Cldn1 (claudin 1) - Rat Genome Database

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Gene: Cldn1 (claudin 1) Rattus norvegicus
Analyze
Symbol: Cldn1
Name: claudin 1
RGD ID: 68422
Description: Predicted to enable identical protein binding activity and virus receptor activity. Involved in several processes, including cellular response to butyrate; cellular response to cytokine stimulus; and endothelial cell development. Located in several cellular components, including apical plasma membrane; bicellular tight junction; and lateral plasma membrane. Biomarker of diabetic retinopathy; liver disease (multiple); non-alcoholic steatohepatitis; and periodontitis. Human ortholog(s) of this gene implicated in Crohn's disease and atopic dermatitis. Orthologous to human CLDN1 (claudin 1); PARTICIPATES IN hepatitis C pathway; INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: claudin-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
mRatBN7.21174,421,569 - 74,436,728 (+)NCBI
Rnor_6.0 Ensembl1177,815,181 - 77,830,416 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01177,815,216 - 77,830,373 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01182,888,890 - 82,904,926 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41176,473,654 - 76,488,809 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11176,531,242 - 76,546,394 (+)NCBI
Celera1173,332,294 - 73,347,451 (+)NCBICelera
Cytogenetic Map11q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(S)-colchicine  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-D  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4,5,3',4',5'-Hexachlorobiphenyl  (EXP)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
3-chloropropane-1,2-diol  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-phenylbutyric acid  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (EXP,ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
aflatoxin B1  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-naphthoflavone  (EXP,ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromobenzene  (EXP)
butan-1-ol  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
cannabidiol  (ISO)
capsaicin  (EXP)
carbon nanotube  (ISO)
casticin  (ISO)
chloropicrin  (ISO)
chloroquine  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clofibric acid  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
decanoic acid  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
disulfiram  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
entinostat  (ISO)
ethanol  (ISO)
flutamide  (EXP)
fonofos  (ISO)
fragrance  (ISO)
genistein  (ISO)
gentamycin  (EXP)
ginsenoside Re  (ISO)
glycidol  (EXP)
hydrogen peroxide  (ISO)
hydroxychloroquine  (ISO)
imidacloprid  (EXP)
indole-3-methanol  (EXP)
indometacin  (EXP)
isobutanol  (ISO)
lead diacetate  (EXP)
leflunomide  (ISO)
levamisole  (ISO)
lipopolysaccharide  (EXP)
lithocholic acid  (ISO)
lucanthone  (ISO)
megestrol acetate  (ISO)
methapyrilene  (EXP)
methotrexate  (ISO)
methylmercury chloride  (ISO)
mifepristone  (EXP)
myricetin  (EXP)
N-acetyl-L-cysteine  (EXP,ISO)
N-nitrosodiethylamine  (EXP)
naphthalene  (EXP)
nickel atom  (ISO)
Nonylphenol  (EXP)
ochratoxin A  (ISO)
ouabain  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
parathion  (ISO)
patulin  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
phenol  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
potassium iodide  (EXP)
progesterone  (ISO)
propiconazole  (EXP)
quercetin  (EXP,ISO)
resorcinol  (ISO)
resveratrol  (EXP,ISO)
rotenone  (EXP)
rottlerin  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
streptozocin  (EXP)
sunitinib  (ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
terbufos  (ISO)
Tesaglitazar  (EXP)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
titanium dioxide  (ISO)
triadimefon  (EXP,ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (EXP)
troglitazone  (EXP,ISO)
valproic acid  (EXP,ISO)
vanadyl sulfate  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
WIN 55212-2  (ISO)
withaferin A  (ISO)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Baker OJ, etal., Am J Physiol Cell Physiol. 2008 Nov;295(5):C1191-201. doi: 10.1152/ajpcell.00144.2008. Epub 2008 Sep 3.
2. Barthelemy J, etal., Mol Reprod Dev. 2007 Apr;74(4):455-67.
3. Bekker V, etal., J Viral Hepat. 2010 Mar;17(3):192-200. doi: 10.1111/j.1365-2893.2009.01166.x. Epub 2009 Aug 7.
4. Bouchagier KA, etal., In Vivo. 2014 May-Jun;28(3):315-26.
5. Campbell SJ, etal., Neuropathol Appl Neurobiol. 2007 Feb;33(1):108-20.
6. Chen M, etal., Clin Nutr. 2020 Apr;39(4):1264-1275. doi: 10.1016/j.clnu.2019.05.020. Epub 2019 May 30.
7. De Benedetto A, etal., J Allergy Clin Immunol. 2011 Mar;127(3):773-86.e1-7. doi: 10.1016/j.jaci.2010.10.018. Epub 2010 Dec 15.
8. Fernandez AL, etal., Alcohol. 2007 Aug;41(5):371-9.
9. Fujita T, etal., J Periodontal Res. 2012 Apr;47(2):222-7. doi: 10.1111/j.1600-0765.2011.01424.x. Epub 2011 Nov 18.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. GOA data from the GO Consortium
12. Gregory M, etal., Endocrinology 2001 Feb;142(2):854-63.
13. Hackel D, etal., Proc Natl Acad Sci U S A. 2012 Jul 17;109(29):E2018-27. doi: 10.1073/pnas.1120800109. Epub 2012 Jun 25.
14. Hadj-Rabia S, etal., Gastroenterology. 2004 Nov;127(5):1386-90.
15. Halász J, etal., Hum Pathol. 2006 May;37(5):555-61. doi: 10.1016/j.humpath.2005.12.015.
16. Higashi Y, etal., J Surg Res. 2007 May 1;139(1):68-76. doi: 10.1016/j.jss.2006.08.038. Epub 2007 Jan 30.
17. Holczbauer Á, etal., Pathol Oncol Res. 2014 Jul;20(3):493-502. doi: 10.1007/s12253-013-9683-4. Epub 2014 Apr 3.
18. Kojima T, etal., Liver Int. 2008 Apr;28(4):534-45. Epub 2007 Nov 21.
19. Li Q, etal., J Cell Mol Med. 2009 Sep;13(9B):4061-76. Epub 2009 Nov 19.
20. Li X, etal., Biochim Biophys Acta. 2012 Feb;1822(2):196-203. doi: 10.1016/j.bbadis.2011.09.019. Epub 2011 Oct 7.
21. Lippoldt A, etal., Neuroreport. 2000 May 15;11(7):1427-31.
22. MGD data from the GO Consortium
23. Nakamuta M, etal., J Med Virol. 2011 May;83(5):921-7. doi: 10.1002/jmv.22042.
24. NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. OMIM Disease Annotation Pipeline
26. Pipeline to import KEGG annotations from KEGG into RGD
27. Poliak S, etal., J Cell Biol 2002 Oct 28;159(2):361-72.
28. Poritz LS, etal., Dig Dis Sci. 2011 Oct;56(10):2802-9. doi: 10.1007/s10620-011-1688-9. Epub 2011 Jul 12.
29. RGD automated data pipeline
30. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
31. RGD automated import pipeline for gene-chemical interactions
32. Shi LZ and Zheng W, Hum Exp Toxicol. 2007 Mar;26(3):159-67.
33. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
34. Tian JY, etal., Zhonghua Yan Ke Za Zhi. 2007 Jul;43(7):646-50.
35. Wang HB, etal., Dig Dis Sci. 2012 Dec;57(12):3126-35. doi: 10.1007/s10620-012-2259-4. Epub 2012 Jun 9.
36. Yadav BK and Shin BS, J Stroke Cerebrovasc Dis. 2015 Jul;24(7):1662-70. doi: 10.1016/j.jstrokecerebrovasdis.2015.03.038. Epub 2015 May 5.
37. Yamamoto T, etal., J Hepatol. 2005 May;42(5):707-18.
38. Yu Z, etal., J Diabetes Res. 2015;2015:518317. doi: 10.1155/2015/518317. Epub 2015 Jan 1.
39. Zadori G, etal., Transplant Proc. 2011 May;43(4):1267-71. doi: 10.1016/j.transproceed.2011.03.066.
40. Zhou Q, etal., Gastroenterology. 2015 Jan;148(1):158-169.e8. doi: 10.1053/j.gastro.2014.09.037. Epub 2014 Sep 30.
Additional References at PubMed
PMID:9647647   PMID:10508613   PMID:10562289   PMID:11090614   PMID:11889141   PMID:12477932   PMID:12673830   PMID:12734665   PMID:15052661   PMID:15489334   PMID:15775979   PMID:16520537  
PMID:17251524   PMID:18036336   PMID:18197414   PMID:18208478   PMID:18367650   PMID:20089884   PMID:20164257   PMID:20375010   PMID:21388515   PMID:21626096   PMID:21983942   PMID:22275141  
PMID:22946046   PMID:23407391   PMID:23685254   PMID:23704991   PMID:25666991   PMID:25849148   PMID:26607202   PMID:27038183   PMID:27164415   PMID:28412298   PMID:30734065  


Genomics

Comparative Map Data
Cldn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21174,421,569 - 74,436,728 (+)NCBI
Rnor_6.0 Ensembl1177,815,181 - 77,830,416 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01177,815,216 - 77,830,373 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01182,888,890 - 82,904,926 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41176,473,654 - 76,488,809 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11176,531,242 - 76,546,394 (+)NCBI
Celera1173,332,294 - 73,347,451 (+)NCBICelera
Cytogenetic Map11q22NCBI
CLDN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3190,305,707 - 190,322,446 (-)EnsemblGRCh38hg38GRCh38
GRCh383190,305,707 - 190,322,446 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh373190,023,496 - 190,040,235 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363191,506,187 - 191,522,909 (-)NCBINCBI36hg18NCBI36
Build 343191,506,195 - 191,522,917NCBI
Celera3188,453,968 - 188,470,713 (-)NCBI
Cytogenetic Map3q28NCBI
HuRef3187,423,222 - 187,439,968 (-)NCBIHuRef
CHM1_13189,986,455 - 190,003,201 (-)NCBICHM1_1
Cldn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391626,175,395 - 26,190,589 (-)NCBIGRCm39mm39
GRCm39 Ensembl1626,175,392 - 26,190,591 (-)Ensembl
GRCm381626,356,645 - 26,371,839 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1626,356,642 - 26,371,841 (-)EnsemblGRCm38mm10GRCm38
MGSCv371626,356,737 - 26,371,925 (-)NCBIGRCm37mm9NCBIm37
MGSCv361626,272,000 - 26,287,188 (-)NCBImm8
Celera1626,899,939 - 26,915,115 (-)NCBICelera
Cytogenetic Map16B2NCBI
Cldn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542017,798,974 - 17,815,205 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542017,798,974 - 17,815,049 (+)NCBIChiLan1.0ChiLan1.0
CLDN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13195,882,239 - 195,898,990 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3195,882,239 - 195,899,248 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03187,328,629 - 187,345,360 (-)NCBIMhudiblu_PPA_v0panPan3
CLDN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13422,303,058 - 22,319,101 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3422,303,850 - 22,319,033 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3426,396,629 - 26,412,654 (-)NCBI
ROS_Cfam_1.03422,237,734 - 22,253,834 (-)NCBI
UMICH_Zoey_3.13422,258,709 - 22,274,790 (-)NCBI
UNSW_CanFamBas_1.03422,245,945 - 22,262,037 (-)NCBI
UU_Cfam_GSD_1.03422,487,908 - 22,503,999 (-)NCBI
Cldn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602114,006,644 - 114,021,281 (+)NCBI
SpeTri2.0NW_00493657898,489 - 113,125 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLDN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13127,712,767 - 127,730,657 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113127,714,857 - 127,730,628 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213136,971,674 - 136,987,446 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLDN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11584,518,464 - 84,533,587 (-)NCBI
ChlSab1.1 Ensembl1584,516,478 - 84,532,969 (-)Ensembl
Vero_WHO_p1.0NW_02366604158,103,316 - 58,119,871 (-)NCBI
Cldn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473066,885,674 - 66,902,345 (+)NCBI

Position Markers
AI535225  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21174,435,141 - 74,435,343 (+)MAPPER
Rnor_6.01177,828,787 - 77,828,988NCBIRnor6.0
Rnor_5.01182,890,275 - 82,890,476UniSTSRnor5.0
RGSC_v3.41176,487,223 - 76,487,424UniSTSRGSC3.4
Celera1173,345,865 - 73,346,066UniSTS
RH 3.4 Map11605.1UniSTS
Cytogenetic Map11q22UniSTS
Cldn1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21174,435,400 - 74,436,490 (+)MAPPER
Rnor_6.01177,829,046 - 77,830,135NCBIRnor6.0
Rnor_5.01182,889,128 - 82,890,217UniSTSRnor5.0
Celera1173,346,124 - 73,347,213UniSTS
Cytogenetic Map11q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111947517979734728Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112831466586994795Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)113043533986714631Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113215552082443118Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113590063480900634Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114309033886714631Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114658320986714631Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
4889859Pur28Proteinuria QTL 2819.50.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114790104978471527Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115785881090463843Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115994302390463843Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)116010984287141948Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)116265336586714475Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116265336586714483Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116449467190463843Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116934231986312439Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116964970890463843Rat
1354656Bvd3Brain ventricular dilatation QTL 33.640.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)117272002986994795Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1512
Count of miRNA genes:359
Interacting mature miRNAs:510
Transcripts:ENSRNOT00000002640
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 44 35 7 35 1 1 5 27 19 1
Low 3 36 13 6 12 6 7 10 69 8 20 11 7
Below cutoff 6 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002640   ⟹   ENSRNOP00000002640
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1177,815,181 - 77,830,416 (+)Ensembl
RefSeq Acc Id: NM_031699   ⟹   NP_113887
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21174,421,569 - 74,436,728 (+)NCBI
Rnor_6.01177,815,216 - 77,830,373 (+)NCBI
Rnor_5.01182,888,890 - 82,904,926 (-)NCBI
RGSC_v3.41176,473,654 - 76,488,809 (+)RGD
Celera1173,332,294 - 73,347,451 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_113887 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF04850 (Get FASTA)   NCBI Sequence Viewer  
  AAH61992 (Get FASTA)   NCBI Sequence Viewer  
  EDL78117 (Get FASTA)   NCBI Sequence Viewer  
  P56745 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_113887   ⟸   NM_031699
- Sequence:
RefSeq Acc Id: ENSRNOP00000002640   ⟸   ENSRNOT00000002640

Transcriptome

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

Promoters
RGD ID:13698238
Promoter ID:EPDNEW_R8762
Type:initiation region
Name:Cldn1_1
Description:claudin 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01177,815,197 - 77,815,257EPDNEW

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:68422 AgrOrtholog
Ensembl Genes ENSRNOG00000001926 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000002640 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000002640 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5599462 IMAGE-MGC_LOAD
InterPro Claudin UniProtKB/Swiss-Prot
  Claudin1 UniProtKB/Swiss-Prot
  Claudin_CS UniProtKB/Swiss-Prot
  PMP22/EMP/MP20/Claudin UniProtKB/Swiss-Prot
KEGG Report rno:65129 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72393 IMAGE-MGC_LOAD
NCBI Gene 65129 ENTREZGENE
PANTHER PTHR12002 UniProtKB/Swiss-Prot
  PTHR12002:SF92 UniProtKB/Swiss-Prot
Pfam PMP22_Claudin UniProtKB/Swiss-Prot
PhenoGen Cldn1 PhenoGen
PRINTS CLAUDIN1 UniProtKB/Swiss-Prot
PROSITE CLAUDIN UniProtKB/Swiss-Prot
TIGR TC211132
UniProt CLD1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q6P6V9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Cldn1  claudin 1      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization transmembrane protein that is localized to tight junctions 634852
gene_cellular_localization associates with Pals-associated tight junction protein in paranodal loop of autotypic tight junctions of myelinating Schwann cells 634852