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    CLDN5 claudin 5 [ Homo sapiens (human) ]

    Gene ID: 7122, updated on 3-Dec-2024

    Summary

    Official Symbol
    CLDN5provided by HGNC
    Official Full Name
    claudin 5provided by HGNC
    Primary source
    HGNC:HGNC:2047
    See related
    Ensembl:ENSG00000184113 MIM:602101; AllianceGenome:HGNC:2047
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    AWAL; BEC1; TMVCF; TMDVCF; CPETRL1
    Summary
    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]
    Expression
    Biased expression in fat (RPKM 51.6), lung (RPKM 14.0) and 6 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CLDN5 in Genome Data Viewer
    Location:
    22q11.21
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (19523024..19525337, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (19899865..19902178, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (19510547..19512860, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene UFD1 antisense RNA 1 Neighboring gene ubiquitin recognition factor in ER associated degradation 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13463 Neighboring gene cell division cycle 45 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:19486137-19486353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19493394-19493894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19493895-19494395 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19502006-19502506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19502507-19503007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19509616-19510548 Neighboring gene MPRA-validated peak4453 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19531837-19532336 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19542168-19542870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19542871-19543573 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:19554961-19555296 Neighboring gene long intergenic non-protein coding RNA 895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19583904-19584446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19585482-19585982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19585983-19586483 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19592881-19593448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19593449-19594016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19594499-19595072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19604675-19605254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19605255-19605833 Neighboring gene Sharpr-MPRA regulatory region 15144 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19607854-19608615 Neighboring gene CRISPRi-validated cis-regulatory element chr22.250 Neighboring gene chromosome 3 open reading frame 38 pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env The exposure to HIV-1 or HIV-1 gp120 results in a significant downregulation of tight junction proteins ZO-1, Occludin, Claudin-1, Claudin-2, Claudin-3, Claudin-4, and Claudin-5 in human retinal pigment epithelial cells PubMed
    env HIV-1 JRFL and HXB2 Env (gp120) downregulates CLDN5 (Claudin-5) in ARPE-19 cells and is dependent upon MMP activation PubMed
    env Cannabinoid inhibits HIV-1 gp120-induced tight junction protein down-regulation of ZO-1, claudin-5, and JAM-1 in human brain micro vascular endothelial cells (HBMEC) PubMed
    env The expression of tight junction proteins ZO-1, JAM-2, Occludin, Claudin-3 and Claudin-5 is modulated by HIV-1 gp120, and the modulated TJ expression involves Rho-A activation PubMed
    Tat tat Exposure of brain micro vascular endothelial cells to HIV-1 Tat results in a decrease of claudin-1, claudin-5, and zonula occludens-2 expression and cellular redistribution of claudin-5, suggesting potential disturbance of the blood-brain barrier by Tat PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables structural molecule activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in bicellular tight junction assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell-cell junction assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in establishment of blood-retinal barrier IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in face morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in learning TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in maintenance of blood-brain barrier IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in maintenance of blood-brain barrier NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in myelination IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of angiogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of gene expression ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of vascular permeability IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in outflow tract morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of bicellular tight junction assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of establishment of endothelial barrier IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of gene expression ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of protein binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to ethanol IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in roof of mouth development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in tight junction assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in transforming growth factor beta receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Schmidt-Lanterman incisure IEA
    Inferred from Electronic Annotation
    more info
     
    located_in apicolateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in bicellular tight junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in bicellular tight junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in bicellular tight junction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cell junction TAS
    Traceable Author Statement
    more info
     
    located_in cell-cell junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cell-cell junction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    colocalizes_with cortical actin cytoskeleton IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lateral plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in paranode region of axon IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in tight junction IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    claudin-5
    Names
    transmembrane protein deleted in VCFS
    transmembrane protein deleted in velocardiofacial syndrome

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001130861.1NP_001124333.1  claudin-5 isoform 1

      See identical proteins and their annotated locations for NP_001124333.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes a protein of 303 aa (isoform 1). A common SNP (rs885985) encodes a stop codon in the 5' coding region and thus, for some haplotypes, translation is predicted to initiate from a downstream AUG to produce a protein of 218 aa (isoform 2).
      Source sequence(s)
      AK092561, AK124019, BU688528
      Consensus CDS
      CCDS13763.2
      UniProtKB/TrEMBL
      D3DX19
      Related
      ENSP00000384554.1, ENST00000403084.1
      Conserved Domains (1) summary
      cl21598
      Location:90266
      PMP22_Claudin; PMP-22/EMP/MP20/Claudin family
    2. NM_001363066.2NP_001349995.1  claudin-5 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) represents the predominant transcript and initiates transcription from a downstream promoter, compared to variant 1. It encodes a protein of 218 aa (isoform 2) with a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC000082, AK124019, BC032363
      Consensus CDS
      CCDS93118.1
      UniProtKB/Swiss-Prot
      B3KS11, O00501, Q53XW2, Q8WUW3
      UniProtKB/TrEMBL
      Q53HW4
      Related
      ENSP00000480623.1, ENST00000618236.2
      Conserved Domains (1) summary
      cl21598
      Location:5181
      PMP22_Claudin; PMP-22/EMP/MP20/Claudin family
    3. NM_001363067.2NP_001349996.1  claudin-5 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1, and encodes a protein (isoform 1) of 303 aa. A common SNP (rs885985) encodes a stop codon in the 5' coding region and thus, for some haplotypes, translation is predicted to initiate from a downstream AUG to produce a protein of 218 aa (isoform 2).
      Source sequence(s)
      AC000082
      Consensus CDS
      CCDS13763.2
      UniProtKB/TrEMBL
      D3DX19
      Conserved Domains (1) summary
      cl21598
      Location:90266
      PMP22_Claudin; PMP-22/EMP/MP20/Claudin family
    4. NM_001426402.1NP_001413331.1  claudin-5 isoform 2

      Status: REVIEWED

      Source sequence(s)
      CP068256
      UniProtKB/Swiss-Prot
      B3KS11, O00501, Q53XW2, Q8WUW3
      UniProtKB/TrEMBL
      Q53HW4
    5. NM_003277.4NP_003268.2  claudin-5 isoform 1

      See identical proteins and their annotated locations for NP_003268.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1, and encodes a protein (isoform 1) of 303 aa. A common SNP (rs885985) encodes a stop codon in the 5' coding region and thus, for some haplotypes, translation is predicted to initiate from a downstream AUG to produce a protein of 218 aa (isoform 2).
      Source sequence(s)
      AK092561, DB023636
      Consensus CDS
      CCDS13763.2
      UniProtKB/TrEMBL
      D3DX19
      Related
      ENSP00000400612.2, ENST00000413119.2
      Conserved Domains (1) summary
      cl21598
      Location:90266
      PMP22_Claudin; PMP-22/EMP/MP20/Claudin family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      19523024..19525337 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      19899865..19902178 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)