Cldn6 (claudin 6) - Rat Genome Database

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Gene: Cldn6 (claudin 6) Rattus norvegicus
Analyze
Symbol: Cldn6
Name: claudin 6
RGD ID: 1308837
Description: Predicted to enable virus receptor activity. Predicted to be involved in bicellular tight junction assembly and cell adhesion. Predicted to act upstream of or within tight junction organization. Predicted to be located in apicolateral plasma membrane. Predicted to be active in bicellular tight junction and plasma membrane. Orthologous to human CLDN6 (claudin 6); PARTICIPATES IN hepatitis C pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: claudin-6; LOC287098
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81013,213,837 - 13,218,578 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1013,213,956 - 13,218,581 (+)EnsemblGRCr8
mRatBN7.21012,710,302 - 12,713,987 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1012,709,960 - 12,715,973 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1017,454,607 - 17,457,368 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01016,943,400 - 16,946,161 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01012,443,841 - 12,446,604 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01012,999,256 - 13,002,860 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1013,000,090 - 13,002,862 (+)Ensemblrn6Rnor6.0
Rnor_5.01012,822,308 - 12,825,905 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41012,944,503 - 12,947,271 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1012,406,544 - 12,409,312 (+)NCBICelera
RGSC_v3.11012,945,821 - 12,946,518 (+)NCBI
Cytogenetic Map10q12NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9892664   PMID:12060405   PMID:12477932   PMID:17130295   PMID:18036336   PMID:20375010  


Genomics

Comparative Map Data
Cldn6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81013,213,837 - 13,218,578 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1013,213,956 - 13,218,581 (+)EnsemblGRCr8
mRatBN7.21012,710,302 - 12,713,987 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1012,709,960 - 12,715,973 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1017,454,607 - 17,457,368 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01016,943,400 - 16,946,161 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01012,443,841 - 12,446,604 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01012,999,256 - 13,002,860 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1013,000,090 - 13,002,862 (+)Ensemblrn6Rnor6.0
Rnor_5.01012,822,308 - 12,825,905 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41012,944,503 - 12,947,271 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1012,406,544 - 12,409,312 (+)NCBICelera
RGSC_v3.11012,945,821 - 12,946,518 (+)NCBI
Cytogenetic Map10q12NCBI
CLDN6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38163,014,712 - 3,018,183 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl163,014,705 - 3,020,071 (-)Ensemblhg38GRCh38
GRCh37163,064,713 - 3,068,184 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36163,004,714 - 3,008,189 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34163,004,714 - 3,008,163NCBI
Celera163,270,273 - 3,273,747 (-)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef163,036,562 - 3,040,036 (-)NCBIHuRef
CHM1_1163,064,587 - 3,068,062 (-)NCBICHM1_1
T2T-CHM13v2.0163,041,284 - 3,044,755 (-)NCBIT2T-CHM13v2.0
Cldn6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391723,898,345 - 23,901,417 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1723,898,223 - 23,901,420 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381723,679,348 - 23,682,446 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1723,679,249 - 23,682,446 (+)Ensemblmm10GRCm38
MGSCv371723,816,332 - 23,819,407 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361723,406,987 - 23,410,062 (+)NCBIMGSCv36mm8
Celera1724,185,577 - 24,188,657 (+)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1711.99NCBI
Cldn6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544214,323,193 - 14,326,311 (+)Ensembl
ChiLan1.0NW_00495544214,323,193 - 14,326,311 (+)NCBIChiLan1.0ChiLan1.0
CLDN6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2183,559,506 - 3,563,127 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1167,337,886 - 7,341,507 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0161,956,556 - 1,960,177 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1163,128,951 - 3,132,503 (-)NCBIPanPan1.1PanPan1.1panPan2
CLDN6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1638,168,793 - 38,171,827 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl638,170,608 - 38,171,273 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha639,409,000 - 39,412,350 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0638,479,077 - 38,482,417 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.1638,164,870 - 38,168,202 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0638,137,368 - 38,140,690 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0638,613,145 - 38,616,477 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cldn6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344105,554,839 - 105,557,401 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366941,153,347 - 1,154,012 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366941,153,189 - 1,154,012 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLDN6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl339,167,853 - 39,172,628 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1339,168,506 - 39,172,631 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2340,527,340 - 40,531,326 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLDN6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.152,758,086 - 2,761,996 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl52,758,702 - 2,759,364 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606828,073,450 - 28,074,745 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cldn6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624824760,798 - 763,142 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624824760,251 - 764,101 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Cldn6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v19987,701 - 988,683 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Cldn6
21 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:234
Count of miRNA genes:160
Interacting mature miRNAs:178
Transcripts:ENSRNOT00000004845
Prediction methods:Microtar, 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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10666111835509383Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10666092373950353Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10687714251877142Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135730538Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10130004247Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10117749933Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138832698Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 2 42 131 86 89 58 74 58 6 289 134 2 119 80 87 31 13 13

Sequence


Ensembl Acc Id: ENSRNOT00000004845   ⟹   ENSRNOP00000004845
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1013,000,090 - 13,002,862 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000004848   ⟹   ENSRNOP00000004848
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1012,709,960 - 12,715,973 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000111504   ⟹   ENSRNOP00000079837
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1012,709,960 - 12,715,973 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000161479   ⟹   ENSRNOP00000110501
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1013,213,956 - 13,218,539 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000169702   ⟹   ENSRNOP00000111498
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1013,216,071 - 13,218,581 (+)Ensembl
RefSeq Acc Id: NM_001102364   ⟹   NP_001095834
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81013,215,808 - 13,218,576 (+)NCBI
mRatBN7.21012,711,216 - 12,713,985 (+)NCBI
Rnor_6.01013,000,090 - 13,002,858 (+)NCBI
Rnor_5.01012,822,308 - 12,825,905 (+)NCBI
RGSC_v3.41012,944,503 - 12,947,271 (+)RGD
Celera1012,406,544 - 12,409,312 (+)RGD
Sequence:
RefSeq Acc Id: XM_008767511   ⟹   XP_008765733
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81013,213,837 - 13,218,578 (+)NCBI
mRatBN7.21012,710,302 - 12,713,987 (+)NCBI
Rnor_6.01012,999,256 - 13,002,860 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063268546   ⟹   XP_063124616
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81013,213,837 - 13,218,578 (+)NCBI
RefSeq Acc Id: NP_001095834   ⟸   NM_001102364
- Peptide Label: precursor
- UniProtKB: B4F7F0 (UniProtKB/TrEMBL),   A0A8I5ZNF5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765733   ⟸   XM_008767511
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000004845   ⟸   ENSRNOT00000004845
Ensembl Acc Id: ENSRNOP00000004848   ⟸   ENSRNOT00000004848
Ensembl Acc Id: ENSRNOP00000079837   ⟸   ENSRNOT00000111504
RefSeq Acc Id: XP_063124616   ⟸   XM_063268546
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZNF5 (UniProtKB/TrEMBL),   B4F7F0 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000110501   ⟸   ENSRNOT00000161479
Ensembl Acc Id: ENSRNOP00000111498   ⟸   ENSRNOT00000169702

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B4F7F0-F1-model_v2 AlphaFold B4F7F0 1-219 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308837 AgrOrtholog
BioCyc Gene G2FUF-25914 BioCyc
Ensembl Genes ENSRNOG00000003648 Ensembl
  ENSRNOG00000003654 Ensembl
  ENSRNOG00000077752 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000161479 ENTREZGENE
  ENSRNOT00000161479.1 UniProtKB/TrEMBL
  ENSRNOT00000169702.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.140.150 UniProtKB/TrEMBL
InterPro Claudin UniProtKB/TrEMBL
  Claudin6 UniProtKB/TrEMBL
  Claudin_CS UniProtKB/TrEMBL
  PMP22/EMP/MP20/Claudin UniProtKB/TrEMBL
KEGG Report rno:287098 UniProtKB/TrEMBL
NCBI Gene 287098 ENTREZGENE
PANTHER Claudin UniProtKB/TrEMBL
Pfam PMP22_Claudin UniProtKB/TrEMBL
PhenoGen Cldn6 PhenoGen
PRINTS CLAUDIN UniProtKB/TrEMBL
  CLAUDIN6 UniProtKB/TrEMBL
PROSITE CLAUDIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000003648 RatGTEx
  ENSRNOG00000003654 RatGTEx
  ENSRNOG00000077752 RatGTEx
UniProt A0A8I5ZNF5 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0M6V2_RAT UniProtKB/TrEMBL
  B4F7F0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Cldn6  claudin 6   Cldn6_predicted  claudin 6 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Cldn6_predicted  claudin 6 (predicted)      Symbol and Name status set to approved 70820 APPROVED