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    CDH9 cadherin 9 [ Homo sapiens (human) ]

    Gene ID: 1007, updated on 15-Jun-2019

    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 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (26880600..27038582, 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 FunctionsWhat'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

    Pathways from BioSystems

    • Adherens junctions interactions, organism-specific biosystem (from REACTOME)
      Adherens junctions interactions, organism-specific biosystemThe adherens junctions (AJ) are multiprotein complexes that promote homotypic cell adhesion in nearly all types of tissue by linking membrane and cytoskeletal components at discrete contact regions (...
    • Cell junction organization, organism-specific biosystem (from REACTOME)
      Cell junction organization, organism-specific biosystem
      Cell junction organization
    • Cell-Cell communication, organism-specific biosystem (from REACTOME)
      Cell-Cell communication, organism-specific biosystemCell-to-Cell communication is crucial for multicellular organisms because it allows organisms to coordinate the activity of their cells. Some cell-to-cell communication requires direct cell-cell cont...
    • Cell-cell junction organization, organism-specific biosystem (from REACTOME)
      Cell-cell junction organization, organism-specific biosystemEpithelial cell-cell contacts consist of three major adhesion systems: adherens junctions (AJs), tight junctions (TJs), and desmosomes. These adhesion systems differ in their function and compositio...

    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 
    cytoskeletal protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    molecular_function ND
    No biological Data available
    more info
     
    protein homodimerization activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell-cell adhesion NAS
    Non-traceable Author Statement
    more info
    PubMed 
    cell-cell adhesion mediated by cadherin IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell-cell junction assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    homophilic cell adhesion via plasma membrane adhesion molecules 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
    catenin complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell-cell adherens junction 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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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
      87617..245599
      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 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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