Human Gene CLDN5 (ENST00000413119.2) from GENCODE V44
  Description: Homo sapiens claudin 5 (CLDN5), transcript variant 2, mRNA. (from RefSeq NM_003277)
RefSeq Summary (NM_003277): 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. Mutations in this gene have been found in patients with velocardiofacial syndrome. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, May 2018].
Gencode Transcript: ENST00000413119.2
Gencode Gene: ENSG00000184113.10
Transcript (Including UTRs)
   Position: hg38 chr22:19,523,052-19,525,423 Size: 2,372 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg38 chr22:19,523,599-19,524,510 Size: 912 Coding Exon Count: 1 

Page IndexSequence and LinksPrimersMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr22:19,523,052-19,525,423)mRNA (may differ from genome)Protein (303 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  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: CLDN5
Diseases sorted by gene-association score: velocardiofacial syndrome (12), gray platelet syndrome (2)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 106.90 RPKM in Adipose - Subcutaneous
Total median expression: 1134.95 RPKM

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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -142.90301-0.475 Picture PostScript Text
3' UTR -255.30547-0.467 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
IPR003551 - Claudin5
IPR017974 - Claudin_CS
IPR004031 - PMP22/EMP/MP20/Claudin

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

ModBase Predicted Comparative 3D Structure on D3DX19
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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005198 structural molecule activity

Biological Process:
GO:0042552 myelination
GO:0045471 response to ethanol

Cellular Component:
GO:0005886 plasma membrane
GO:0005923 bicellular tight junction
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016328 lateral plasma membrane
GO:0030054 cell junction
GO:0033270 paranode region of axon
GO:0043220 Schmidt-Lanterman incisure

-  Descriptions from all associated GenBank mRNAs
  AF000959 - Homo sapiens transmembrane protein mRNA, complete cds.
BC002404 - Homo sapiens claudin 5, mRNA (cDNA clone MGC:8543 IMAGE:2822745), complete cds.
BC019290 - Homo sapiens claudin 5, mRNA (cDNA clone MGC:4051 IMAGE:2822745), complete cds.
BC032363 - Homo sapiens claudin 5, mRNA (cDNA clone MGC:40358 IMAGE:5242567), complete cds.
AK092561 - Homo sapiens cDNA FLJ35242 fis, clone PROST2002651, highly similar to CLAUDIN-5.
AK124019 - Homo sapiens cDNA FLJ42025 fis, clone SPLEN2036326, highly similar to CLAUDIN-5.
JD519155 - Sequence 500179 from Patent EP1572962.
JD324867 - Sequence 305891 from Patent EP1572962.
JD286140 - Sequence 267164 from Patent EP1572962.
JD219849 - Sequence 200873 from Patent EP1572962.
JD219848 - Sequence 200872 from Patent EP1572962.
AK222466 - Homo sapiens mRNA for claudin 5 variant, clone: adKA02848.
JD200867 - Sequence 181891 from Patent EP1572962.
JD297480 - Sequence 278504 from Patent EP1572962.
CR456420 - Homo sapiens CLDN5 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.CLDN5.V3).
JD129763 - Sequence 110787 from Patent EP1572962.
JD464807 - Sequence 445831 from Patent EP1572962.
JD407758 - Sequence 388782 from Patent EP1572962.
JD107799 - Sequence 88823 from Patent EP1572962.
JD452347 - Sequence 433371 from Patent EP1572962.
CU012981 - Homo sapiens CLDN5, mRNA (cDNA clone IMAGE:100000142), complete cds, with stop codon, in Gateway system.
BT007254 - Homo sapiens claudin 5 (transmembrane protein deleted in velocardiofacial syndrome) mRNA, complete cds.
CU013269 - Homo sapiens CLDN5, mRNA (cDNA clone IMAGE:100000046), complete cds, without stop codon, in Gateway system.
AB528106 - Synthetic construct DNA, clone: pF1KE0494, Homo sapiens CLDN5 gene for claudin 5, without stop codon, in Flexi system.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04514 - Cell adhesion molecules (CAMs)
hsa04530 - Tight junction
hsa04670 - Leukocyte transendothelial migration

-  Other Names for This Gene
  Alternate Gene Symbols: D3DX19, D3DX19_HUMAN, ENST00000413119.1, hCG_17893, NM_003277, uc002zpu.1, uc002zpu.2, uc002zpu.3
UCSC ID: ENST00000413119.2
RefSeq Accession: NM_003277
Protein: D3DX19 CCDS: CCDS13763.2

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