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CDH9 cadherin 9 [ Homo sapiens (human) ]

Gene ID: 1007, updated on 4-Jun-2020

Summary

Official Symbol
CDH9provided by HGNC
Official Full Name
cadherin 9provided by HGNC
Primary source
HGNC:HGNC:1768
See related
Ensembl:ENSG00000113100 MIM:609974
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

Genomic context

See CDH9 in Genome Data Viewer
Location:
5p14.1
Exon count:
12
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (26880597..27038586, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (26880709..27038689, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene RNA, U4 small nuclear 43, pseudogene Neighboring gene cyclin B3 pseudogene 1 Neighboring gene RNA, U6 small nuclear 738, pseudogene Neighboring gene uncharacterized LOC105374695

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC125386

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cadherin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
molecular_function ND
No biological Data available
more info
 
Process Evidence Code Pubs
adherens junction organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
adherens junction organization TAS
Traceable Author Statement
more info
 
calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell adhesion NAS
Non-traceable Author Statement
more info
PubMed 
cell-cell adhesion via plasma-membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell junction assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synapse assembly IEA
Inferred from Electronic Annotation
more info
 
synaptic membrane adhesion IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
catenin complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of presynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
cadherin-9
Names
T1-cadherin

NCBI Reference Sequences (RefSeq)

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
    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: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

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