Cdh6 cadherin 6 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Cdh6provided by MGI
Official Full Name: cadherin 6provided by MGI
Primary source: MGI:MGI:107435
See related: Ensembl:ENSMUSG00000039385 AllianceGenome:MGI:107435
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: cad6
Summary: This gene encodes a member of the cadherin family of calcium-dependent glycoproteins that mediate cell adhesion and regulate many morphogenetic events during development. The encoded preproprotein is further processed to generate a mature protein. Mice lacking the encoded protein exhibit delay in mesenchyme-to-epithelial conversion and a loss of nephrons. Multiple distinct genes of the cadherin family, including this gene, are found on chromosome 15. [provided by RefSeq, Oct 2015]
Expression: Biased expression in frontal lobe adult (RPKM 1.6), limb E14.5 (RPKM 1.6) and 12 other tissues See more
Orthologs: human all
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Genomic context

Location:: 15 A1; 15 6.11 cM

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	15	NC_000081.7 (13028785..13176493, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	15	NC_000081.6 (13028699..13176407, complement)

Chromosome 15 - NC_000081.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Cadherin 6 expression in the nascent cortical plate may serve solidification of the protomap for cortical functional areas.
Title: A sharp cadherin-6 gene expression boundary in the developing mouse cortical plate demarcates the future functional areal border.
cadherin-6 plays essential roles in locomotor activity and ultrasonic vocalization
Title: Defects in ultrasonic vocalization of cadherin-6 knockout mice.
role of cadherin 6 as a novel ligand for alpha(IIb)beta(3) and highlights its function in thrombus formation.
Title: Cadherin 6 has a functional role in platelet aggregation and thrombus formation.
Data show that during development, the adhesion molecule cadherin-6 is expressed by a subset of retinal ganglion cells and also by their targets in the brain.
Title: Cadherin-6 mediates axon-target matching in a non-image-forming visual circuit.
These results suggest the role of Cdh6 in coordinating mouse hindbrain compartments possibly under the control of Hox gene regulatory network.
Title: Genetic labeling of mouse rhombomeres by Cadherin-6::EGFP-BAC transgenesis underscores the role of cadherins in hindbrain compartmentalization.
Results describe the genetic control of Cdh6 expression by systematic integration of a reporter cassette into bacterial artificial chromosomes, with reporter activities evaluated in stable transgenic mouse lines.
Title: Cadherin-6 gene regulatory patterns in the postnatal mouse brain.
identified a short 79-bp region that is implicated in regulating expression in cells once they have emigrated from the neural tube
Title: Analysis of mouse Cdh6 gene regulation by transgenesis of modified bacterial artificial chromosomes.
Cadherin 6 is expressed in the floor and roof plates of the motor columns of the spinal cord.
Title: Complementary expression and regulation of cadherins 6 and 11 during specific steps of motoneuron differentiation.

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Variation

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Alleles

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

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

General gene information

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Markers

Cdh6 (e-PCR), detects polymorphism
- UniSTS:265061

Cdh6 (e-PCR), detects polymorphism
- UniSTS:545911

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 calcium ion binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within Notch signaling pathway	IDA Inferred from Direct Assay more info	PubMed
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
acts_upstream_of_or_within cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cell adhesion	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation 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 multicellular organism development	IBA Inferred from Biological aspect of Ancestor 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

Component	Evidence Code	Pubs
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
part_of catenin complex	IBA Inferred from Biological aspect of Ancestor more info
located_in cell junction	ISO Inferred from Sequence Orthology more info
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
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma 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-6

Names: K-cadherin; kidney 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_007666.4 → NP_031692.2 cadherin-6 preproprotein

See identical proteins and their annotated locations for NP_031692.2

Status: REVIEWED

Source sequence(s)

AC139574, AK134611, BI134319, CN531307

Consensus CDS

CCDS27393.1

UniProtKB/Swiss-Prot

P70393, P97326, Q3KNY8

UniProtKB/TrEMBL

Q3KNZ1

Related

ENSMUSP00000037113.5, ENSMUST00000036439.6

Conserved Domains (3) summary

cd11304
Location:163 → 264

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:79 → 157

CA; Cadherin repeats

pfam01049
Location:637 → 783

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

13028785..13176493 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017316421.2 → XP_017171910.1 cadherin-6 isoform X3

Conserved Domains (2) summary

cd11304
Location:102 → 209

Cadherin_repeat; Cadherin tandem repeat domain

pfam01049
Location:467 → 613

Cadherin_C; Cadherin cytoplasmic region
XM_006520018.4 → XP_006520081.1 cadherin-6 isoform X2

Conserved Domains (2) summary

cd11304
Location:163 → 264

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:79 → 157

CA; Cadherin repeats
XM_036159108.1 → XP_036015001.1 cadherin-6 isoform X1

UniProtKB/Swiss-Prot

P70393, P97326, Q3KNY8

UniProtKB/TrEMBL

Q3KNZ1

Conserved Domains (3) summary

cd11304
Location:163 → 264

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:79 → 157

CA; Cadherin repeats

pfam01049
Location:637 → 783

Cadherin_C; Cadherin cytoplasmic region
XM_006520017.2 → XP_006520080.1 cadherin-6 isoform X1

See identical proteins and their annotated locations for XP_006520080.1

UniProtKB/Swiss-Prot

P70393, P97326, Q3KNY8

UniProtKB/TrEMBL

Q3KNZ1

Conserved Domains (3) summary

cd11304
Location:163 → 264

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:79 → 157

CA; Cadherin repeats

pfam01049
Location:637 → 783

Cadherin_C; Cadherin cytoplasmic region
XM_017316420.2 → XP_017171909.1 cadherin-6 isoform X2

Conserved Domains (2) summary

cd11304
Location:163 → 264

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:79 → 157

CA; Cadherin repeats