Human Gene CLDN2 (ENST00000336803.2_4) from GENCODE V47lift37
  Description: claudin 2, transcript variant 1 (from RefSeq NM_020384.4)
Gencode Transcript: ENST00000336803.2_4
Gencode Gene: ENSG00000165376.12_9
Transcript (Including UTRs)
   Position: hg19 chrX:106,163,632-106,174,091 Size: 10,460 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chrX:106,171,459-106,172,151 Size: 693 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:106,163,632-106,174,091)mRNA (may differ from genome)Protein (230 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CLD2_HUMAN
DESCRIPTION: RecName: Full=Claudin-2; AltName: Full=SP82;
FUNCTION: Plays a major role in tight junction-specific obliteration of the intercellular space, through calcium- independent cell-adhesion activity (By similarity).
SUBUNIT: Can form homo- and heteropolymers with other CLDN. Homopolymers interact with CLDN3, but not CLDN1, homopolymers. Directly interacts with TJP1/ZO-1, TJP2/ZO-2 and TJP3/ZO-3 (By similarity).
SUBCELLULAR LOCATION: Cell junction, tight junction (By similarity). Cell membrane; Multi-pass membrane protein (By similarity).
SIMILARITY: Belongs to the claudin family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CLDN2
Diseases sorted by gene-association score: osmotic diarrhea (8)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 32.11 RPKM in Kidney - Cortex
Total median expression: 74.06 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -110.80328-0.338 Picture PostScript Text
3' UTR -664.001940-0.342 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR006187 - Claudin
IPR005411 - Claudin2
IPR017974 - Claudin_CS
IPR004031 - PMP22/EMP/MP20/Claudin

Pfam Domains:
PF00822 - PMP-22/EMP/MP20/Claudin family

SCOP Domains:
53067 - Actin-like ATPase domain

ModBase Predicted Comparative 3D Structure on P57739
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005198 structural molecule activity
GO:0005515 protein binding
GO:0042802 identical protein binding

Biological Process:
GO:0016338 calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules

Cellular Component:
GO:0005886 plasma membrane
GO:0005923 bicellular tight junction
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction


-  Descriptions from all associated GenBank mRNAs
  AF177340 - Homo sapiens clone SP82 claudin 2 mRNA, complete cds.
AK312515 - Homo sapiens cDNA, FLJ92880, Homo sapiens claudin 2 (CLDN2), mRNA.
BC071747 - Homo sapiens claudin 2, mRNA (cDNA clone MGC:88250 IMAGE:30322852), complete cds.
AK075405 - Homo sapiens cDNA PSEC0096 fis, clone NT2RP2002060, highly similar to Claudin-2.
AK075371 - Homo sapiens cDNA PSEC0059 fis, clone NT2RP2000601, highly similar to Mus musculus claudin-2 mRNA.
BC014424 - Homo sapiens claudin 2, mRNA (cDNA clone MGC:20191 IMAGE:4645075), complete cds.
AY358474 - Homo sapiens clone DNA64886 Claudin-2 (UNQ705) mRNA, complete cds.
JD446840 - Sequence 427864 from Patent EP1572962.
JD499735 - Sequence 480759 from Patent EP1572962.
JD339710 - Sequence 320734 from Patent EP1572962.
JD072839 - Sequence 53863 from Patent EP1572962.
JD042968 - Sequence 23992 from Patent EP1572962.
AB463528 - Synthetic construct DNA, clone: pF1KB0998, Homo sapiens CLDN2 gene for claudin 2, without stop codon, in Flexi system.
DQ892216 - Synthetic construct clone IMAGE:100004846; FLH184142.01X; RZPDo839C08144D claudin 2 (CLDN2) gene, encodes complete protein.
DQ895412 - Synthetic construct Homo sapiens clone IMAGE:100009872; FLH184138.01L; RZPDo839C08143D claudin 2 (CLDN2) gene, encodes complete protein.
KJ904619 - Synthetic construct Homo sapiens clone ccsbBroadEn_14013 CLDN2-like gene, encodes complete protein.
AF250558 - Homo sapiens claudin-2 mRNA, complete cds.
JD486799 - Sequence 467823 from Patent EP1572962.
JD222981 - Sequence 204005 from Patent EP1572962.
JD470020 - Sequence 451044 from Patent EP1572962.
JD232360 - Sequence 213384 from Patent EP1572962.
JD403897 - Sequence 384921 from Patent EP1572962.
JD036817 - Sequence 17841 from Patent EP1572962.
JD250538 - Sequence 231562 from Patent EP1572962.
JD355822 - Sequence 336846 from Patent EP1572962.
JD561634 - Sequence 542658 from Patent EP1572962.
JD130417 - Sequence 111441 from Patent EP1572962.
JD449347 - Sequence 430371 from Patent EP1572962.
JD216111 - Sequence 197135 from Patent EP1572962.
JD152902 - Sequence 133926 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P57739 (Reactome details) participates in the following event(s):

R-HSA-420019 Claudins create paired strands through homophilic and heterophilic cis and trans interactions
R-HSA-420029 Tight junction interactions
R-HSA-421270 Cell-cell junction organization
R-HSA-446728 Cell junction organization
R-HSA-1500931 Cell-Cell communication

-  Other Names for This Gene
  Alternate Gene Symbols: B2R6B9, CLD2_HUMAN, ENST00000336803.1, NM_020384, P57739, PSEC0059, SP82, uc317ups.1, uc317ups.2, UNQ705/PRO1356
UCSC ID: ENST00000336803.2_4
RefSeq Accession: NM_020384.4
Protein: P57739 (aka CLD2_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CLDN2:
pancreatitis-ov (Pancreatitis Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.