Cldn16 (claudin 16) - Rat Genome Database

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Pathways
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Gene: Cldn16 (claudin 16) Rattus norvegicus
Analyze
Symbol: Cldn16
Name: claudin 16
RGD ID: 620322
Description: Predicted to enable identical protein binding activity. Involved in positive regulation of calcium ion transport and transepithelial transport. Located in bicellular tight junction. Used to study hypertension. Human ortholog(s) of this gene implicated in renal hypomagnesemia 3 and renal tubular transport disease. Orthologous to human CLDN16 (claudin 16); PARTICIPATES IN hepatitis C pathway; INTERACTS WITH bisphenol A; tributylstannane; vinclozolin.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: claudin-16; paracellin-1; Pcln1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81187,795,106 - 87,814,396 (-)NCBIGRCr8
mRatBN7.21174,290,298 - 74,309,588 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1174,290,298 - 74,309,588 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1183,098,900 - 83,118,197 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01175,733,942 - 75,753,237 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01174,795,644 - 74,814,832 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01177,683,942 - 77,703,232 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1177,681,794 - 77,703,255 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01183,013,610 - 83,035,155 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41176,313,985 - 76,334,074 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11176,371,576 - 76,391,663 (-)NCBI
Celera1173,208,029 - 73,227,202 (-)NCBICelera
Cytogenetic Map11q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
bicellular tight junction  (IBA,IDA,IEA,ISO,ISS,TAS)
plasma membrane  (IBA,IEA)

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. Association of paracellin-1 with ZO-1 augments the reabsorption of divalent cations in renal epithelial cells. Ikari A, etal., J Biol Chem. 2004 Dec 24;279(52):54826-32. Epub 2004 Oct 20.
3. Dysfunction of paracellin-1 by dephosphorylation in Dahl salt-sensitive hypertensive rats. Ikari A, etal., J Physiol Sci. 2006 Oct;56(5):379-83. Epub 2006 Sep 9.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Paracellin-1, a renal tight junction protein required for paracellular Mg2+ resorption. Simon DB, etal., Science. 1999 Jul 2;285(5424):103-6.
12. Primary gene structure and expression studies of rodent paracellin-1. Weber S, etal., J Am Soc Nephrol 2001 Dec;12(12):2664-72.
Additional References at PubMed
PMID:16520537   PMID:18036336   PMID:19914201   PMID:24659781   PMID:28623232   PMID:29991461  


Genomics

Comparative Map Data
Cldn16
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81187,795,106 - 87,814,396 (-)NCBIGRCr8
mRatBN7.21174,290,298 - 74,309,588 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1174,290,298 - 74,309,588 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1183,098,900 - 83,118,197 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01175,733,942 - 75,753,237 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01174,795,644 - 74,814,832 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01177,683,942 - 77,703,232 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1177,681,794 - 77,703,255 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01183,013,610 - 83,035,155 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41176,313,985 - 76,334,074 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11176,371,576 - 76,391,663 (-)NCBI
Celera1173,208,029 - 73,227,202 (-)NCBICelera
Cytogenetic Map11q22NCBI
CLDN16
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383190,290,361 - 190,412,138 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3190,322,541 - 190,412,138 (+)EnsemblGRCh38hg38GRCh38
GRCh373190,008,150 - 190,129,927 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363191,588,535 - 191,611,027 (+)NCBINCBI36Build 36hg18NCBI36
Build 343191,588,542 - 191,611,035NCBI
Celera3188,536,131 - 188,560,428 (+)NCBICelera
Cytogenetic Map3q28NCBI
HuRef3187,505,460 - 187,529,668 (+)NCBIHuRef
CHM1_13190,068,819 - 190,093,110 (+)NCBICHM1_1
T2T-CHM13v2.03193,106,655 - 193,228,453 (+)NCBIT2T-CHM13v2.0
Cldn16
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391626,281,885 - 26,301,515 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1626,281,885 - 26,301,515 (+)EnsemblGRCm39 Ensembl
GRCm381626,463,135 - 26,482,765 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1626,463,135 - 26,482,765 (+)EnsemblGRCm38mm10GRCm38
MGSCv371626,463,246 - 26,482,853 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361626,378,509 - 26,398,125 (+)NCBIMGSCv36mm8
Celera1627,006,449 - 27,026,198 (+)NCBICelera
Cytogenetic Map16B2NCBI
cM Map1618.1NCBI
Cldn16
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542017,693,573 - 17,715,211 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542017,684,752 - 17,714,639 (-)NCBIChiLan1.0ChiLan1.0
CLDN16
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22188,257,031 - 188,282,805 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13188,261,748 - 188,287,522 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03187,141,710 - 187,436,909 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13195,964,400 - 195,990,065 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3195,964,178 - 195,990,065 (+)Ensemblpanpan1.1panPan2
CLDN16
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13422,392,108 - 22,414,250 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3422,317,474 - 22,412,665 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3426,433,682 - 26,507,764 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03422,274,616 - 22,348,804 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3422,252,125 - 22,347,219 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13422,295,774 - 22,370,096 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03422,282,808 - 22,357,000 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03422,524,777 - 22,598,893 (+)NCBIUU_Cfam_GSD_1.0
Cldn16
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602113,913,789 - 113,933,582 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365785,774 - 25,350 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365785,774 - 25,621 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLDN16
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13127,808,599 - 127,830,717 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113127,808,599 - 127,831,081 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213137,065,482 - 137,087,589 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLDN16
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11584,529,660 - 84,619,707 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1584,593,857 - 84,619,660 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604158,118,538 - 58,210,830 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cldn16
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473066,741,550 - 66,768,921 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473066,741,687 - 66,768,589 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cldn16
161 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:61
Count of miRNA genes:50
Interacting mature miRNAs:58
Transcripts:ENSRNOT00000042994
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 (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
D11Rat104  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21174,291,260 - 74,291,612 (+)MAPPERmRatBN7.2
Rnor_6.01177,684,905 - 77,685,256NCBIRnor6.0
Rnor_5.01183,031,842 - 83,032,193UniSTSRnor5.0
RGSC_v3.41176,314,948 - 76,315,299UniSTSRGSC3.4
Celera1173,208,992 - 73,209,227UniSTS
SHRSP x BN Map1135.7599UniSTS
SHRSP x BN Map1135.7599RGD
Cytogenetic Map11q22UniSTS


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

endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 27
Low 2 8 16
Below cutoff 2 1 2 1 1 1 17 8 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000083319   ⟹   ENSRNOP00000074628
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1174,290,298 - 74,309,588 (-)Ensembl
Rnor_6.0 Ensembl1177,681,794 - 77,703,255 (-)Ensembl
RefSeq Acc Id: NM_131905   ⟹   NP_571980
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81187,795,106 - 87,814,396 (-)NCBI
mRatBN7.21174,290,298 - 74,309,588 (-)NCBI
Rnor_6.01177,683,942 - 77,703,232 (-)NCBI
Rnor_5.01183,013,610 - 83,035,155 (+)NCBI
RGSC_v3.41176,313,985 - 76,334,074 (-)RGD
Celera1173,208,029 - 73,227,202 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_571980 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK52459 (Get FASTA)   NCBI Sequence Viewer  
  EDL78118 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000074628
  ENSRNOP00000074628.1
GenBank Protein Q91Y55 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_571980   ⟸   NM_131905
- UniProtKB: Q91Y55 (UniProtKB/Swiss-Prot),   A0A0G2K8J2 (UniProtKB/TrEMBL),   A6JRY9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074628   ⟸   ENSRNOT00000083319

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q91Y55-F1-model_v2 AlphaFold Q91Y55 1-235 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:620322 AgrOrtholog
BioCyc Gene G2FUF-20938 BioCyc
Ensembl Genes ENSRNOG00000055138 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000083319 ENTREZGENE
  ENSRNOT00000083319.2 UniProtKB/TrEMBL
Gene3D-CATH 1.20.140.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Claudin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Claudin16 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Claudin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PMP22/EMP/MP20/Claudin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:155268 UniProtKB/TrEMBL
NCBI Gene 155268 ENTREZGENE
PANTHER PTHR12002 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR12002:SF56 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PMP22_Claudin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cldn16 PhenoGen
PRINTS CLAUDIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CLAUDIN16 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CLAUDIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000055138 RatGTEx
UniProt A0A0G2K8J2 ENTREZGENE, UniProtKB/TrEMBL
  A6JRY9 ENTREZGENE, UniProtKB/TrEMBL
  CLD16_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Cldn16  claudin 16      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Cldn16  claudin 16      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in distal tubular segments including the thick ascending limb of Henle's loop, the distal tubule, and the collecting duct 727232