Cldn1 (claudin 1) - Rat Genome Database

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Gene: Cldn1 (claudin 1) Rattus norvegicus
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 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; 17beta-estradiol.
Type: protein-coding
Previously known as: claudin-1
RGD Orthologs
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.21174,421,569 - 74,436,728 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1174,421,569 - 74,436,724 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1183,230,293 - 83,245,398 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01175,865,333 - 75,880,440 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01174,926,942 - 74,942,078 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01177,815,216 - 77,830,373 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1177,815,181 - 77,830,416 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01182,888,890 - 82,904,926 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41176,473,654 - 76,488,809 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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)

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  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
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-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
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-(ethoxymethylene)-2-phenyloxazol-5-one  (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)
amitrole  (EXP)
ammonium chloride  (EXP)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (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)
CGP 52608  (ISO)
chlordecone  (ISO)
chloropicrin  (ISO)
chloroquine  (ISO)
cholic acid  (EXP)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clofibric acid  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
corn oil  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (ISO)
decanoic acid  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
Didecyldimethylammonium  (ISO)
disulfiram  (ISO)
diuron  (EXP)
dodecanoic acid  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
entinostat  (ISO)
epoxiconazole  (ISO)
ethanol  (ISO)
flutamide  (EXP)
fonofos  (ISO)
fragrance  (ISO)
genistein  (ISO)
gentamycin  (EXP)
ginsenoside Re  (ISO)
glycidol  (EXP)
glyphosate  (EXP)
hydrogen peroxide  (ISO)
hydroxychloroquine  (ISO)
hydroxysafflor yellow A  (ISO)
imidacloprid  (EXP)
indole-3-methanol  (EXP)
indometacin  (EXP)
isobutanol  (ISO)
ivermectin  (ISO)
lead diacetate  (EXP)
leflunomide  (ISO)
levamisole  (ISO)
lipopolysaccharide  (EXP,ISO)
lithium chloride  (ISO)
lithocholic acid  (ISO)
loxoprofen  (ISO)
lucanthone  (ISO)
luteolin  (ISO)
megestrol acetate  (ISO)
methapyrilene  (EXP)
methimazole  (EXP)
methotrexate  (ISO)
methylmercury chloride  (ISO)
mifepristone  (EXP)
mono(2-ethylhexyl) phthalate  (ISO)
Muraglitazar  (EXP)
myricetin  (EXP)
N-acetyl-L-cysteine  (EXP,ISO)
N-nitrosodiethylamine  (EXP)
naphthalene  (EXP)
nickel atom  (ISO)
nitrofen  (EXP)
Nonylphenol  (EXP)
ochratoxin A  (ISO)
ouabain  (ISO)
ozone  (ISO)
panobinostat  (ISO)
paracetamol  (EXP,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)
procymidone  (ISO)
progesterone  (ISO)
propiconazole  (EXP)
prothioconazole  (ISO)
Prothioconazole-desthio  (ISO)
quercetin  (EXP,ISO)
resorcinol  (ISO)
resveratrol  (EXP,ISO)
rotenone  (EXP)
rottlerin  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium propionate  (ISO)
streptozocin  (EXP)
sulfadimethoxine  (EXP)
sunitinib  (ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
terbufos  (ISO)
Tesaglitazar  (EXP)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
thioacetamide  (EXP)
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 - curated
# Reference Title Reference Citation
1. Proinflammatory cytokines tumor necrosis factor-alpha and interferon-gamma alter tight junction structure and function in the rat parotid gland Par-C10 cell line. 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. In utero exposure to tributyltin alters the expression of e-cadherin and localization of claudin-1 in intercellular junctions of the rat ventral prostate. Barthelemy J, etal., Mol Reprod Dev. 2007 Apr;74(4):455-67.
3. Genetic variation in CLDN1 and susceptibility to hepatitis C virus infection. 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. Expression of claudins-1, -4, -5, -7 and occludin in hepatocellular carcinoma and their relation with classic clinicopathological features and patients' survival. Bouchagier KA, etal., In Vivo. 2014 May-Jun;28(3):315-26.
5. Loss of the atypical inflammatory response in juvenile and aged rats. Campbell SJ, etal., Neuropathol Appl Neurobiol. 2007 Feb;33(1):108-20.
6. Resveratrol attenuates high-fat diet-induced non-alcoholic steatohepatitis by maintaining gut barrier integrity and inhibiting gut inflammation through regulation of the endocannabinoid system. Chen M, etal., Clin Nutr. 2020 Apr;39(4):1264-1275. doi: 10.1016/j.clnu.2019.05.020. Epub 2019 May 30.
7. Tight junction defects in patients with atopic dermatitis. 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. Chronic alcohol ingestion alters claudin expression in the alveolar epithelium of rats. Fernandez AL, etal., Alcohol. 2007 Aug;41(5):371-9.
9. Loss of claudin-1 in lipopolysaccharide-treated periodontal epithelium. 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. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
12. Claudin-1 is not restricted to tight junctions in the rat epididymis. Gregory M, etal., Endocrinology 2001 Feb;142(2):854-63.
13. Transient opening of the perineurial barrier for analgesic drug delivery. 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. Claudin-1 gene mutations in neonatal sclerosing cholangitis associated with ichthyosis: a tight junction disease. Hadj-Rabia S, etal., Gastroenterology. 2004 Nov;127(5):1386-90.
15. Claudin-1 and claudin-2 differentiate fetal and embryonal components in human hepatoblastoma. Halász J, etal., Hum Pathol. 2006 May;37(5):555-61. doi: 10.1016/j.humpath.2005.12.015.
16. Loss of claudin-1 expression correlates with malignancy of hepatocellular carcinoma. 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. Increased expression of claudin-1 and claudin-7 in liver cirrhosis and hepatocellular carcinoma. Holczbauer Á, etal., Pathol Oncol Res. 2014 Jul;20(3):493-502. doi: 10.1007/s12253-013-9683-4. Epub 2014 Apr 3.
18. Transforming growth factor-beta induces epithelial to mesenchymal transition by down-regulation of claudin-1 expression and the fence function in adult rat hepatocytes. Kojima T, etal., Liver Int. 2008 Apr;28(4):534-45. Epub 2007 Nov 21.
19. Altered distribution of tight junction proteins after intestinal ischaemia/reperfusion injury in rats. Li Q, etal., J Cell Mol Med. 2009 Sep;13(9B):4061-76. Epub 2009 Nov 19.
20. Alteration in intestine tight junction protein phosphorylation and apoptosis is associated with increase in IL-18 levels following alcohol intoxication and burn injury. 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. Organization of choroid plexus epithelial and endothelial cell tight junctions and regulation of claudin-1, -2 and -5 expression by protein kinase C. Lippoldt A, etal., Neuroreport. 2000 May 15;11(7):1427-31.
22. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
23. Expression profiles of genes associated with viral entry in HCV-infected human liver. Nakamuta M, etal., J Med Virol. 2011 May;83(5):921-7. doi: 10.1002/jmv.22042.
24. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
26. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
27. Distinct claudins and associated PDZ proteins form different autotypic tight junctions in myelinating Schwann cells. Poliak S, etal., J Cell Biol 2002 Oct 28;159(2):361-72.
28. Increase in the tight junction protein claudin-1 in intestinal inflammation. Poritz LS, etal., Dig Dis Sci. 2011 Oct;56(10):2802-9. doi: 10.1007/s10620-011-1688-9. Epub 2011 Jul 12.
29. GOA pipeline RGD automated data pipeline
30. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
31. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
32. Early lead exposure increases the leakage of the blood-cerebrospinal fluid barrier, in vitro. Shi LZ and Zheng W, Hum Exp Toxicol. 2007 Mar;26(3):159-67.
33. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
34. [Dexamethasone intensify the tight junctions in rat retinal vascular endothelial cells in vitro]. Tian JY, etal., Zhonghua Yan Ke Za Zhi. 2007 Jul;43(7):646-50.
35. Butyrate enhances intestinal epithelial barrier function via up-regulation of tight junction protein Claudin-1 transcription. Wang HB, etal., Dig Dis Sci. 2012 Dec;57(12):3126-35. doi: 10.1007/s10620-012-2259-4. Epub 2012 Jun 9.
36. Single-Nucleotide Polymorphisms of Tight Junction Component Claudin-1 Associated with Leukoaraiosis. 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. p38 MAP-kinase regulates function of gap and tight junctions during regeneration of rat hepatocytes. Yamamoto T, etal., J Hepatol. 2005 May;42(5):707-18.
38. Dendrobium chrysotoxum Lindl. alleviates diabetic retinopathy by preventing retinal inflammation and tight junction protein decrease. Yu Z, etal., J Diabetes Res. 2015;2015:518317. doi: 10.1155/2015/518317. Epub 2015 Jan 1.
39. Examination of claudin-1 expression in patients undergoing liver transplantation owing to hepatitis C virus cirrhosis. Zadori G, etal., Transplant Proc. 2011 May;43(4):1267-71. doi: 10.1016/j.transproceed.2011.03.066.
40. MicroRNA 29 targets nuclear factor-kappaB-repressing factor and Claudin 1 to increase intestinal permeability. 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   PMID:34018017  
PMID:34789399   PMID:35370461  


Comparative Map Data
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.21174,421,569 - 74,436,728 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1174,421,569 - 74,436,724 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1183,230,293 - 83,245,398 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01175,865,333 - 75,880,440 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01174,926,942 - 74,942,078 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01177,815,216 - 77,830,373 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1177,815,181 - 77,830,416 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01182,888,890 - 82,904,926 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41176,473,654 - 76,488,809 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11176,531,242 - 76,546,394 (+)NCBI
Celera1173,332,294 - 73,347,451 (+)NCBICelera
Cytogenetic Map11q22NCBI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh383190,305,707 - 190,322,446 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3190,305,707 - 190,322,446 (-)EnsemblGRCh38hg38GRCh38
GRCh373190,023,496 - 190,040,235 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363191,506,187 - 191,522,909 (-)NCBINCBI36Build 36hg18NCBI36
Build 343191,506,195 - 191,522,917NCBI
Celera3188,453,968 - 188,470,713 (-)NCBICelera
Cytogenetic Map3q28NCBI
HuRef3187,423,222 - 187,439,968 (-)NCBIHuRef
CHM1_13189,986,455 - 190,003,201 (-)NCBICHM1_1
T2T-CHM13v2.03193,121,997 - 193,138,734 (-)NCBIT2T-CHM13v2.0
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm391626,175,395 - 26,190,589 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1626,175,392 - 26,190,591 (-)EnsemblGRCm39 Ensembl
GRCm381626,356,645 - 26,371,839 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1626,356,642 - 26,371,841 (-)EnsemblGRCm38mm10GRCm38
MGSCv371626,356,737 - 26,371,925 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361626,272,000 - 26,287,188 (-)NCBIMGSCv36mm8
Celera1626,899,939 - 26,915,115 (-)NCBICelera
Cytogenetic Map16B2NCBI
cM Map1618.0NCBI
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
ChiLan1.0 EnsemblNW_00495542017,798,974 - 17,815,205 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542017,798,974 - 17,815,049 (+)NCBIChiLan1.0ChiLan1.0
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
NHGRI_mPanPan13188,179,246 - 188,196,102 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03187,328,629 - 187,345,360 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13195,882,239 - 195,898,990 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3195,882,239 - 195,899,248 (-)Ensemblpanpan1.1panPan2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03422,237,734 - 22,253,834 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3422,238,526 - 22,254,024 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13422,258,709 - 22,274,790 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03422,245,945 - 22,262,037 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03422,487,908 - 22,503,999 (-)NCBIUU_Cfam_GSD_1.0
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
HiC_Itri_2NW_024405602114,006,644 - 114,021,281 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493657898,273 - 113,153 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493657898,489 - 113,125 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
Sscrofa11.1 Ensembl13127,712,777 - 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
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
ChlSab1.11584,518,464 - 84,533,587 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1584,516,478 - 84,532,969 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604158,103,316 - 58,119,871 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
HetGla_female_1.0 EnsemblNW_00462473066,885,319 - 66,903,079 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473066,885,674 - 66,902,345 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Variants in Cldn1
105 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1512
Count of miRNA genes:359
Interacting mature miRNAs:510
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 (
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)
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)111897620886241447Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)115980279482566545Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)115980279482566553Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116611332182169223Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat
1354656Bvd3Brain ventricular dilatation QTL 33.640.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116944607082846715Rat

Markers in Region
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21174,435,141 - 74,435,343 (+)MAPPERmRatBN7.2
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
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21174,435,400 - 74,436,490 (+)MAPPERmRatBN7.2
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


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
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


RefSeq Acc Id: ENSRNOT00000002640   ⟹   ENSRNOP00000002640
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1174,421,569 - 74,436,724 (+)Ensembl
Rnor_6.0 Ensembl1177,815,181 - 77,830,416 (+)Ensembl
RefSeq Acc Id: NM_031699   ⟹   NP_113887
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
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  
RefSeq Acc Id: NP_113887   ⟸   NM_031699
- UniProtKB: P56745 (UniProtKB/Swiss-Prot),   Q6P6V9 (UniProtKB/Swiss-Prot),   A6JRZ0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002640   ⟸   ENSRNOT00000002640

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P56745-F1-model_v2 AlphaFold P56745 1-211 view protein structure


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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:68422 AgrOrtholog
BioCyc Gene G2FUF-20936 BioCyc
Ensembl Genes ENSRNOG00000001926 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000002640 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000002640 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Claudin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Claudin1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Claudin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PMP22/EMP/MP20/Claudin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:65129 UniProtKB/Swiss-Prot
  PTHR12002 UniProtKB/Swiss-Prot
  PTHR12002:SF92 UniProtKB/Swiss-Prot
Pfam PMP22_Claudin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cldn1 PhenoGen
  CLAUDIN1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC211132
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