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CLDN9 claudin 9 [ Homo sapiens (human) ]

Gene ID: 9080, updated on 17-Sep-2024

Summary

Official Symbol
CLDN9provided by HGNC
Official Full Name
claudin 9provided by HGNC
Primary source
HGNC:HGNC:2051
See related
Ensembl:ENSG00000213937 MIM:615799; AllianceGenome:HGNC:2051
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
DFNB116
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, 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]
Orthologs
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Genomic context

See CLDN9 in Genome Data Viewer
Location:
16p13.3
Exon count:
1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (3012923..3014505)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (3039495..3041077)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (3062924..3064506)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene progestin and adipoQ receptor family member 4 Neighboring gene protein kinase, membrane associated tyrosine/threonine 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3029137-3030013 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3030014-3030889 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3030890-3031766 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3032811-3033312 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7098 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:3033737-3033923 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3037455-3038406 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3038407-3039356 Neighboring gene glycine rich extracellular protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3043721-3044222 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3045542-3046514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3048182-3048682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3048683-3049183 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3051481-3052017 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr16:3053764-3054722 Neighboring gene Sharpr-MPRA regulatory region 8596 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3057599-3058558 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3058559-3059516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3061783-3062608 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:3064184-3064351 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3065208-3065772 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:3066992-3067588 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:3067589-3068185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3068783-3069378 Neighboring gene claudin 6 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:3070698-3071897 Neighboring gene TNF receptor superfamily member 12A

Genomic regions, transcripts, and products

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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
 
enables virus receptor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 symbiont entry into host cell IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in bicellular tight junction IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in bicellular tight junction ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in cell junction IDA
Inferred from Direct Assay
more info
 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
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 plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 

NCBI Reference Sequences (RefSeq)

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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_020982.4NP_066192.1  claudin-9

    See identical proteins and their annotated locations for NP_066192.1

    Status: REVIEWED

    Source sequence(s)
    AI791760, AK091002, BC051870
    Consensus CDS
    CCDS10487.1
    UniProtKB/Swiss-Prot
    O95484
    Related
    ENSP00000398017.2, ENST00000445369.3
    Conserved Domains (1) summary
    cl21598
    Location:4163
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    3012923..3014505
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    3039495..3041077
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)