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Aliases for CDH9 Gene

Aliases for CDH9 Gene

  • Cadherin 9, Type 2 (T1-Cadherin) 2 3
  • T1-Cadherin 3
  • Cadherin-9 3

External Ids for CDH9 Gene

Previous GeneCards Identifiers for CDH9 Gene

  • GC05M026567
  • GC05M027314
  • GC05M026880
  • GC05M026926

Summaries for CDH9 Gene

Entrez Gene Summary for CDH9 Gene

  • This gene encodes a type II classical cadherin from the cadherin superfamily, integral membrane proteins that mediate calcium-dependent cell-cell adhesion. Mature cadherin proteins are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. The extracellular domain consists of 5 subdomains, each containing a cadherin motif, and appears to determine the specificity of the protein's homophilic cell adhesion activity. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. [provided by RefSeq, Jul 2008]

GeneCards Summary for CDH9 Gene

CDH9 (Cadherin 9, Type 2 (T1-Cadherin)) is a Protein Coding gene. Diseases associated with CDH9 include benign epilepsy with centrotemporal spikes. Among its related pathways are ERK Signaling and ERK Signaling. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is CDH19.

UniProtKB/Swiss-Prot for CDH9 Gene

  • Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types

Gene Wiki entry for CDH9 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDH9 Gene

Genomics for CDH9 Gene

Genomic Location for CDH9 Gene

26,880,600 bp from pter
27,121,150 bp from pter
240,551 bases
Minus strand

Genomic View for CDH9 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CDH9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDH9 Gene

Proteins for CDH9 Gene

  • Protein details for CDH9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • Q3B7I5

    Protein attributes for CDH9 Gene

    789 amino acids
    Molecular mass:
    88689 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CDH9 Gene

Proteomics data for CDH9 Gene at MOPED

Post-translational modifications for CDH9 Gene

  • Glycosylation at Asn255, Asn437, Asn455, and Asn536
  • Modification sites at PhosphoSitePlus

Other Protein References for CDH9 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for CDH9 Gene

Domains for CDH9 Gene

Gene Families for CDH9 Gene

  • MCDH :Cadherins / Major cadherins

Suggested Antigen Peptide Sequences for CDH9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Q9ULB4
  • Three calcium ions are usually bound at the interface of each cadherin domain and rigidify the connections, imparting a strong curvature to the full-length ectodomain.
  • Contains 5 cadherin domains.
genes like me logo Genes that share domains with CDH9: view

Function for CDH9 Gene

Molecular function for CDH9 Gene

UniProtKB/Swiss-Prot Function: Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types

Gene Ontology (GO) - Molecular Function for CDH9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with CDH9: view

Phenotypes for CDH9 Gene

GenomeRNAi human phenotypes for CDH9:
genes like me logo Genes that share phenotypes with CDH9: view

Animal Model Products

miRNA for CDH9 Gene

miRTarBase miRNAs that target CDH9

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for CDH9 Gene

Localization for CDH9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDH9 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

Jensen Localization Image for CDH9 Gene COMPARTMENTS Subcellular localization image for CDH9 gene
Compartment Confidence
plasma membrane 5
cytosol 1
golgi apparatus 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for CDH9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CDH9: view

Pathways for CDH9 Gene

genes like me logo Genes that share pathways with CDH9: view

Gene Ontology (GO) - Biological Process for CDH9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0016337 single organismal cell-cell adhesion NAS 10861224
GO:0034329 cell junction assembly TAS --
GO:0034332 adherens junction organization TAS --
GO:0045216 cell-cell junction organization TAS --
genes like me logo Genes that share ontologies with CDH9: view

Compounds for CDH9 Gene

(1) HMDB Compounds for CDH9 Gene

Compound Synonyms Cas Number PubMed IDs
  • Ca
genes like me logo Genes that share compounds with CDH9: view

Transcripts for CDH9 Gene

mRNA/cDNA for CDH9 Gene

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

Unigene Clusters for CDH9 Gene

Cadherin 9, type 2 (T1-cadherin):
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CDH9

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for CDH9

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CDH9 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13
SP1: -

Relevant External Links for CDH9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CDH9 Gene

mRNA expression in normal human tissues for CDH9 Gene

mRNA differential expression in normal tissues according to GTEx for CDH9 Gene

This gene is overexpressed in Brain - Anterior cingulate cortex (BA24) (8.3), Brain - Nucleus accumbens (basal ganglia) (7.6), Brain - Cortex (7.5), Brain - Frontal Cortex (BA9) (7.2), Brain - Amygdala (5.2), and Brain - Putamen (basal ganglia) (4.2).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for CDH9 Gene

SOURCE GeneReport for Unigene cluster for CDH9 Gene Hs.272212

genes like me logo Genes that share expressions with CDH9: view

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for CDH9 Gene

Orthologs for CDH9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CDH9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CDH9 35
  • 99.7 (n)
  • 99.75 (a)
CDH9 36
  • 100 (a)
(Bos Taurus)
Mammalia CDH9 35
  • 91.14 (n)
  • 94.84 (a)
CDH9 36
  • 95 (a)
(Canis familiaris)
Mammalia CDH9 35
  • 91.85 (n)
  • 94.93 (a)
CDH9 36
  • 95 (a)
(Mus musculus)
Mammalia Cdh9 35
  • 86.47 (n)
  • 91.22 (a)
Cdh9 16
Cdh9 36
  • 91 (a)
(Monodelphis domestica)
Mammalia CDH9 36
  • 90 (a)
(Ornithorhynchus anatinus)
Mammalia CDH9 36
  • 84 (a)
(Rattus norvegicus)
Mammalia Cdh9 35
  • 86.97 (n)
  • 92.13 (a)
(Gallus gallus)
Aves CDH9 35
  • 79.26 (n)
  • 83.65 (a)
CDH9 36
  • 84 (a)
(Anolis carolinensis)
Reptilia CDH9 36
  • 83 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cdh9 35
  • 71.79 (n)
  • 72.05 (a)
(Danio rerio)
Actinopterygii CABZ01067945.1 36
  • 65 (a)
cdh10 36
  • 62 (a)
cdh6 36
  • 61 (a)
Species with no ortholog for CDH9:
  • 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)
  • 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)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CDH9 Gene

Gene Tree for CDH9 (if available)
Gene Tree for CDH9 (if available)

Paralogs for CDH9 Gene

Paralogs for CDH9 Gene

Selected SIMAP similar genes for CDH9 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with CDH9: view

Variants for CDH9 Gene

Sequence variations from dbSNP and Humsavar for CDH9 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type MAF
rs765947 -- 27,015,613(-) TTTAG(G/T)AACAG intron-variant
rs765948 -- 27,015,556(-) TGATA(A/T)ATATA intron-variant
rs891030 -- 27,013,812(-) ACACT(A/G)TTACA intron-variant
rs891031 -- 27,013,012(-) TGGCC(C/T)GTGCT intron-variant
rs919338 -- 26,983,550(-) GAGGC(A/G)AGTTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CDH9 Gene

Variant ID Type Subtype PubMed ID
nsv462021 CNV Gain 19166990
nsv880920 CNV Loss 21882294
dgv5993n71 CNV Loss 21882294
dgv1787e1 CNV Complex 17122850
nsv880473 CNV Loss 21882294
nsv462023 CNV Loss 19166990
nsv462024 CNV Loss 19166990
esv1001329 CNV Insertion 20482838
nsv880889 CNV Loss 21882294
dgv5995n71 CNV Loss 21882294
nsv881006 CNV Loss 21882294

Relevant External Links for CDH9 Gene

HapMap Linkage Disequilibrium report

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDH9 Gene

Disorders for CDH9 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (1) Diseases for CDH9 Gene including...

Search for CDH9 Gene in MalaCards »

(2) University of Copenhagen DISEASES for CDH9 Gene

Relevant External Links for CDH9

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with CDH9: view

No data available for UniProtKB/Swiss-Prot for CDH9 Gene

Publications for CDH9 Gene

  1. Identification of three human type-II classic cadherins and frequent heterophilic interactions between different subclasses of type-II classic cadherins. (PMID: 10861224) Shimoyama Y. … Natori M. (Biochem. J. 2000) 3 4 23
  2. Cadherin-9 is a novel cell surface marker for the heterogeneous pool of renal fibroblasts. (PMID: 17668045) Thedieck C. … Klein G. (PLoS ONE 2007) 3 23
  3. Diversity of the cadherin family: evidence for eight new cadherins in nervous tissue. (PMID: 2059658) Suzuki S. … Tanihara H. (Cell Regul. 1991) 2 3
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  5. Common genetic variants on 5p14.1 associate with autism spectrum disorders. (PMID: 19404256) Wang K. … Hakonarson H. (Nature 2009) 3 48

Products for CDH9 Gene

Sources for CDH9 Gene

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