   PMID:23018187   PMID:23171401   PMID:23288152   PMID:23297502   PMID:23345400  
PMID:23417864   PMID:23708107   PMID:24008412   PMID:24081143   PMID:24398936   PMID:24567356   PMID:24854121   PMID:24889144   PMID:25278303   PMID:25304966   PMID:25471013   PMID:25617501  
PMID:25649016   PMID:26585695   PMID:26607202   PMID:28079139   PMID:28718701   PMID:29179201   PMID:29258088   PMID:29845266   PMID:30452951   PMID:30734065   PMID:31506421   PMID:32716860  
PMID:32807750   PMID:33343804  


Genomics

Comparative Map Data
Ocln
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2231,657,217 - 31,707,466 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl231,657,220 - 31,764,150 (-)Ensembl
Rnor_6.0230,527,327 - 30,577,218 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl230,527,715 - 30,577,218 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0249,686,707 - 49,737,380 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4231,317,090 - 31,367,485 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1231,237,461 - 31,287,854 (-)NCBI
Celera227,670,881 - 27,719,967 (-)NCBICelera
Cytogenetic Map2q12NCBI
OCLN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl569,492,292 - 69,558,104 (+)EnsemblGRCh38hg38GRCh38
GRCh38569,492,547 - 69,558,104 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37568,788,374 - 68,853,931 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36568,823,875 - 68,885,889 (+)NCBINCBI36hg18NCBI36
Build 34568,823,874 - 68,885,887NCBI
Cytogenetic Map5q13.2NCBI
HuRef565,744,381 - 65,800,380 (+)NCBIHuRef
HuRef565,800,577 - 65,803,347 (+)NCBIHuRef
CHM1_1568,787,783 - 68,853,763 (+)NCBICHM1_1
Ocln
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3913100,633,012 - 100,689,226 (-)NCBIGRCm39mm39
GRCm39 Ensembl13100,633,015 - 100,689,226 (-)Ensembl
GRCm3813100,496,504 - 100,552,718 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl13100,496,507 - 100,552,718 (-)EnsemblGRCm38mm10GRCm38
MGSCv3713101,267,322 - 101,322,453 (-)NCBIGRCm37mm9NCBIm37
MGSCv3613101,597,624 - 101,652,755 (-)NCBImm8
Celera13104,112,684 - 104,167,697 (-)NCBICelera
Cytogenetic Map13D1NCBI
cM Map1353.23NCBI
Ocln
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955575163,646 - 210,379 (+)NCBIChiLan1.0ChiLan1.0
OCLN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1546,022,538 - 46,080,549 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl546,023,437 - 46,069,342 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0544,447,230 - 44,509,637 (-)NCBIMhudiblu_PPA_v0panPan3
OCLN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1254,500,299 - 54,545,430 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl254,500,299 - 54,545,430 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha251,466,637 - 51,511,781 (+)NCBI
ROS_Cfam_1.0255,004,936 - 55,058,838 (+)NCBI
UMICH_Zoey_3.1252,076,201 - 52,121,488 (+)NCBI
UNSW_CanFamBas_1.0252,843,313 - 52,888,432 (+)NCBI
UU_Cfam_GSD_1.0253,733,721 - 53,779,092 (+)NCBI
Ocln
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213191,162,311 - 191,216,242 (-)NCBI
SpeTri2.0NW_00493648099,516 - 152,834 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OCLN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1647,600,498 - 47,654,033 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11647,600,175 - 47,652,435 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21651,547,473 - 51,598,116 (+)NCBISscrofa10.2Sscrofa10.2susScr3
OCLN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1465,581,943 - 65,641,516 (+)NCBI
ChlSab1.1 Ensembl465,582,460 - 65,644,787 (+)Ensembl
Vero_WHO_p1.0NW_02366604914,326,566 - 14,386,556 (+)NCBI
Ocln
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624905333,853 - 388,990 (+)NCBI

Position Markers
D2Rat193  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2231,685,805 - 31,685,914 (+)MAPPERmRatBN7.2
Rnor_6.0230,555,907 - 30,556,013NCBIRnor6.0
Rnor_5.0249,715,234 - 49,715,340UniSTSRnor5.0
RGSC_v3.4231,346,066 - 31,346,173RGDRGSC3.4
RGSC_v3.4231,346,067 - 31,346,173UniSTSRGSC3.4
RGSC_v3.1231,266,436 - 31,266,542RGD
Celera227,699,448 - 27,699,554UniSTS
RH 3.4 Map277.5UniSTS
RH 3.4 Map277.5RGD
SHRSP x BN Map210.5399UniSTS
SHRSP x BN Map210.5399RGD
Cytogenetic Map2q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22490385374786777Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22691781781754745Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
1331764Bp205Blood pressure QTL 2053.476arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22699957143154682Rat
1643006Pain1Pain QTL 13.630.005mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)22699957148268661Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22715716072157160Rat
1300160Hrtrt3Heart rate QTL 33.62heart pumping trait (VT:2000009)absolute change in heart rate (CMO:0000534)22997159351729300Rat
10755434Coatc7Coat color QTL 70.04794coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23064806575648065Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:819
Count of miRNA genes:316
Interacting mature miRNAs:410
Transcripts:ENSRNOT00000024674
Prediction methods:Microtar, Miranda, 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 16 16 10 16 2 35 22 11
Low 34 41 25 9 25 3 3 72 19 3
Below cutoff 9 5 7 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024674   ⟹   ENSRNOP00000024674
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl231,657,220 - 31,707,120 (-)Ensembl
Rnor_6.0 Ensembl230,527,715 - 30,577,218 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077537   ⟹   ENSRNOP00000070680
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl231,742,653 - 31,759,468 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084667   ⟹   ENSRNOP00000068691
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl231,657,220 - 31,760,321 (-)Ensembl
Rnor_6.0 Ensembl230,528,242 - 30,576,591 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085488   ⟹   ENSRNOP00000073691
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl231,725,984 - 31,764,150 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106737   ⟹   ENSRNOP00000078336
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl231,742,653 - 31,764,002 (-)Ensembl
RefSeq Acc Id: NM_031329   ⟹   NP_112619
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2231,657,217 - 31,707,120 (-)NCBI
Rnor_6.0230,527,327 - 30,577,218 (-)NCBI
Rnor_5.0249,686,707 - 49,737,380 (-)NCBI
RGSC_v3.4231,317,090 - 31,367,485 (-)RGD
Celera227,670,881 - 27,719,967 (-)RGD
Sequence:
RefSeq Acc Id: XM_006231853   ⟹   XP_006231915
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2231,658,558 - 31,707,019 (-)NCBI
Rnor_6.0230,528,283 - 30,577,084 (-)NCBI
Rnor_5.0249,686,707 - 49,737,380 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006231854   ⟹   XP_006231916
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2231,658,558 - 31,706,965 (-)NCBI
Rnor_6.0230,528,283 - 30,577,061 (-)NCBI
Rnor_5.0249,686,707 - 49,737,380 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006231855   ⟹   XP_006231917
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2231,658,558 - 31,706,508 (-)NCBI
Rnor_6.0230,528,283 - 30,576,129 (-)NCBI
Rnor_5.0249,686,707 - 49,737,380 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039103242   ⟹   XP_038959170
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2231,658,558 - 31,707,466 (-)NCBI
RefSeq Acc Id: XM_039103244   ⟹   XP_038959172
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2231,658,558 - 31,706,508 (-)NCBI
RefSeq Acc Id: XM_039103245   ⟹   XP_038959173
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2231,658,558 - 31,707,019 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_112619   ⟸   NM_031329
- UniProtKB: Q6P6T5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006231915   ⟸   XM_006231853
- Peptide Label: isoform X1
- UniProtKB: Q6P6T5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006231916   ⟸   XM_006231854
- Peptide Label: isoform X1
- UniProtKB: Q6P6T5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006231917   ⟸   XM_006231855
- Peptide Label: isoform X1
- UniProtKB: Q6P6T5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068691   ⟸   ENSRNOT00000084667
RefSeq Acc Id: ENSRNOP00000024674   ⟸   ENSRNOT00000024674
RefSeq Acc Id: XP_038959170   ⟸   XM_039103242
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038959173   ⟸   XM_039103245
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038959172   ⟸   XM_039103244
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000070680   ⟸   ENSRNOT00000077537
RefSeq Acc Id: ENSRNOP00000078336   ⟸   ENSRNOT00000106737
RefSeq Acc Id: ENSRNOP00000073691   ⟸   ENSRNOT00000085488
Protein Domains
MARVEL

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/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
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)
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
LN/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
LN/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
M520/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
M520/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
M520/NRrrcMcwi (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
MHS/Gib (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
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)
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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
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)
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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)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
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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 (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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620089 AgrOrtholog
Ensembl Genes ENSRNOG00000018297 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000024674 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000068691 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000024674 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000084667 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5623744 IMAGE-MGC_LOAD
InterPro ELL/occludin UniProtKB/Swiss-Prot
  Marvel UniProtKB/Swiss-Prot
  Occludin UniProtKB/Swiss-Prot
  Occludin_ELL UniProtKB/Swiss-Prot
KEGG Report rno:83497 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72407 IMAGE-MGC_LOAD
NCBI Gene 83497 ENTREZGENE
PANTHER PTHR23288 UniProtKB/Swiss-Prot
  PTHR23288:SF4 UniProtKB/Swiss-Prot
Pfam MARVEL UniProtKB/Swiss-Prot
  Occludin_ELL UniProtKB/Swiss-Prot
PhenoGen Ocln PhenoGen
PIRSF Occludin UniProtKB/Swiss-Prot
PRINTS OCCLUDIN UniProtKB/Swiss-Prot
PROSITE MARVEL UniProtKB/Swiss-Prot
UniProt OCLN_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q9Z303 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-09-11 Ocln  occludin  Tpmt  thiopurine methyltransferase  Symbol and Name updated 1299863 APPROVED
2005-01-20 Tpmt  thiopurine methyltransferase  Ocln  occludin  Symbol and Name updated 1299863 APPROVED
2002-08-07 Ocln  occludin      Symbol and Name status set to provisional 70820 PROVISIONAL