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Aliases for CLDN9 Gene

Aliases for CLDN9 Gene

  • Claudin 9 2 3 5
  • Claudin-9 3

External Ids for CLDN9 Gene

Previous GeneCards Identifiers for CLDN9 Gene

  • GC16P003083
  • GC16P003096
  • GC16P003062
  • GC16P003064
  • GC16P003002
  • GC16P003035

Summaries for CLDN9 Gene

Entrez Gene Summary for CLDN9 Gene

  • 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 protein is one of the entry cofactors for hepatitis C virus. Mouse studies revealed that this gene is required for the preservation of sensory cells in the hearing organ and the gene deficiency is associated with deafness. [provided by RefSeq, Jun 2010]

GeneCards Summary for CLDN9 Gene

CLDN9 (Claudin 9) is a Protein Coding gene. Diseases associated with CLDN9 include Hepatitis C and Hepatitis. Among its related pathways are Blood-Brain Barrier and Immune Cell Transmigration: VCAM-1/CD106 Signaling Pathways and Sertoli-Sertoli Cell Junction Dynamics. Gene Ontology (GO) annotations related to this gene include identical protein binding and structural molecule activity. An important paralog of this gene is CLDN6.

UniProtKB/Swiss-Prot for CLDN9 Gene

  • Plays a major role in tight junction-specific obliteration of the intercellular space, through calcium-independent cell-adhesion activity.

  • (Microbial infection) Acts as a receptor for hepatitis C virus (HCV) entry into hepatic cells.

Gene Wiki entry for CLDN9 Gene

Additional gene information for CLDN9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLDN9 Gene

Genomics for CLDN9 Gene

GeneHancer (GH) Regulatory Elements for CLDN9 Gene

Promoters and enhancers for CLDN9 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J003012 Enhancer 1 Ensembl ENCODE 650.7 +0.4 430 1.7 CTCF KLF1 KLF17 MAX SIN3A BMI1 ZIC2 RAD21 YY1 HIC1 CLDN9 PIR52190 ENSG00000272079 IL32 PGP TNFRSF12A
GH16J003013 Enhancer 0.6 ENCODE 650.7 +1.4 1376 0.1 RXRA USF2 MAX RAD21 YY1 SP1 ZGPAT POLR2A HNF4A ZBTB33 CLDN9 PIR52190 TNFRSF12A
GH16J003003 Promoter/Enhancer 2.1 FANTOM5 Ensembl ENCODE dbSUPER 7.1 -4.6 -4640 8.4 CLOCK MLX DMAP1 YY1 E2F8 ZNF143 SP3 NFYC MEF2D GLIS1 ENSG00000272079 LOC105371056 CREBBP ZNF597 MMP25 AMDHD2 SRRM2 ZNF598 ZNF263 ZNF200
GH16J003052 Enhancer 1 Ensembl ENCODE dbSUPER 11.7 +42.0 41980 3.7 BCOR ZBTB21 ZMYM3 GABPA ZNF366 POLR2A ZNF184 GABPB1 CREM ZBTB17 GC16P003540 MMP25 BICDL2 IL32 CLDN6 TNFRSF12A ZNF205 CLDN9 PKMYT1 MMP25-AS1
GH16J003017 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 0.4 +5.5 5459 1.8 ATF1 SIN3A RAD21 ETS1 ZNF143 ATF7 CREM THAP11 SP5 REST CLDN6 TNFRSF12A PKMYT1 BICDL2 ENSG00000272079 CLDN9
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CLDN9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLDN9 gene promoter:

Genomic Locations for CLDN9 Gene

Genomic Locations for CLDN9 Gene
chr16:3,012,456-3,014,505
(GRCh38/hg38)
Size:
2,050 bases
Orientation:
Plus strand
chr16:3,062,457-3,064,506
(GRCh37/hg19)

Genomic View for CLDN9 Gene

Genes around CLDN9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLDN9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLDN9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLDN9 Gene

Proteins for CLDN9 Gene

  • Protein details for CLDN9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95484-CLD9_HUMAN
    Recommended name:
    Claudin-9
    Protein Accession:
    O95484

    Protein attributes for CLDN9 Gene

    Size:
    217 amino acids
    Molecular mass:
    22848 Da
    Quaternary structure:
    • Interacts with CLDN1, CD81 and OCLN (PubMed:20375010).

neXtProt entry for CLDN9 Gene

Post-translational modifications for CLDN9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLDN9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLDN9 Gene

Domains & Families for CLDN9 Gene

Gene Families for CLDN9 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for CLDN9 Gene

Suggested Antigen Peptide Sequences for CLDN9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O95484

UniProtKB/Swiss-Prot:

CLD9_HUMAN :
  • Belongs to the claudin family.
Family:
  • Belongs to the claudin family.
genes like me logo Genes that share domains with CLDN9: view

Function for CLDN9 Gene

Molecular function for CLDN9 Gene

UniProtKB/Swiss-Prot Function:
Plays a major role in tight junction-specific obliteration of the intercellular space, through calcium-independent cell-adhesion activity.
UniProtKB/Swiss-Prot Function:
(Microbial infection) Acts as a receptor for hepatitis C virus (HCV) entry into hepatic cells.
GENATLAS Biochemistry:
claudin 9,clostridium perfringens enterotoxin receptor,integral membrane protein,claudin family of major structural components of tight junction (TJ) strands

Gene Ontology (GO) - Molecular Function for CLDN9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001618 virus receptor activity IMP 20375010
GO:0005198 structural molecule activity IEA --
GO:0005515 protein binding IPI 20375010
GO:0042802 identical protein binding ISS --
genes like me logo Genes that share ontologies with CLDN9: view
genes like me logo Genes that share phenotypes with CLDN9: view

Animal Model Products

CRISPR Products

miRNA for CLDN9 Gene

miRTarBase miRNAs that target CLDN9

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLDN9

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CLDN9 Gene

Localization for CLDN9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLDN9 Gene

Cell junction, tight junction. Cell membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLDN9 gene
Compartment Confidence
plasma membrane 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (3)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLDN9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IDA,IEA 20375010
GO:0005923 bicellular tight junction ISS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA,IDA --
genes like me logo Genes that share ontologies with CLDN9: view

Pathways & Interactions for CLDN9 Gene

genes like me logo Genes that share pathways with CLDN9: view

Gene Ontology (GO) - Biological Process for CLDN9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016032 viral process IEA --
GO:0016338 calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules ISS --
GO:0045216 cell-cell junction organization IEA --
GO:0046718 viral entry into host cell IEA --
genes like me logo Genes that share ontologies with CLDN9: view

No data available for SIGNOR curated interactions for CLDN9 Gene

Drugs & Compounds for CLDN9 Gene

(1) Drugs for CLDN9 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with CLDN9: view

Transcripts for CLDN9 Gene

mRNA/cDNA for CLDN9 Gene

(2) Selected AceView cDNA sequences:
(4) Additional mRNA sequences :
(1) REFSEQ mRNAs :
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CLDN9 Gene

Claudin 9:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLDN9

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLDN9 Gene

No ASD Table

Relevant External Links for CLDN9 Gene

GeneLoc Exon Structure for
CLDN9
ECgene alternative splicing isoforms for
CLDN9

Expression for CLDN9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLDN9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLDN9 Gene

This gene is overexpressed in Whole Blood (x12.2), Pituitary (x9.2), Brain - Cerebellum (x7.0), and Brain - Cerebellar Hemisphere (x6.9).

NURSA nuclear receptor signaling pathways regulating expression of CLDN9 Gene:

CLDN9

SOURCE GeneReport for Unigene cluster for CLDN9 Gene:

Hs.296949

mRNA Expression by UniProt/SwissProt for CLDN9 Gene:

O95484-CLD9_HUMAN
Tissue specificity: Expressed in the liver, in peripheral blood mononuclear cells and hepatocarcinoma cell lines.

Evidence on tissue expression from TISSUES for CLDN9 Gene

  • Eye(4.1)
  • Nervous system(4)
genes like me logo Genes that share expression patterns with CLDN9: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLDN9 Gene

Orthologs for CLDN9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLDN9 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLDN9 34 33
  • 99.08 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CLDN9 34
  • 93 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CLDN9 34 33
  • 91.71 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CLDN9 34 33
  • 90.17 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Cldn9 33
  • 87.56 (n)
mouse
(Mus musculus)
Mammalia Cldn9 16 34 33
  • 86.94 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 64 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii cldnc 33
  • 62.37 (n)
Species where no ortholog for CLDN9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CLDN9 Gene

ENSEMBL:
Gene Tree for CLDN9 (if available)
TreeFam:
Gene Tree for CLDN9 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLDN9: view image

Paralogs for CLDN9 Gene

Paralogs for CLDN9 Gene

(19) SIMAP similar genes for CLDN9 Gene using alignment to 1 proteins:

  • CLD9_HUMAN
genes like me logo Genes that share paralogs with CLDN9: view

Variants for CLDN9 Gene

Sequence variations from dbSNP and Humsavar for CLDN9 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1000419818 -- 3,011,243(+) C/T upstream_transcript_variant
rs1001541212 -- 3,010,897(+) C/G upstream_transcript_variant
rs1002111012 -- 3,014,343(+) A/C 3_prime_UTR_variant
rs1002201661 -- 3,012,913(+) G/A 5_prime_UTR_variant
rs1002891854 -- 3,012,741(+) T/C 5_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for CLDN9 Gene

Variant ID Type Subtype PubMed ID
nsv509588 CNV insertion 20534489
nsv510673 CNV deletion 20534489
nsv952906 CNV deletion 24416366

Variation tolerance for CLDN9 Gene

Residual Variation Intolerance Score: 37.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.89; 18.45% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLDN9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLDN9

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLDN9 Gene

Disorders for CLDN9 Gene

MalaCards: The human disease database

(4) MalaCards diseases for CLDN9 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
hepatitis c
  • chronic hepatitis c
hepatitis
  • hepatitis a
hepatitis c virus
  • hepatitis c virus, susceptibility to
deafness, autosomal recessive 49
  • dfnb49
- elite association - COSMIC cancer census association via MalaCards
Search CLDN9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CLDN9

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CLDN9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLDN9 Gene

Publications for CLDN9 Gene

  1. Claudin association with CD81 defines hepatitis C virus entry. (PMID: 20375010) Harris HJ … McKeating JA (The Journal of biological chemistry 2010) 3 4 58
  2. Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity. (PMID: 19773279) Hosgood HD … Lan Q (Occupational and environmental medicine 2009) 3 44 58
  3. The tight junction proteins claudin-1, -6, and -9 are entry cofactors for hepatitis C virus. (PMID: 18234789) Meertens L … Dragic T (Journal of virology 2008) 2 3 58
  4. Claudin-6 and claudin-9 function as additional coreceptors for hepatitis C virus. (PMID: 17804490) Zheng A … Deng H (Journal of virology 2007) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for CLDN9 Gene

Sources for CLDN9 Gene

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