Cldn20 (claudin 20) - Rat Genome Database

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Gene: Cldn20 (claudin 20) Rattus norvegicus
Analyze
Symbol: Cldn20
Name: claudin 20
RGD ID: 1595446
Description: Predicted to enable structural molecule activity. Predicted to be involved in bicellular tight junction assembly and cell adhesion. Predicted to be located in tight junction. Predicted to be active in bicellular tight junction and plasma membrane. Orthologous to human CLDN20 (claudin 20); PARTICIPATES IN hepatitis C pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; paracetamol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: claudin-20; LOC680178; similar to claudin 20
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
GRCr8146,539,039 - 46,539,698 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl146,536,236 - 46,540,949 (+)EnsemblGRCr8
mRatBN7.2144,133,769 - 44,134,428 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl144,133,769 - 44,134,428 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx144,674,720 - 44,675,379 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0150,661,954 - 50,662,613 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0144,750,218 - 44,750,877 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0144,443,218 - 44,447,595 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl144,446,765 - 44,447,424 (+)Ensemblrn6Rnor6.0
Rnor_5.0145,773,397 - 45,777,686 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4138,528,300 - 38,528,959 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera139,767,484 - 39,768,143 (+)NCBICelera
Cytogenetic Map1q11NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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
# 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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:18036336   PMID:30734065  


Genomics

Comparative Map Data
Cldn20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8146,539,039 - 46,539,698 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl146,536,236 - 46,540,949 (+)EnsemblGRCr8
mRatBN7.2144,133,769 - 44,134,428 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl144,133,769 - 44,134,428 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx144,674,720 - 44,675,379 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0150,661,954 - 50,662,613 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0144,750,218 - 44,750,877 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0144,443,218 - 44,447,595 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl144,446,765 - 44,447,424 (+)Ensemblrn6Rnor6.0
Rnor_5.0145,773,397 - 45,777,686 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4138,528,300 - 38,528,959 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera139,767,484 - 39,768,143 (+)NCBICelera
Cytogenetic Map1q11NCBI
CLDN20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386155,264,013 - 155,276,548 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6155,264,013 - 155,276,548 (+)Ensemblhg38GRCh38
GRCh376155,585,147 - 155,597,682 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366155,626,839 - 155,639,374 (+)NCBIBuild 36Build 36hg18NCBI36
Build 346155,677,259 - 155,689,792NCBI
Celera6156,319,443 - 156,331,976 (+)NCBICelera
Cytogenetic Map6q25.3NCBI
HuRef6153,147,422 - 153,160,302 (+)NCBIHuRef
CHM1_16155,847,762 - 155,860,297 (+)NCBICHM1_1
T2T-CHM13v2.06156,466,034 - 156,478,569 (+)NCBIT2T-CHM13v2.0
Cldn20
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39173,582,829 - 3,583,488 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl173,582,829 - 3,583,488 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38173,532,554 - 3,533,213 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl173,532,554 - 3,533,213 (+)Ensemblmm10GRCm38
MGSCv37173,532,554 - 3,533,213 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36173,489,036 - 3,489,695 (+)NCBIMGSCv36mm8
Celera174,067,361 - 4,068,020 (+)NCBICelera
Cytogenetic Map17A1NCBI
cM Map172.01NCBI
Cldn20
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554396,923,157 - 6,924,098 (-)NCBIChiLan1.0ChiLan1.0
CLDN20
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25175,295,703 - 175,308,733 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16173,187,143 - 173,194,630 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06153,089,106 - 153,093,580 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16159,045,062 - 159,057,687 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6159,056,863 - 159,057,522 (+)EnsemblpanPan2panpan1.1
CLDN20
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1145,013,689 - 45,020,882 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl145,018,095 - 45,018,754 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha145,851,739 - 45,858,033 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0145,198,080 - 45,204,376 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl145,201,449 - 45,202,108 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1145,065,245 - 45,071,541 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0144,936,971 - 44,943,267 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0145,493,216 - 45,499,511 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cldn20
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946140,225,114 - 140,226,850 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364897,477,904 - 7,478,563 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364897,477,160 - 7,478,843 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLDN20
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl111,617,807 - 11,618,550 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1111,617,807 - 11,618,550 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2113,591,814 - 13,596,741 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLDN20
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11382,840,409 - 82,841,307 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1382,840,480 - 82,841,139 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604055,215,518 - 55,216,467 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cldn20
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247853,063,991 - 3,064,650 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247853,063,852 - 3,065,040 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Cldn20
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12195,231,140 - 195,231,973 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Cldn20
3 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:19
Count of miRNA genes:18
Interacting mature miRNAs:19
Transcripts:ENSRNOT00000030132
Prediction methods:Miranda, Rnahybrid, 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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)14345783787558729Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1774611852746118Rat
1357397Bw41Body weight QTL 414.190.0001body mass (VT:0001259)body weight (CMO:0000012)12940927974409279Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)139728272132889942Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14630261591302615Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)14345783787558729Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)14630261591302615Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)14350995288509952Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)14212296887122968Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)14630261591302615Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1694102251941022Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)1690935351909353Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)14630261591302615Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)11731537851816258Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)1690935351909353Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134184556172281316Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)14630261591302615Rat
5684999Bss102Bone structure and strength QTL 1025.57e-07tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)1690935351909353Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134565911208798288Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14345783787558729Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)14630261591302615Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12050832665508326Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)11168446456684464Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)13070837587558729Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13456572679565726Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1774612152746121Rat
1558642Prcr2Prostate cancer resistance QTL 24.3prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)11037949255379492Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)14630261591302615Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)14630261591302615Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)14350995288509952Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)14212296887122968Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11282049457820494Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)14630261591302615Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)14350995288509952Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)12065642065656420Rat


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
10 10 24 67 44 45 15 68 15 3 198 116 7 52 49 42 30 11 11

Sequence


Ensembl Acc Id: ENSRNOT00000030132   ⟹   ENSRNOP00000030893
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl144,133,769 - 44,134,428 (+)Ensembl
Rnor_6.0 Ensembl144,446,765 - 44,447,424 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000125202   ⟹   ENSRNOP00000100062
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl146,538,059 - 46,540,949 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000168490   ⟹   ENSRNOP00000105337
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl146,536,236 - 46,540,949 (+)Ensembl
RefSeq Acc Id: NM_001109394   ⟹   NP_001102864
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8146,539,039 - 46,539,698 (+)NCBI
mRatBN7.2144,133,769 - 44,134,428 (+)NCBI
Rnor_6.0144,446,765 - 44,447,424 (+)NCBI
Rnor_5.0145,773,397 - 45,777,686 (+)NCBI
RGSC_v3.4138,528,300 - 38,528,959 (+)RGD
Celera139,767,484 - 39,768,143 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102864 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92823 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000100062.1
  ENSRNOP00000105337
  ENSRNOP00000105337.1
RefSeq Acc Id: NP_001102864   ⟸   NM_001109394
- Peptide Label: precursor
- UniProtKB: D3ZT28 (UniProtKB/TrEMBL),   A6KIQ7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000030893   ⟸   ENSRNOT00000030132
Ensembl Acc Id: ENSRNOP00000105337   ⟸   ENSRNOT00000168490
Ensembl Acc Id: ENSRNOP00000100062   ⟸   ENSRNOT00000125202

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZT28-F1-model_v2 AlphaFold D3ZT28 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:1595446 AgrOrtholog
BioCyc Gene G2FUF-61663 BioCyc
Ensembl Genes ENSRNOG00000023531 Ensembl
  ENSRNOG00000073115 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000125202.1 UniProtKB/TrEMBL
  ENSRNOT00000168490 ENTREZGENE
  ENSRNOT00000168490.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.140.150 UniProtKB/TrEMBL
InterPro Claudin UniProtKB/TrEMBL
  Claudin_CS UniProtKB/TrEMBL
  PMP22/EMP/MP20/Claudin UniProtKB/TrEMBL
KEGG Report rno:680178 UniProtKB/TrEMBL
NCBI Gene 680178 ENTREZGENE
PANTHER Claudin UniProtKB/TrEMBL
Pfam PMP22_Claudin UniProtKB/TrEMBL
PhenoGen Cldn20 PhenoGen
PRINTS CLAUDIN UniProtKB/TrEMBL
PROSITE CLAUDIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000023531 RatGTEx
  ENSRNOG00000073115 RatGTEx
UniProt A0ABK0LI52_RAT UniProtKB/TrEMBL
  A6KIQ7 ENTREZGENE, UniProtKB/TrEMBL
  D3ZT28 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-07-08 Cldn20  claudin 20  LOC682962  similar to claudin 20  Data merged from RGD:1592782 1643240 APPROVED
2008-03-05 Cldn20  claudin 20  LOC680178  similar to claudin 20  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC680178  similar to claudin 20      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC682962  similar to claudin 20      Symbol and Name status set to provisional 70820 PROVISIONAL