CDH9 cadherin 9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CDH9provided by HGNC
Official Full Name: cadherin 9provided by HGNC
Primary source: HGNC:HGNC:1768
See related: Ensembl:ENSG00000113100 MIM:609974; AllianceGenome:HGNC:1768
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
Summary: 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]
Expression: Biased expression in brain (RPKM 3.5) and kidney (RPKM 1.9) See more
Orthologs: mouse all
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Genomic context

Location:: 5p14.1

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (26880597..27038586, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (26985312..27143345, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (26880706..27038693, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

MiR-130b-3p promotes colorectal cancer progression by targeting CHD9.
Title: MiR-130b-3p promotes colorectal cancer progression by targeting CHD9.
The CC genotype of rs4307059 located in the region between CDH9 and CDH10 is associated with completed suicide in a Polish cohort
Title: Analysis of four genes involved in the neurodevelopment shows association of rs4307059 polymorphism in the cadherin 9/10 region with completed suicide.
Cadherin-9 is a reliable cell surface marker for fibroblasts in healthy and diseased kidneys.
Title: Cadherin-9 is a novel cell surface marker for the heterogeneous pool of renal fibroblasts.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: A genome-wide association study on common SNPs and rare CNVs in anorexia nervosa.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study on common SNPs and rare CNVs in anorexia nervosa. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common genetic variants on 5p14.1 associate with autism spectrum disorders. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic determinants of plasma &#x003b2;&#x02082;-glycoprotein I levels: a genome-wide association study in extended pedigrees from Spain. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetics of coronary artery calcification among African Americans, a meta-analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of prognosis in advanced non-small cell lung cancer patients receiving platinum-based chemotherapy. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH118785 (e-PCR)
- UniSTS:138286

CDH9_3 (e-PCR)
- UniSTS:277090

WI-14975 (e-PCR)
- UniSTS:47971

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables beta-catenin binding	IBA Inferred from Biological aspect of Ancestor more info
enables cadherin binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in adherens junction organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell adhesion	NAS Non-traceable Author Statement more info	PubMed
involved_in cell-cell adhesion mediated by cadherin	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell junction assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info
involved_in synapse assembly	IEA Inferred from Electronic Annotation more info
involved_in synaptic membrane adhesion	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
part_of catenin complex	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in postsynaptic membrane	IEA Inferred from Electronic Annotation more info
located_in presynaptic membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: cadherin-9

Names: T1-cadherin

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.