Tjp1 (tight junction protein 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Tjp1 (tight junction protein 1) Rattus norvegicus
Analyze
Symbol: Tjp1
Name: tight junction protein 1
RGD ID: 1306305
Description: Exhibits protein C-terminus binding activity. Involved in several processes, including cellular response to glucose stimulus; negative regulation of vascular permeability; and response to lipopolysaccharide. Localizes to bicellular tight junction; cytoplasm; and gap junction. Biomarker of several diseases, including brain ischemia; cholestasis; peptic esophagitis; perinatal necrotizing enterocolitis; and uveitis. Orthologous to human TJP1 (tight junction protein 1); PARTICIPATES IN E-cadherin signaling pathway; INTERACTS WITH (+)-pilocarpine; (R)-carnitine; (S)-nicotine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: tight junction protein ZO-1; ZO-1; zona occludens 1; zona occludens protein 1; zonula occludens protein 1
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
mRatBN7.21118,849,838 - 119,094,492 (-)NCBI
Rnor_6.0 Ensembl1126,146,489 - 126,227,469 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01126,146,489 - 126,515,359 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01127,243,076 - 127,607,938 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41119,684,774 - 119,750,532 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11119,763,121 - 119,845,891 (-)NCBI
Celera1111,069,963 - 111,134,894 (-)NCBICelera
Cytogenetic Map1q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(R)-carnitine  (EXP)
(S)-nicotine  (EXP,ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-(5-isoquinolinesulfonyl)-2-methylpiperazine  (EXP)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP)
17beta-estradiol 17-glucosiduronic acid  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-D  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-hydroxypropanoic acid  (ISO)
2-methoxy-17beta-estradiol  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP,ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-hydroxynon-2-enal  (ISO)
5-(1,4-diazepane-1-sulfonyl)isoquinoline  (EXP,ISO)
5-(2-methylpiperazine-1-sulfonyl)isoquinoline  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetaldehyde  (ISO)
acrylamide  (EXP)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
alpha,alpha-trehalose  (ISO)
alpha-D-galactose  (ISO)
anthocyanin  (EXP)
antirheumatic drug  (ISO)
apocynin  (ISO)
Aroclor 1254  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
bucladesine  (EXP)
cadmium atom  (EXP)
cadmium dichloride  (EXP,ISO)
calciol  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
cannabidiol  (ISO)
carbamazepine  (ISO)
carrageenan  (ISO)
chelerythrine  (ISO)
chlorogenic acid  (EXP)
chlorpyrifos  (EXP)
cisplatin  (ISO)
clopidogrel  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
cortisol  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cycloheximide  (ISO)
cyclophosphamide  (EXP,ISO)
cyclosporin A  (EXP,ISO)
D-glucose  (ISO)
decabromodiphenyl ether  (ISO)
Deoxycorticosterone acetate  (ISO)
deoxynivalenol  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
diclofenac  (ISO)
dicrotophos  (ISO)
dieldrin  (EXP)
diiodine  (ISO)
dimethyl sulfoxide  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
ethanol  (ISO)
fasudil hydrochloride  (EXP,ISO)
flavonoids  (ISO)
folic acid  (ISO)
folpet  (ISO)
furan  (ISO)
galactose  (ISO)
gamma-hexachlorocyclohexane  (EXP,ISO)
gamma-linolenic acid  (ISO)
genistein  (EXP)
Ginkgolide A  (ISO)
ginsenoside Re  (ISO)
glucose  (ISO)
glycyrrhizinic acid  (ISO)
Goe 6976  (EXP)
hexadecanoic acid  (ISO)
homocysteine  (ISO)
hydrogen peroxide  (ISO)
hydrogen sulfide  (ISO)
hydroquinone  (EXP)
imidacloprid  (EXP)
indometacin  (EXP,ISO)
kaempferol  (ISO)
L-ascorbic acid  (EXP)
lead diacetate  (ISO)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
levamisole  (ISO)
lipopolysaccharide  (EXP,ISO)
lithium atom  (EXP)
lithium hydride  (EXP)
lithocholic acid  (ISO)
losartan  (EXP)
LY294002  (ISO)
malaoxon  (EXP)
malathion  (EXP)
menadione  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
microcystin-LR  (EXP,ISO)
mifepristone  (ISO)
ML-7  (ISO)
mono(2-ethylhexyl) phthalate  (EXP)
Monobutylphthalate  (EXP,ISO)
myricetin  (EXP)
N(6),N(6)-dimethyladenine  (EXP)
N-acetyl-L-cysteine  (EXP,ISO)
nicotine  (EXP,ISO)
nitric oxide  (EXP,ISO)
Nonylphenol  (EXP)
ochratoxin A  (ISO)
okadaic acid  (ISO)
oroxylin A  (EXP)
oxaliplatin  (EXP)
paracetamol  (ISO)
paraquat  (EXP,ISO)
patulin  (ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (EXP)
phenobarbital  (EXP)
phenol  (ISO)
phosgene  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
potassium iodide  (EXP)
probenecid  (ISO)
quercetin  (EXP,ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
rifampicin  (ISO)
ritonavir  (EXP)
rotenone  (ISO)
rottlerin  (ISO)
Salidroside  (ISO)
salubrinal  (ISO)
saquinavir  (EXP)
SB 203580  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
serpentine asbestos  (ISO)
sodium chloride  (ISO)
sodium fluoride  (ISO)
sodium sulfide (anhydrous)  (ISO)
sorafenib  (ISO)
staurosporine  (EXP)
streptozocin  (ISO)
tamoxifen  (ISO)
telmisartan  (ISO)
tert-butyl hydroperoxide  (EXP)
tetrachloromethane  (ISO)
thalidomide  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
tributylstannane  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
Triptolide  (ISO)
troglitazone  (ISO)
valproic acid  (EXP,ISO)
vitamin E  (EXP)
vorinostat  (ISO)
wortmannin  (ISO)
zafirlukast  (ISO)
zardaverine  (EXP)
zileuton  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Chen W, etal., J Neurochem. 2009 Nov;111(3):726-36. Epub 2009 Aug 27.
2. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. GOA data from the GO Consortium
4. Jin H, etal., FASEB J. 2010 Feb;24(2):451-63. Epub 2009 Oct 13.
5. Khailova L, etal., Pediatr Res. 2009 Aug;66(2):140-4.
6. Khan M, etal., J Neuroinflammation. 2009 Nov 4;6:32.
7. Laing JG, etal., Cell Commun Adhes 2001;8(4-6):209-12.
8. Li FY and Li Y, World J Gastroenterol. 2009 Aug 7;15(29):3621-30.
9. Li Q, etal., J Cell Mol Med. 2009 Sep;13(9B):4061-76. Epub 2009 Nov 19.
10. Maly IP and Landmann L, Histochem Cell Biol. 2008 Mar;129(3):289-99. Epub 2008 Jan 15.
11. MGD data from the GO Consortium
12. Nemeth Z, etal., Pathol Oncol Res. 2009 Sep;15(3):533-9. Epub .
13. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
14. Qiao X, etal., Cell Cycle. 2014;13(19):3059-75. doi: 10.4161/15384101.2014.949091.
15. Qiu LB, etal., Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi. 2009 Sep;27(9):539-43.
16. Qu YZ, etal., Eur J Pharmacol. 2009 Mar 15;606(1-3):137-41. Epub 2009 Jan 25.
17. RGD automated data pipeline
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. Rincon-Choles H, etal., Diabetes. 2006 Apr;55(4):894-900.
21. Ronaldson PT, etal., J Cereb Blood Flow Metab. 2009 Jun;29(6):1084-98. Epub 2009 Mar 25.
22. Simard JM, etal., J Cereb Blood Flow Metab. 2009 Feb;29(2):317-30. Epub 2008 Oct 15.
23. Singh D, etal., J Biol Chem. 2005 Aug 26;280(34):30416-21. Epub 2005 Jun 26.
24. 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.
25. 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.
26. Suzuki T, etal., J Pharmacol Sci. 2008 Mar;106(3):469-77.
27. Thévenin AF, etal., Mol Biol Cell. 2017 Dec 1;28(25):3595-3608. doi: 10.1091/mbc.E16-07-0496. Epub 2017 Oct 11.
28. Trinh L, etal., Mol Vis. 2008 Jun 16;14:1149-56.
29. Uehara K and Uehara A, Histochem Cell Biol. 2008 Jan;129(1):95-103. Epub 2007 Sep 25.
30. Wu Z, etal., Neurobiol Dis. 2008 Dec;32(3):543-51. Epub 2008 Sep 21.
31. Xia W, etal., J Biol Chem. 2006 Jun 16;281(24):16799-813. Epub 2006 Apr 13.
32. Zhang YL, etal., Shock. 2007 Aug;28(2):245-52.
Additional References at PubMed
PMID:8636221   PMID:9531559   PMID:9582296   PMID:10395790   PMID:10873669   PMID:11025210   PMID:11090614   PMID:11689568   PMID:11706048   PMID:11731229   PMID:11734628   PMID:12060405  
PMID:12064589   PMID:12068294   PMID:12203721   PMID:12507281   PMID:12633933   PMID:12673830   PMID:12717711   PMID:12832289   PMID:14622136   PMID:14685273   PMID:14699011   PMID:14757759  
PMID:15052661   PMID:15084279   PMID:15173637   PMID:15492000   PMID:15702233   PMID:15728677   PMID:15775979   PMID:15788452   PMID:15950600   PMID:16105026   PMID:16199027   PMID:16275913  
PMID:16364283   PMID:16427635   PMID:16510873   PMID:16520537   PMID:16931598   PMID:17000770   PMID:17122142   PMID:17130295   PMID:17138661   PMID:17397395   PMID:17541973   PMID:17666436  
PMID:18183615   PMID:18308723   PMID:18423437   PMID:18603586   PMID:18706176   PMID:18823282   PMID:18855986   PMID:18922801   PMID:19017651   PMID:19129494   PMID:19213829   PMID:19507189  
PMID:19590046   PMID:20080746   PMID:20089884   PMID:20473291   PMID:20551175   PMID:20599605   PMID:20868367   PMID:20970449   PMID:21131473   PMID:21285373   PMID:21318404   PMID:21334421  
PMID:21336719   PMID:21411630   PMID:21454477   PMID:21725876   PMID:21884682   PMID:21947081   PMID:22006950   PMID:22512338   PMID:22559818   PMID:22611033   PMID:22855531   PMID:22946046  
PMID:23434913   PMID:23610556   PMID:23801859   PMID:23824537   PMID:23863479   PMID:23885123   PMID:23963446   PMID:23979167   PMID:24008412   PMID:24098443   PMID:24191021   PMID:24339795  
PMID:24580804   PMID:24854121   PMID:24889144   PMID:25468996   PMID:25512490   PMID:25753039   PMID:26464396   PMID:26609154   PMID:26977812   PMID:27037668   PMID:27452368   PMID:28169360  
PMID:29258088   PMID:29524637   PMID:29749551   PMID:29803674   PMID:30734065   PMID:31506421   PMID:31540688   PMID:31795317   PMID:31975378  


Genomics

Comparative Map Data
Tjp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21118,849,838 - 119,094,492 (-)NCBI
Rnor_6.0 Ensembl1126,146,489 - 126,227,469 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01126,146,489 - 126,515,359 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01127,243,076 - 127,607,938 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41119,684,774 - 119,750,532 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11119,763,121 - 119,845,891 (-)NCBI
Celera1111,069,963 - 111,134,894 (-)NCBICelera
Cytogenetic Map1q22NCBI
TJP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1529,699,367 - 29,968,915 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1529,699,367 - 29,968,865 (-)EnsemblGRCh38hg38GRCh38
GRCh381529,699,367 - 29,969,049 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371529,991,571 - 30,261,252 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361527,779,648 - 27,901,998 (-)NCBINCBI36hg18NCBI36
Build 341527,779,650 - 27,901,998NCBI
Celera157,633,694 - 7,756,038 (-)NCBI
Cytogenetic Map15q13.1NCBI
HuRef157,657,688 - 7,779,970 (-)NCBIHuRef
CHM1_11529,958,165 - 30,228,633 (-)NCBICHM1_1
Tjp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39764,945,913 - 65,177,629 (-)NCBIGRCm39mm39
GRCm39 Ensembl764,945,913 - 65,177,529 (-)Ensembl
GRCm38765,296,165 - 65,527,850 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl765,296,165 - 65,527,781 (-)EnsemblGRCm38mm10GRCm38
MGSCv37772,441,051 - 72,516,130 (-)NCBIGRCm37mm9NCBIm37
MGSCv36765,175,118 - 65,250,189 (-)NCBImm8
Celera762,713,602 - 62,789,529 (-)NCBICelera
Cytogenetic Map7CNCBI
cM Map735.02NCBI
Tjp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541628,654,905 - 28,870,555 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541628,640,807 - 28,869,717 (+)NCBIChiLan1.0ChiLan1.0
TJP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11526,479,294 - 26,598,886 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1526,344,878 - 26,598,878 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v015981,198 - 1,249,292 (-)NCBIMhudiblu_PPA_v0panPan3
TJP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1338,997,122 - 39,076,617 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl338,997,076 - 39,241,574 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha341,683,799 - 41,794,039 (-)NCBI
ROS_Cfam_1.0339,375,018 - 39,624,615 (-)NCBI
UMICH_Zoey_3.1338,917,559 - 39,028,158 (-)NCBI
UNSW_CanFamBas_1.0339,155,559 - 39,266,003 (-)NCBI
UU_Cfam_GSD_1.0339,363,904 - 39,474,165 (-)NCBI
Tjp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640144,288,679 - 144,519,613 (+)NCBI
SpeTri2.0NW_0049364831,814,870 - 2,045,802 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TJP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1144,930,368 - 145,195,836 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11144,930,387 - 145,195,857 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21161,175,436 - 161,284,250 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TJP1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12652,623,751 - 52,750,037 (-)NCBI
ChlSab1.1 Ensembl2652,622,743 - 52,749,950 (-)Ensembl
Tjp1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247682,826,848 - 3,034,195 (-)NCBI

Position Markers
TJP1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21118,849,893 - 118,850,058 (+)MAPPER
Rnor_6.01126,146,545 - 126,146,709NCBIRnor6.0
Rnor_5.01127,243,132 - 127,243,296UniSTSRnor5.0
RGSC_v3.41119,684,830 - 119,684,994UniSTSRGSC3.4
Celera1111,070,019 - 111,070,183UniSTS
Cytogenetic Map1q22UniSTS
TJP1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21118,849,996 - 118,850,097 (+)MAPPER
Rnor_6.01126,146,648 - 126,146,748NCBIRnor6.0
Rnor_5.01127,243,235 - 127,243,335UniSTSRnor5.0
RGSC_v3.41119,684,933 - 119,685,033UniSTSRGSC3.4
Celera1111,070,122 - 111,070,222UniSTS
Cytogenetic Map1q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143579208126240667Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143579208126240667Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143579208126240667Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143579208126240667Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143579208126240667Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)183502376128502376Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)183656882126240667Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)185779320130779320Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)185917265130917265Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)186776571131776571Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)190804143161321256Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)number of 20 x 20 cm floor squares crossed into, out of or within a discrete space in an experimental apparatus (CMO:0001514)191093646136093646Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)194201400184846632Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)194201400197187904Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)194225372130917265Rat
1300153Bp171Blood pressure QTL 1713.37arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)194364073153076991Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)195304961156446783Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)199983293127203999Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)199983293188289386Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)199983293198656062Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)199983293216213510Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)199983293216325819Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100131562236763528Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100354344145354344Rat
8655649Arrd1Age-related retinal degeneration QTL 14.89retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1106002252202571904Rat
61370Mcs3Mammary carcinoma susceptibility QTL 32.15mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1108057233167517487Rat
1641897Alcrsp1Alcohol response QTL 1response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1108417193153417193Rat
2317833Alcrsp19Alcohol response QTL 1912.40.001response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1108417193153417193Rat
1354623Rf46Renal function QTL 463.8blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)1108986301161784422Rat
1354591Cm36Cardiac mass QTL 364.1heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1108986301219232156Rat
1354615Cm32Cardiac mass QTL 325.2heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1108986301219232156Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1108986301238830534Rat
2303591Gluco41Glucose level QTL 412blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1109634374154634374Rat
9590300Scort16Serum corticosterone level QTL 164.390.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1110620749155620749Rat
8694370Bw154Body weight QTL 1548.910.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)1110620749155620749Rat
61399Tcat1Tongue tumor resistance QTL 13.3tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 5 mm (CMO:0001879)1111446783156446783Rat
61346Rf2Renal disease susceptibility QTL 23.7urine protein amount (VT:0005160)urine protein level (CMO:0000591)1111446783156446783Rat
631569Bp93Blood pressure QTL 930.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1113593576129209407Rat
631496Bp97Blood pressure QTL 973.08arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1113593576158593576Rat
1300158Bp173Blood pressure QTL 1733.48arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1122614824201146953Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1122614824262664716Rat
2313060Bss71Bone structure and strength QTL 712.60.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)1124090312169090312Rat
631199Cm23Cardiac mass QTL 234.60.0004heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1124603592188289386Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1125875758262433692Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1126240667217054291Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:139
Count of miRNA genes:119
Interacting mature miRNAs:128
Transcripts:ENSRNOT00000014988
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 48 38 13 38 8 8 74 35 41 11 8
Low 9 3 6 3 3
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001106266 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229330 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229331 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229332 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229333 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588930 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588931 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588932 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588934 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588935 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105261 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105265 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105279 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105288 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105296 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105302 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105325 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105332 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105338 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105341 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105346 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005501920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473980 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000039 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000014988   ⟹   ENSRNOP00000014988
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1126,146,489 - 126,211,439 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087332   ⟹   ENSRNOP00000072324
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1126,147,386 - 126,227,469 (-)Ensembl
RefSeq Acc Id: NM_001106266   ⟹   NP_001099736
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,849,838 - 118,914,869 (-)NCBI
Rnor_6.01126,146,489 - 126,211,439 (-)NCBI
Rnor_5.01127,243,076 - 127,607,938 (-)NCBI
RGSC_v3.41119,684,774 - 119,750,532 (-)RGD
Celera1111,069,963 - 111,134,894 (-)RGD
Sequence:
RefSeq Acc Id: XM_006229330   ⟹   XP_006229392
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01126,146,491 - 126,249,535 (-)NCBI
Rnor_5.01127,243,076 - 127,607,938 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229331   ⟹   XP_006229393
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01126,146,491 - 126,227,220 (-)NCBI
Rnor_5.01127,243,076 - 127,607,938 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229332   ⟹   XP_006229394
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01126,146,491 - 126,227,764 (-)NCBI
Rnor_5.01127,243,076 - 127,607,938 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229333   ⟹   XP_006229395
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01126,146,491 - 126,226,450 (-)NCBI
Rnor_5.01127,243,076 - 127,607,938 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588930   ⟹   XP_017444419
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01126,146,491 - 126,515,359 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588931   ⟹   XP_017444420
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01126,146,491 - 126,515,359 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588932   ⟹   XP_017444421
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01126,146,491 - 126,515,359 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588933   ⟹   XP_017444422
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01126,146,491 - 126,515,359 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588934   ⟹   XP_017444423
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01126,146,491 - 126,515,359 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588935   ⟹   XP_017444424
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,849,840 - 119,094,477 (-)NCBI
Rnor_6.01126,146,491 - 126,403,469 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017588936   ⟹   XP_017444425
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01126,146,491 - 126,402,812 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039105261   ⟹   XP_038961189
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,849,840 - 119,094,492 (-)NCBI
RefSeq Acc Id: XM_039105265   ⟹   XP_038961193
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,849,840 - 119,094,492 (-)NCBI
RefSeq Acc Id: XM_039105279   ⟹   XP_038961207
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,849,840 - 119,094,492 (-)NCBI
RefSeq Acc Id: XM_039105288   ⟹   XP_038961216
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,849,840 - 119,094,492 (-)NCBI
RefSeq Acc Id: XM_039105296   ⟹   XP_038961224
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,849,844 - 119,094,477 (-)NCBI
RefSeq Acc Id: XM_039105302   ⟹   XP_038961230
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,849,840 - 119,090,974 (-)NCBI
RefSeq Acc Id: XM_039105314   ⟹   XP_038961242
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,849,840 - 119,094,492 (-)NCBI
RefSeq Acc Id: XM_039105325   ⟹   XP_038961253
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,849,840 - 118,931,943 (-)NCBI
RefSeq Acc Id: XM_039105332   ⟹   XP_038961260
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,849,840 - 118,953,602 (-)NCBI
RefSeq Acc Id: XM_039105338   ⟹   XP_038961266
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,849,840 - 119,094,492 (-)NCBI
RefSeq Acc Id: XM_039105341   ⟹   XP_038961269
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,849,840 - 118,931,943 (-)NCBI
RefSeq Acc Id: XM_039105346   ⟹   XP_038961274
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,849,840 - 119,094,492 (-)NCBI
RefSeq Acc Id: XR_005501920
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,849,840 - 119,094,492 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001099736   ⟸   NM_001106266
- UniProtKB: F1M4A0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229392   ⟸   XM_006229330
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_006229394   ⟸   XM_006229332
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_006229393   ⟸   XM_006229331
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_006229395   ⟸   XM_006229333
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017444423   ⟸   XM_017588934
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017444422   ⟸   XM_017588933
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017444421   ⟸   XM_017588932
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017444420   ⟸   XM_017588931
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017444419   ⟸   XM_017588930
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017444424   ⟸   XM_017588935
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017444425   ⟸   XM_017588936
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: ENSRNOP00000014988   ⟸   ENSRNOT00000014988
RefSeq Acc Id: ENSRNOP00000072324   ⟸   ENSRNOT00000087332
RefSeq Acc Id: XP_038961274   ⟸   XM_039105346
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038961266   ⟸   XM_039105338
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038961242   ⟸   XM_039105314
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038961216   ⟸   XM_039105288
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038961207   ⟸   XM_039105279
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038961193   ⟸   XM_039105265
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038961189   ⟸   XM_039105261
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038961230   ⟸   XM_039105302
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038961260   ⟸   XM_039105332
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038961253   ⟸   XM_039105325
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038961269   ⟸   XM_039105341
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038961224   ⟸   XM_039105296
- Peptide Label: isoform X6
Protein Domains
Guanylate kinase-like   PDZ   SH3   ZU5

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 (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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)
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
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
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/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
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 (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
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
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
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
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
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)
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
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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: 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)
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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/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
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 127259223 127259224 T A snv GH/OmrMcwi (MCW), F344/Jcl (KyushuU), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), MHS/Gib (KNAW), WAG/Rij (KNAW), BBDP/WorN (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), F344/NRrrc (Illumina) (KNAW), BUF/N (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), M520/N (KNAW), MNS/Gib (KNAW), F344/DuCrlCrlj (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), F344/Stm (KyushuU), SBH/Ygl (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 126153352 126153353 C T snv CDR
1 126162636 126162637 T A snv WAG/Rij (RGD), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), CDR, CDS, Buf/N (MCW), F344/NRrrc (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (RGD), SBH/Ygl (RGD), MNS/Gib (RGD), MHS/Gib (RGD), LEW/NCrlBR (RGD), LEW/Crl (RGD), M520/N (MCW), FHL/EurMcwi (RGD), BBDP/Wor (RGD), FHH/EurMcwi (RGD)
1 126515228 126515229 C T snv F344/NCrl (RGD), BBDP/Wor (RGD), SBN/Ygl (RGD), MNS/Gib (RGD), M520/N (MCW), SBH/Ygl (RGD), F344/NRrrc (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 119700939 119700940 T A snv FHH/EurMcwi (MDC), F344/NHsd (ICAHN), F344/NRrrc (KNAW), M520/N (KNAW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), BUF/N (KNAW), GH/OmrMcwi (MCW), BBDP/WorN (ICL), F344/NCrl (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), MHS/Gib (ICL), MNS/Gib (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), WAG/Rij (ICL), HCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich)
1 119702616 119702617 A C snv SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306305 AgrOrtholog
Ensembl Genes ENSRNOG00000011077 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000014988 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072324 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000014988 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000087332 UniProtKB/Swiss-Prot
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro GK/Ca_channel_bsu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Guanylate_kin-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IPR005417 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZO-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZO-1_SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZU5_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:292994 UniProtKB/TrEMBL
NCBI Gene 292994 ENTREZGENE
PANTHER PTHR13865:SF25 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Guanylate_kin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZU5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tjp1 PhenoGen
PRINTS ZONOCCLUDNS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZONOCCLUDNS1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE GUANYLATE_KINASE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZU5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART GuKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZU5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50044 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50156 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K2P5 ENTREZGENE
  F1M4A0 ENTREZGENE, UniProtKB/TrEMBL
  ZO1_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Tjp1  tight junction protein 1   Tjp1_predicted  tight junction protein 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Tjp1_predicted  tight junction protein 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED