Cdh9 cadherin 9 [Mus musculus (house mouse)] - Gene

Summary

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, Dec 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
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Genomic context

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_000081.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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

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Alleles

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

Endonuclease-mediated (4) 1 citation
Targeted (3) 1 citation

General gene information

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Markers

Cdh9 (e-PCR), detects polymorphism
- UniSTS:265062

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

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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.

mRNA and Protein(s)

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

NC_000081.7 Reference GRCm39 C57BL/6J

Range

16728641..16857224

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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