Cdh16 cadherin 16 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Cdh16provided by MGI
Official Full Name: cadherin 16provided by MGI
Primary source: MGI:MGI:106671
See related: Ensembl:ENSMUSG00000031881 AllianceGenome:MGI:106671
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: Predicted to enable calcium ion binding activity. Acts upstream of or within calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules. Located in basolateral plasma membrane. Is expressed in foregut; genitourinary system; and lung. Orthologous to human CDH16 (cadherin 16). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Restricted expression toward kidney adult (RPKM 275.2) See more
Orthologs: human all
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Genomic context

Location:: 8 D3; 8 53.04 cM

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	8	NC_000074.7 (105328547..105351028, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	8	NC_000074.6 (104601915..104624396, complement)

Chromosome 8 - NC_000074.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

Deletion of Cdh16 Ksp-cadherin leads to a developmental delay in the ability to maximally concentrate urine in mouse.
Title: Deletion of Cdh16 Ksp-cadherin leads to a developmental delay in the ability to maximally concentrate urine in mouse.
study concludes that Cadherin-16 is a novel downstream target of the transcription factor Pax8, likely since the early steps of thyroid development, and that its expression is associated with the fully differentiated state of the thyroid cell
Title: An essential role for Pax8 in the transcriptional regulation of cadherin-16 in thyroid cells.
In the developing thyroid, CDH16 is expressed at embryonic day 10.5, 1-2 d after the main thyroid-specific transcription factors involved in thyroid cell differentiation.
Title: CDH16/Ksp-cadherin is expressed in the developing thyroid gland and is strongly down-regulated in thyroid carcinomas.
Ksp-cadherin induces homotypic and Ca2+-dependent cell-cell adhesion that can be specifically blocked with antibodies raised against the cadherin repeats EC1 and EC2
Title: Ksp-cadherin is a functional cell-cell adhesion molecule related to LI-cadherin.
identify Ksp-cadherin as the first kidney-specific promoter that has been shown to be regulated by hepatocyte nuclear factor-1
Title: Regulation of kidney-specific Ksp-cadherin gene promoter by hepatocyte nuclear factor-1beta.

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Variation

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Alleles

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

Targeted (1)
Endonuclease-mediated (6) 1 citation

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
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 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in basolateral plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: cadherin-16

Names: KSP-cadherin; kidney-specific 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_001252627.1 → NP_001239556.1 cadherin-16 isoform 2 precursor

See identical proteins and their annotated locations for NP_001239556.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.

Source sequence(s)

AJ609635, AK164546

Consensus CDS

CCDS85594.1

UniProtKB/TrEMBL

Q3TPA4

Related

ENSMUSP00000129663.4, ENSMUST00000163783.4

Conserved Domains (2) summary

cd11304
Location:314 → 417

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:37 → 96

CA; Cadherin repeats
NM_001252628.1 → NP_001239557.1 cadherin-16 isoform 3 precursor

See identical proteins and their annotated locations for NP_001239557.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 3' UTR and 3' coding region differences, compared to variant 1, which results in a frameshift. The resulting protein (isoform 3) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AK052636, AK164546

Consensus CDS

CCDS85595.1

UniProtKB/TrEMBL

Q8C730

Related

ENSMUSP00000148726.2, ENSMUST00000212882.2

Conserved Domains (2) summary

cd11304
Location:344 → 447

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:67 → 126

CA; Cadherin repeats
NM_007663.3 → NP_031689.1 cadherin-16 isoform 1 precursor

See identical proteins and their annotated locations for NP_031689.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AJ609635, AK164546

Consensus CDS

CCDS22583.1

UniProtKB/Swiss-Prot

O88338, Q9JLZ5

UniProtKB/TrEMBL

Q546A8

Related

ENSMUSP00000148478.2, ENSMUST00000211903.2

Conserved Domains (2) summary

cd11304
Location:344 → 447

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:67 → 126

CA; Cadherin repeats

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_000074.7 Reference GRCm39 C57BL/6J

Range

105328547..105351028 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006530629.1 → XP_006530692.1 cadherin-16 isoform X1

Conserved Domains (2) summary

cd11304
Location:344 → 447

Cadherin_repeat; Cadherin tandem repeat domain

smart00112
Location:67 → 126

CA; Cadherin repeats