Human Gene CLDN23 (uc003wsi.3) Description and Page Index
  Description: Homo sapiens claudin 23 (CLDN23), mRNA.
RefSeq Summary (NM_194284): 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. This gene is expressed in germinal center B-cells, placenta and stomach as well as in colon tumor. This gene is down-regulated in intestinal type gastric cancer. [provided by RefSeq, Aug 2010]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript is intronless :: SRR6380200.29125.21, SRR7346977.1094289.1 [ECO:0000345] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr8:8,559,666-8,561,617 Size: 1,952 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr8:8,559,909-8,560,787 Size: 879 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:8,559,666-8,561,617)mRNA (may differ from genome)Protein (292 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: CLD23_HUMAN
DESCRIPTION: RecName: Full=Claudin-23;
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 (By similarity). Cell membrane; Multi-pass membrane protein (By similarity).
TISSUE SPECIFICITY: Expressed in germinal center B-cells, placenta, stomach as well as in colon tumor.
SIMILARITY: Belongs to the claudin family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CLDN23
CDC HuGE Published Literature: CLDN23
Positive Disease Associations: Stroke
Related Studies:
  1. Stroke
    , , . [PubMed 0]

-  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: 12.22 RPKM in Stomach
Total median expression: 116.72 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 -111.20243-0.458 Picture PostScript Text
3' UTR -241.33830-0.291 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

ModBase Predicted Comparative 3D Structure on Q96B33
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  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


-  Descriptions from all associated GenBank mRNAs
  LF208089 - JP 2014500723-A/15592: Polycomb-Associated Non-Coding RNAs.
LF212197 - JP 2014500723-A/19700: Polycomb-Associated Non-Coding RNAs.
LF208088 - JP 2014500723-A/15591: Polycomb-Associated Non-Coding RNAs.
LF213937 - JP 2014500723-A/21440: Polycomb-Associated Non-Coding RNAs.
AK123547 - Homo sapiens cDNA FLJ41553 fis, clone COLON2005126.
BC125148 - Homo sapiens claudin 23, mRNA (cDNA clone MGC:150404 IMAGE:40120346), complete cds.
BC125149 - Homo sapiens claudin 23, mRNA (cDNA clone MGC:150405 IMAGE:40120347), complete cds.
JD389997 - Sequence 371021 from Patent EP1572962.
BC016047 - Homo sapiens claudin 23, mRNA (cDNA clone IMAGE:4639904), containing frame-shift errors.
LF372049 - JP 2014500723-A/179552: Polycomb-Associated Non-Coding RNAs.
LF213121 - JP 2014500723-A/20624: Polycomb-Associated Non-Coding RNAs.
Z36835 - H.sapiens (XS77) mRNA, 347bp.
JD344798 - Sequence 325822 from Patent EP1572962.
JD528281 - Sequence 509305 from Patent EP1572962.
LF372048 - JP 2014500723-A/179551: Polycomb-Associated Non-Coding RNAs.
JD566774 - Sequence 547798 from Patent EP1572962.
JD082309 - Sequence 63333 from Patent EP1572962.
JD370584 - Sequence 351608 from Patent EP1572962.
JD259821 - Sequence 240845 from Patent EP1572962.
JD163333 - Sequence 144357 from Patent EP1572962.
MA449514 - JP 2018138019-A/21440: Polycomb-Associated Non-Coding RNAs.
MA607626 - JP 2018138019-A/179552: Polycomb-Associated Non-Coding RNAs.
MA607625 - JP 2018138019-A/179551: Polycomb-Associated Non-Coding RNAs.
MA443666 - JP 2018138019-A/15592: Polycomb-Associated Non-Coding RNAs.
MA447774 - JP 2018138019-A/19700: Polycomb-Associated Non-Coding RNAs.
MA443665 - JP 2018138019-A/15591: Polycomb-Associated Non-Coding RNAs.
MA448698 - JP 2018138019-A/20624: Polycomb-Associated Non-Coding RNAs.

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

Reactome (by CSHL, EBI, and GO)

Protein Q96B33 (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: CLD23_HUMAN, NM_194284, NP_919260, Q08AJ3, Q96B33
UCSC ID: uc003wsi.3
RefSeq Accession: NM_194284
Protein: Q96B33 (aka CLD23_HUMAN or CLDN_HUMAN)
CCDS: CCDS55195.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_194284.2
exon count: 1CDS single in 3' UTR: no RNA size: 1972
ORF size: 879CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1940.00frame shift in genome: no % Coverage: 98.99
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.