Human Gene CLDN20 (ENST00000367165.3_3) from GENCODE V45lift37 (2024)

Human Gene CLDN20 (ENST00000367165.3_3) from GENCODE V45lift37

Description: hom*o sapiens claudin 20 (CLDN20), mRNA. (from RefSeq NM_001001346)
RefSeq Summary (NM_001001346): This gene encodes a member of the claudin family. Claudins are integral membrane proteins and components of tight junction strands. Tight junction strands serve as a physical barrier to prevent solutes and water from passing freely through the paracellular space between epithelial or endothelial cell sheets, and also play critical roles in maintaining cell polarity and signal transductions. [provided by RefSeq, Jun 2010].
Gencode Transcript: ENST00000367165.3_3
Gencode Gene: ENSG00000171217.5_4
Transcript (Including UTRs)
Position:hg19 chr6:155,585,147-155,597,682Size:12,536Total Exon Count:2Strand:+
Coding Region
Position:hg19 chr6:155,596,854-155,597,513Size:660Coding Exon Count:1

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC:2024-04-24 11:59:55

Sequence and Links to Tools and Databases

Genomic Sequence (chr6:155,585,147-155,597,682)			mRNA (may differ from genome)		Protein (219 aa)
Gene Sorter	Genome Browser	Other Species FASTA	Gene interactions	Table Schema	AlphaFold
BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards	GeneNetwork
HGNC	MGI	PubMed	Reactome	UniProtKB	Wikipedia
BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: CLD20_HUMAN DESCRIPTION: RecName: Full=Claudin-20; FUNCTION: Plays a major role in tight junction-specific obliteration of the intercellular space, through calcium- independent cell-adhesion activity (By similarity). SUBCELLULAR LOCATION: Cell junction, tight junction. Cell membrane; Multi-pass membrane protein. 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

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

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D007854Lead

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 0.99 RPKM in Nerve - Tibial Total median expression: 10.98 RPKM View in GTEx track of Genome BrowserView at GTEx portalView GTEx Body Map

Highest median expression: 0.99 RPKM in Nerve - Tibial
Total median expression: 10.98 RPKM

View in GTEx track of Genome BrowserView at GTEx portalView GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-110.40	380	-0.291	Picture	PostScript	Text
3' UTR	-21.60	169	-0.128	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
IPR017974 - Claudin_CS
IPR004031 - PMP22/EMP/MP20/Claudin

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

SCOP Domains:
48726 - Immunoglobulin
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on P56880


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0005198 structural molecule activity 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

Molecular Function:
GO:0005198 structural molecule activity
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


	BC020838 - homo sapiens claudin 20, mRNA (cDNA clone MGC:23949 IMAGE:4243903), complete cds. HM005642 - homo sapiens clone HTL-S-229n testis secretory sperm-binding protein Li 229n mRNA, complete cds. CU676742 - Synthetic construct homo sapiens gateway clone IMAGE:100021824 5' read CLDN20 mRNA. HQ447712 - Synthetic construct homo sapiens clone IMAGE:100071042; CCSB012825_01 claudin 20 (CLDN20) gene, encodes complete protein. KJ893747 - Synthetic construct hom*o sapiens clone ccsbBroadEn_03141 CLDN20 gene, encodes complete protein. CS123437 - Sequence 8 from Patent WO2005058362.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein P56880 (Reactome details) participates in the following event(s): R-HSA-420019 Claudins create paired strands through hom*ophilic 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

Reactome (by CSHL, EBI, and GO)

Protein P56880 (Reactome details) participates in the following event(s):

R-HSA-420019 Claudins create paired strands through hom*ophilic 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: CLD20_HUMAN, ENST00000367165.1, ENST00000367165.2, NM_001001346, P56880, uc318frs.1 UCSC ID: ENST00000367165.3_3 RefSeq Accession: NM_001001346 Protein: P56880 (aka CLD20_HUMAN or CLDK_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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