Cldn16 (claudin 16) - Rat Genome Database

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Gene: Cldn16 (claudin 16) Mus musculus
Analyze
Symbol: Cldn16
Name: claudin 16
RGD ID: 733040
MGI Page MGI
Description: Predicted to enable structural molecule activity. Predicted to be involved in several processes, including bicellular tight junction assembly; positive regulation of calcium ion transport; and transepithelial transport. Predicted to act upstream of or within monoatomic ion transport. Located in bicellular tight junction. Is expressed in metanephros and stomach. Used to study renal hypomagnesemia 3. Human ortholog(s) of this gene implicated in renal hypomagnesemia 3 and renal tubular transport disease. Orthologous to human CLDN16 (claudin 16).
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: claudi; claudin-16; H59D2a protein; paracellin-1; PC; PCLN1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. 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.
2. MGDs mouse GO annotations MGD data from the GO Consortium
3. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. Mouse MP Annotation Import Pipeline RGD automated import pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Paracellin-1, a renal tight junction protein required for paracellular Mg2+ resorption. Simon DB, etal., Science. 1999 Jul 2;285(5424):103-6.
10. 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:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12477932   PMID:16141072   PMID:16141073   PMID:16234325   PMID:16520537   PMID:16602821   PMID:17033971   PMID:17442678  
PMID:18036336   PMID:18480174   PMID:18784260   PMID:19538300   PMID:19706201   PMID:19706394   PMID:20147368   PMID:20511716   PMID:21677750   PMID:21873635   PMID:22155109   PMID:22275141  
PMID:25557732   PMID:26398943   PMID:26426912   PMID:28028216   PMID:29129401   PMID:30973865   PMID:34737342   PMID:36889572  


Genomics

Comparative Map Data
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
(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
(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
(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
650 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:96
Count of miRNA genes:46
Interacting mature miRNAs:48
Transcripts:ENSMUST00000115302, ENSMUST00000161053
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301384Dice1_mdetermination of interleukin 4 commitment 1 (mouse)Not determined16128434358Mouse
10402497Lmr23_mleishmaniasis resistance 23 (mouse)Not determined16129674200Mouse
1301559Bbaa19_mB.burgdorferi-associated arthritis 19 (mouse)Not determined16130066977Mouse
10412289Ppsl_mplasma P-selectin levels (mouse)Not determined16130814572Mouse
27095908Scvln7_msacral vertebrae length 2, 5 week (mouse)16331786439820362Mouse
27226768Tibl9_mtibia length 9, 5 week (mouse)16331786451420363Mouse
27226785Feml12_mfemur length 12, 5 week (mouse)16331786464620363Mouse
26884432Zlq7_mzygomatic length QTL 7, 10 week (mouse)16381786464620363Mouse
38501069Tip4_mtuberculosis immunophenotype 4, IFN-g level (mouse)16431786444520363Mouse
1301443Mopkd2_mmodifier of polycystic kidney disease progression 2 (mouse)Not determined16464631438646414Mouse
1300656Bgeq15_mbody growth early QTL 15 (mouse)Not determined16577525239775440Mouse
1301945Skl7_mskeletal size (tail length) 7 (mouse)Not determined16577525239775440Mouse
1300943Skts9_mskin tumor susceptibility 9 (mouse)Not determined16577525239775440Mouse
1300987Skull23_mskull morphology 23 (mouse)Not determined16577525239775440Mouse
4141010Bbq1_mbrain and behavior QTL 1 (mouse)Not determined16647700935021216Mouse
1357763Lp1_mlymphocyte proliferation 1 (mouse)Not determined16654297965466552Mouse
4142460Nilac10_mnicotine induced locomotor activity 10 (mouse)Not determined16713690629225471Mouse
11251724Ewc6_methanol withdrawal and consumption 6 (mouse)16822605242226052Mouse
26884376Skwq4_mskull length QTL 4, 5 week (mouse)16841786490896888Mouse
10043978Obq35_mobesity QTL 35 (mouse)Not determined16988163143881631Mouse
1301086Lprm5_mlymphoproliferation modifier 5 (mouse)Not determined161184882445848923Mouse
1301841Lrnx9_mlearning-contextual 9 (mouse)Not determined161222536046225471Mouse
10045614Rapop6_mradiation-induced apoptosis 6 (mouse)Not determined161480292148803032Mouse
4142236Pstc4_mperiosteal circumference 4 (mouse)Not determined161552290949523112Mouse
11565820Vasr1_mvariability in acoustic startle response 1 (mouse)161969865726368664Mouse
1357517Bwtn1_mbody weight at necropsy 1 (mouse)Not determined162001932985600826Mouse
1300534Bmd15_mbone mineral density 15 (mouse)Not determined162193838355938574Mouse
4141179Ipng3_mimprinted postnatal growth 3 (mouse)Not determined2277525257594076Mouse
15092062Egrme4_mearly growth rate, maternal effect 4 (mouse)162521866444220250Mouse

Markers in Region
Cldn16  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map16B2UniSTS
cM Map16 UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000115302   ⟹   ENSMUSP00000110957
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1626,282,006 - 26,301,513 (+)Ensembl
GRCm38.p6 Ensembl1626,463,256 - 26,482,763 (+)Ensembl
RefSeq Acc Id: ENSMUST00000161053   ⟹   ENSMUSP00000124528
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1626,281,885 - 26,301,515 (+)Ensembl
GRCm38.p6 Ensembl1626,463,135 - 26,482,765 (+)Ensembl
RefSeq Acc Id: NM_053241   ⟹   NP_444471
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391626,281,885 - 26,301,515 (+)NCBI
GRCm381626,463,135 - 26,482,765 (+)ENTREZGENE
MGSCv371626,463,246 - 26,482,853 (+)RGD
Celera1627,006,424 - 27,026,196 (+)ENTREZGENE
cM Map16 ENTREZGENE
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_444471   ⟸   NM_053241
- UniProtKB: Q542L7 (UniProtKB/Swiss-Prot),   Q925N4 (UniProtKB/Swiss-Prot),   Q14BW2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000110957   ⟸   ENSMUST00000115302
RefSeq Acc Id: ENSMUSP00000124528   ⟸   ENSMUST00000161053

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q925N4-F1-model_v2 AlphaFold Q925N4 1-235 view protein structure

Promoters
RGD ID:8685886
Promoter ID:EPDNEW_M20974
Type:initiation region
Name:Cldn16_1
Description:Mus musculus claudin 16 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381626,463,082 - 26,463,142EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2148742 AgrOrtholog
Ensembl Genes ENSMUSG00000038148 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000115302.2 UniProtKB/Swiss-Prot
  ENSMUST00000161053 ENTREZGENE
  ENSMUST00000161053.8 UniProtKB/Swiss-Prot
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 mmu:114141 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:2148742 ENTREZGENE
NCBI Gene 114141 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
UniProt CLD16_MOUSE UniProtKB/Swiss-Prot
  Q14BW2 ENTREZGENE, UniProtKB/TrEMBL
  Q542L7 ENTREZGENE
  Q925N4 ENTREZGENE
UniProt Secondary Q542L7 UniProtKB/Swiss-Prot