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CDH9 cadherin 9 [ Homo sapiens (human) ]

Gene ID: 1007, updated on 4-Jan-2025

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
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Genomic context

See CDH9 in Genome Data Viewer
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_000005.10Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak5190 silencer Neighboring gene cyclin B3 pseudogene 1 Neighboring gene uncharacterized LOC124901159 Neighboring gene MPRA-validated peak5192 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:27094263-27094762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:27119569-27120128 Neighboring gene RNA, U6 small nuclear 738, pseudogene Neighboring gene MPRA-validated peak5193 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:27290183-27290742 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:27315951-27316500 Neighboring gene uncharacterized LOC105374695

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
A genome-wide association study on common SNPs and rare CNVs in anorexia nervosa.
EBI GWAS Catalog
Common genetic variants on 5p14.1 associate with autism spectrum disorders.
EBI GWAS Catalog
Genetic determinants of plasma β₂-glycoprotein I levels: a genome-wide association study in extended pedigrees from Spain.
EBI GWAS Catalog
Genetics of coronary artery calcification among African Americans, a meta-analysis.
EBI GWAS Catalog
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
EBI GWAS Catalog
Genome-wide association study of prognosis in advanced non-small cell lung cancer patients receiving platinum-based chemotherapy.
EBI GWAS Catalog

Interactions

General gene information

Clone Names

  • MGC125386

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables beta-catenin binding  
enables cadherin binding  
enables calcium ion binding  
Process Evidence Code Pubs
involved_in adherens junction organization  
involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules  
involved_in cell migration  
involved_in cell morphogenesis  
involved_in cell-cell adhesion PubMed 
involved_in cell-cell adhesion mediated by cadherin  
involved_in cell-cell junction assembly  
involved_in homophilic cell adhesion via plasma membrane adhesion molecules  
involved_in synapse assembly  
involved_in synaptic membrane adhesion  
Component Evidence Code Pubs
is_active_in adherens junction  
part_of catenin complex  
located_in plasma membrane  
located_in postsynaptic membrane  
located_in presynaptic membrane  

General protein information

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.

Genomic

  1. NG_046968.1 RefSeqGene

    Range
    87613..245602
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_016279.4NP_057363.3  cadherin-9 preproprotein

    See identical proteins and their annotated locations for NP_057363.3

    Status: REVIEWED

    Source sequence(s)
    AB035302, AC010470, AC022450, BC107594, DA165253
    Consensus CDS
    CCDS3893.1
    UniProtKB/Swiss-Prot
    Q3B7I5, Q9ULB4
    Related
    ENSP00000231021.4, ENST00000231021.9
    Conserved Domains (2) summary
    cd11304
    Location:164264
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam01049
    Location:645782
    Cadherin_C; Cadherin cytoplasmic region

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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    26880597..27038586 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    26985312..27143345 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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