U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Cdh9 cadherin 9 [ Mus musculus (house mouse) ]

    Gene ID: 12565, updated on 2-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Cdh9provided by MGI
    Official Full Name
    cadherin 9provided by MGI
    Primary source
    MGI:MGI:107433
    See related
    Ensembl:ENSMUSG00000025370 AllianceGenome:MGI:107433
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Summary
    Enables cadherin binding activity involved in cell-cell adhesion and identical protein binding activity. Involved in synapse assembly and synaptic membrane adhesion. Located in axon and dendrite. Is active in glutamatergic synapse; hippocampal mossy fiber to CA3 synapse; and synaptic membrane. Is expressed in several structures, including limb; nervous system; sensory organ; and testis. Orthologous to human CDH9 (cadherin 9). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in frontal lobe adult (RPKM 2.5), CNS E18 (RPKM 2.4) and 6 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Cdh9 in Genome Data Viewer
    Location:
    15 A2; 15 7.91 cM
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (16728641..16857224)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (16728550..16857138)

    Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 41276 Neighboring gene STARR-seq mESC enhancer starr_38080 Neighboring gene STARR-seq mESC enhancer starr_38081 Neighboring gene STARR-seq mESC enhancer starr_38082 Neighboring gene predicted gene 2611 Neighboring gene STARR-seq mESC enhancer starr_38085 Neighboring gene STARR-seq mESC enhancer starr_38086 Neighboring gene STARR-seq mESC enhancer starr_38087 Neighboring gene STARR-seq mESC enhancer starr_38088 Neighboring gene STARR-seq mESC enhancer starr_38089 Neighboring gene STARR-seq mESC enhancer starr_38090 Neighboring gene STARR-seq mESC enhancer starr_38091 Neighboring gene predicted gene, 52225 Neighboring gene STARR-seq mESC enhancer starr_38093 Neighboring gene STARR-seq mESC enhancer starr_38094 Neighboring gene STARR-seq mESC enhancer starr_38095 Neighboring gene STARR-seq mESC enhancer starr_38096 Neighboring gene STARR-seq mESC enhancer starr_38097 Neighboring gene transcription factor EC pseudogene

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Association of CDH11 with Autism Spectrum Disorder Revealed by Matched-gene Co-expression Analysis and Mouse Behavioral Studies. Wu N, et al. Neurosci Bull, 2022 Jan. PMID 34523068, Free PMC Article
    2. Cadherin-9 regulates synapse-specific differentiation in the developing hippocampus. Williams ME, et al. Neuron, 2011 Aug 25. PMID 21867881, Free PMC Article
    3. Segregated expressions of autism risk genes Cdh11 and Cdh9 in autism-relevant regions of developing cerebellum. Wang C, et al. Mol Brain, 2019 May 2. PMID 31046797, Free PMC Article
    4. Breathing control center neurons that promote arousal in mice. Yackle K, et al. Science, 2017 Mar 31. PMID 28360327, Free PMC Article
    5. Cadherin Combinations Recruit Dendrites of Distinct Retinal Neurons to a Shared Interneuronal Scaffold. Duan X, et al. Neuron, 2018 Sep 19. PMID 30197236, Free PMC Article

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. mRNA expression profiles of two autism spectrum disorder-associated cadherins, Cdh9 and Cdh11, in the developing cerebellum, were examined.
      Title: Segregated expressions of autism risk genes Cdh11 and Cdh9 in autism-relevant regions of developing cerebellum.
    2. Study shows that bipolar cells BC2s and BC5s deliver visual input to neurons that compute direction of motion and demonstrate that Cdh8 and Cdh9 are required for assembly of the circuit.
      Title: Type II cadherins guide assembly of a direction-selective retinal circuit.
    3. These observations indicate that cadherin-9 bidirectionally regulates DG-CA3 synapse development and highlight the critical role of differentially expressed molecular cues in establishing specific connections in the mammalian brain.
      Title: Cadherin-9 regulates synapse-specific differentiation in the developing hippocampus.
    Submit: New GeneRIF Correction

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by MGI

    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 cadherin binding involved in cell-cell adhesion IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in synapse assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in synapse assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in synaptic membrane adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synaptic membrane adhesion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in synaptic membrane adhesion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in synaptic membrane adhesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in axon IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of catenin complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in dendrite IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in glutamatergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    is_active_in hippocampal mossy fiber to CA3 synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in hippocampal mossy fiber to CA3 synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in hippocampal mossy fiber to CA3 synapse IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    is_active_in postsynaptic membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in postsynaptic membrane IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in postsynaptic membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in presynaptic membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in presynaptic membrane IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in presynaptic membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in synapse IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

    Go to the top of the page Help
    Preferred Names
    cadherin-9
    Names
    T1-cadherin

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_009869.2 → NP_033999.1  cadherin-9 preproprotein

      See identical proteins and their annotated locations for NP_033999.1

      Status: VALIDATED

      Source sequence(s)
      AC116724, AC123645
      Consensus CDS
      CCDS49584.1
      UniProtKB/Swiss-Prot
      P70407
      UniProtKB/TrEMBL
      F8WHU6
      Related
      ENSMUSP00000154022.2, ENSMUST00000228307.2
      Conserved Domains (2) summary
      cd11304
      Location:163 → 263
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam01049
      Location:636 → 782
      Cadherin_C; Cadherin cytoplasmic region

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000081.7 Reference GRCm39 C57BL/6J

      Range
      16728641..16857224
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011245337.4 → XP_011243639.1  cadherin-9 isoform X1

      UniProtKB/Swiss-Prot
      P70407
      Conserved Domains (2) summary
      cd11304
      Location:242 → 342
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam01049
      Location:715 → 861
      Cadherin_C; Cadherin cytoplasmic region

    2. XM_006520020.4 → XP_006520083.1  cadherin-9 isoform X2

      See identical proteins and their annotated locations for XP_006520083.1

      UniProtKB/Swiss-Prot
      P70407
      UniProtKB/TrEMBL
      F8WHU6
      Conserved Domains (2) summary
      cd11304
      Location:163 → 263
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam01049
      Location:636 → 782
      Cadherin_C; Cadherin cytoplasmic region
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P70407.2 GenPept UniProtKB/Swiss-Prot:P70407

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools