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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

CLDN9 Gene

protein-coding GIFtS: 53
GCID: GC16P003062

claudin 9

Explore 7 diseases affiliated with
CLDN9 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Claudin 9¹ ²
Claudin-9¹

External Ids:	HGNC: 2051¹	Entrez Gene: 9080²	Ensembl: ENSG00000213937⁷	UniProtKB: O95484³

Export aliases for CLDN9 gene to outside databases

Previous GC identifers: GC16P003083 GC16P003096 GC16P003064 GC16P003002 GC16P003035

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for CLDN9:

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)

UniProtKB/Swiss-Prot: CLD9_HUMAN, O95484

Function: Plays a major role in tight junction-specific obliteration of the intercellular space, through

calcium-independent cell-adhesion activity (By similarity)

Gene Wiki entry for CLDN9

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000016.9 NC_018927.1 NT_010393.16

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the CLDN9 gene promoter:
COUP-TF1 AP-1 ATF-2 MyoD COUP HNF-4alpha2 HNF-4alpha1 COUP-TF c-Jun
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: CLDN9 promoter sequence

Search SABiosciences Chromatin IP Primers for CLDN9

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CLDN9

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16p13.3 Ensembl cytogenetic band: 16p13.3 HGNC cytogenetic band: 16p13.3

CLDN9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLDN9 gene location

GeneLoc information about chromosome 16 GeneLoc Exon Structure

GeneLoc location for GC16P003062: view genomic region (about GC identifiers)

Start:	3,062,457 bp from pter	End:	3,064,506 bp from pter
Size:	2,050 bases	Orientation:	plus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: CLD9_HUMAN, O95484 (See protein sequence)

Recommended Name: Claudin-9

Size: 217 amino acids; 22848 Da

Subcellular location: Cell junction, tight junction. Cell membrane; Multi-pass membrane protein

Explore the universe of human proteins at neXtProt for CLDN9: NX_O95484

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_O95484

CLDN9 Protein expression data from MOPED and PaxDb: --

REFSEQ proteins: NP_066192.1

ENSEMBL proteins:

ENSP00000398017

Reactome Protein details: O95484
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Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005886	plasma membrane	IEA	--
GO:0005923	tight junction	ISS	--
GO:0016021	integral to membrane	IEA	--

CLDN9 for ontologies About GeneDecksing

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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

CLDN9 for domains About GeneDecksing

4 InterPro domains/families:

IPR017974 Claudin_CS

IPR003553 Claudin9

IPR006187 Claudin

IPR004031 PMP22/EMP/MP20/Claudin

Graphical View of Domain Structure for InterPro Entry O95484

ProtoNet protein and cluster: O95484

2 Blocks protein families:

IPB003553 Claudin-9 signature

IPB006187 Claudin family signature

UniProtKB/Swiss-Prot: CLD9_HUMAN, O95484

Similarity: Belongs to the claudin family

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

UniProtKB/Swiss-Prot: CLD9_HUMAN, O95484

Function: Plays a major role in tight junction-specific obliteration of the intercellular space, through

calcium-independent cell-adhesion activity (By similarity)

Genatlas biochemistry entry for CLDN9:

claudin 9,clostridium perfringens enterotoxin receptor,integral membrane protein,claudin family of major structural

components of tight junction (TJ) strands

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		1 QIAGEN miScript miRNA Assays for microRNA that regulate CLDN9:
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In Situ Assay
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLDN9

Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005198	structural molecule activity	IEA	--
GO:0042802	identical protein binding	ISS	--

CLDN9 for ontologies About GeneDecksing

Animal Models:
3 MGI mutant phenotypes (inferred from 1 allele) (MGI details for Cldn9):

behavior/neurological

hearing/vestibular/ear

nervous system

CLDN9 for phenotypes About GeneDecksing

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways - 5/7 super-pathways (see all 7) About this table

See pathways by source

Super-pathway

contained gene-specific pathways

Cell-cell junction organization

	Cell-cell junction organization	1.00			Tight junction interactions	0.49
	Cell junction organization	0.69			Cell-Cell communication	0.45

Sertoli-Sertoli Cell Junction Dynamics

Sertoli-Sertoli Cell Junction Dynamics

1.00

Epithelial Tight Junctions

0.36

Hepatitis C

Hepatitis C

1.00

Leukocyte transendothelial migration

Leukocyte transendothelial migration

1.00

Tight junction

Tight junction

1.00

Pathway sources
See GeneCards unified pathways
Show all pathways

3 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for CLDN9

	Sertoli-Sertoli Cell Junction Dynamics
	Epithelial Tight Junctions
	Transendothelial Migration of Leukocytes

4 Reactome Pathways for CLDN9

	Tight junction interactions
	Cell junction organization
	Cell-Cell communication
	Cell-cell junction organization

4 Kegg Pathways (Kegg details for CLDN9):

	Cell adhesion molecules (CAMs)
	Tight junction
	Leukocyte transendothelial migration
	Hepatitis C

CLDN9 for pathways About GeneDecksing

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for CLDN9

Gene Ontology (GO): 4 biological process terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0016338	calcium-independent cell-cell adhesion	ISS	--
GO:0034329	cell junction assembly	TAS	--
GO:0045216	cell-cell junction organization	TAS	--
GO:0070830	tight junction assembly	TAS	--

CLDN9 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for CLDN9

1 HMDB Compound for CLDN9 About this table

Compound	Synonyms	CAS #	PubMed Ids
Calcium	Ca (see all 2)	7440-70-2	--

Search CenterWatch for drugs/clinical trials and news about CLDN9 / CLD9

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for CLDN9 gene:

NM_020982.3

Unigene Cluster for CLDN9:

Claudin 9

Hs.296949 [show with all ESTs]

Unigene Representative Sequence: NM_020982

1 Ensembl transcript including schematic representation, and UCSC links where relevant:

ENST00000445369(uc010uwo.1)

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		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat CLDN9
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		hsa-miR-105
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Additional cDNA sequence:

AK091002.1 AY390431.1 BC051870.1 BC065830.1

2 DOTS entries:

DT.100711963 DT.40127055

2 AceView cDNA sequences:

AY390431 AK091002

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

CLDN9 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: CCCTCCCAAC

About this image

CLDN9 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

2 LifeMap In Vivo Development Anatomical Compartments/Cells

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Yolk Sac

Definitive Yolk Sac

Definitive Hematopoietic Stem Cells

Blood

Head Mesenchyme

Frontonasal Process

Head Mesenchyme

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

Genevestigator expression for CLDN9

SOURCE GeneReport for Unigene cluster: Hs.296949

SABiosciences Expression via Pathway-Focused PCR Arrays including CLDN9:

Tight Junctions in human mouse rat

Cell Junction PathwayFinder in human mouse rat

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In Situ
Assay Products:

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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of chordates.

Orthologs for CLDN9 gene from 2/9 species (see all 9) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	LOC417474¹	claudin-3-like	69.31(n) 61.21(a)		417474 XM_003642385.1 XP_003642433.1
zebrafish (Danio rerio)	Actinopterygii	cldnc¹	claudin c	62.37(n) 62.21(a)		81582 NM_131764.1 NP_571839.1

ENSEMBL Gene Tree for CLDN9 (if available)
TreeFam Gene Tree for CLDN9 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for CLDN9 gene

CLDN4² CLDN8² CLDN20² CLDN17² CLDN5² CLDN2² CLDN10² CLDN15²

CLDN3² CLDN1² CLDN14² CLDN6² CLDN7² CLDN19²

18/19 SIMAP similar genes for CLDN9 using alignment to 1 protein entry: CLD9_HUMAN(see all similar genes):

CLDN4 CLDN3 CLDN6 CLDN7 CLDN5 CLDN8

CLDN2 CLDN1 CLDN17 CLDN19 CLDN14 CLDN18

CLDN10 CLDN20 CLDN22 CLDN24 CLDN15 CLDN25

CLDN9 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 16 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs80021503^1,2		--	3060483(+)	`ATGGAG/TTGCGG`	1	--	us2k¹		0	--	--	--	--
rs187868099^1,2		--	3060514(+)	`GCAGAC/TTCTAA`	1	--	us2k¹		0	--	--	--	--
rs2023913^1,2	C,F,A,H,	--	3060543(-)	`GAGGTA/GGGAGG`	1	--	us2k¹		4		NA WA CSA EA	126
rs57156178^1,2	F,	--	3060608(+)	`TGTGTA/GTATAT`	1	--	us2k¹		1		WA	118
rs200635505^1,2		--	3060620(+)	`ATATA-/TTATAT`	1	--	us2k¹		0	--	--	--	--
rs201253961^1,2		--	3060622(+)	`ATATA-/TTATTT`	1	--	us2k¹		0	--	--	--	--
rs148424713^1,2		--	3060623(+)	`ATATA-/TTTTTT`	1	--	us2k¹		0	--	--	--	--
rs34118424^1,2	C,	--	3060624(+)	`TATAT-/ATTTTT`	1	--	us2k¹		0	--	--	--	--
rs1548539^1,2		--	3060626(-)	`aaaaaA/Tatata`	1	--	us2k¹		1		NA	2
rs201914952^1,2		--	3060627(+)	`TATTT-/ATTTTT`	1	--	us2k¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for CLDN9 (3062457 - 3064506 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for CLDN9: --

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing CLDN9

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

CLDN9 for disorders About GeneDecksing

7 diseases for CLDN9: About MalaCards

hepatitis c endolymphatic hydrops hepatitis gastric adenocarcinoma

gastric cancer adenocarcinoma prostatitis

1 disease from the University of Copenhagen DISEASES database for CLDN9:

Endolymphatic hydrops

Human Genome Epidemiology (HuGE) Navigator: CLDN9 (1 document)

Export disorders for CLDN9 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for CLDN9 gene, integrated from 9 sources (see all 23):
(articles sorted by number of sources associating them with CLDN9)

Utopia: connect your pdf to the dynamic
world of online information

The tight junction proteins claudin-1, -6, and -9 are entry cofactors for hepatitis C virus. (PubMed id 18234789)^{1, 3} Meertens L....Dragic T. (2008)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S....Malek J. (2004)
Analysis of a human gene homologous to rat ventral prostate.1 protein. (PubMed id 9441748)^{1, 3} Peacock R.E.... Inglehearn C.F. (1997)
Claudin-6, 7, or 9 overexpression in the human gastri c adenocarcinoma cell line AGS increases its invasiveness, migration, and proli feration rate. (PubMed id 20874001)¹ Zavala-Zendejas V.E....Rendon-Huerta E.P. (2011)
Distribution and expression pattern of claudins 6, 7, and 9 in diffuse- and intestinal-type gastric adenocarcinomas. (PubMed id 19960275)¹ RendA^n-Huerta E....MontaA+o L.F. (2010)
A claudin-9-based ion permeability barrier is essenti al for hearing. (PubMed id 19696885)¹ Nakano Y....BA!nfi B. (2009)
Association between genetic variants in VEGF, ERCC3 a nd occupational benzene haematotoxicity. (PubMed id 19773279)¹ Hosgood H.D....Lan Q. (2009)
The claudins. (PubMed id 19706201)¹ Lal-Nag M. and Morin P.J. (2009)
Structure and function of claudins. (PubMed id 18036336)¹ Krause G....Blasig I.E. (2008)
Claudin-6 and claudin-9 function as additional coreceptors for hepatitis C virus. (PubMed id 17804490)¹ Zheng A....Deng H. (2007)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 9080	HGNC: 2051	AceView: CLDN9	Ensembl:ENSG00000213937	euGenes: HUgn9080
ECgene: CLDN9	Kegg: 9080	H-InvDB: CLDN9

(According to HUGE)
About This Section

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for CLDN9	Pharmacogenomics, SNPs, Pathways

Intellectual Property for CLDN9 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for CLDN9 gene:
Search GeneIP for patents involving CLDN9

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section


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	Browse OriGene Antibodies		OriGene shRNA RFP for CLDN9
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	QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat CLDN9
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GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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Category			VWF (GIFTS: 73) von Willebrand factor
GIFtS Group

The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

The GeneCards Human Gene Database

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

Hot genes Disease genes CLDN9 gene at Home site.

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CLDN9 Gene

claudin 9

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CLDN9 Gene

claudin 9

Aliasesfor CLDN9 gene

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