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CDH16 cadherin 16 [ Homo sapiens (human) ]

Gene ID: 1014, updated on 21-Dec-2019

Summary

Official Symbol
CDH16provided by HGNC
Official Full Name
cadherin 16provided by HGNC
Primary source
HGNC:HGNC:1755
See related
Ensembl:ENSG00000166589 MIM:603118
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 is a member of the cadherin superfamily, genes encoding calcium-dependent, membrane-associated glycoproteins. Mapped to a previously identified cluster of cadherin genes on chromosome 16q22.1, the gene localizes with superfamily members CDH1, CDH3, CDH5, CDH8 and CDH11. The protein consists of an extracellular domain containing 6 cadherin domains, a transmembrane region and a truncated cytoplasmic domain but lacks the prosequence and tripeptide HAV adhesion recognition sequence typical of most classical cadherins. Expression is exclusively in kidney, where the protein functions as the principal mediator of homotypic cellular recognition, playing a role in the morphogenic direction of tissue development. Alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Mar 2011]
Expression
Restricted expression toward kidney (RPKM 177.1) See more
Orthologs

Genomic context

See CDH16 in Genome Data Viewer
Location:
16q22.1
Exon count:
18
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (66908122..66918885, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (66942025..66952887, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene pyruvate dehyrogenase phosphatase catalytic subunit 2 Neighboring gene uncharacterized LOC107984821 Neighboring gene VISTA enhancer hs1760 Neighboring gene RRAD, Ras related glycolysis inhibitor and calcium channel regulator Neighboring gene cytosolic iron-sulfur assembly component 2B

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 Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules IEA
Inferred from Electronic Annotation
more info
 
cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
basolateral plasma membrane IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
cadherin-16
Names
KSP-cadherin
cadherin 16, KSP-cadherin
kidney-specific 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.

mRNA and Protein(s)

  1. NM_001204744.2NP_001191673.1  cadherin-16 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001191673.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame segment in the 3' coding region, as compared to variant 1. The resulting isoform (2) lacks an internal segment, as compared to isoform 1.
    Source sequence(s)
    AY358911, BC027912
    Consensus CDS
    CCDS56002.1
    UniProtKB/Swiss-Prot
    O75309
    Related
    ENSP00000377619.3, ENST00000394055.7
    Conserved Domains (2) summary
    cd11304
    Location:342445
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:47124
    CA; Cadherin repeats
  2. NM_001204745.2NP_001191674.1  cadherin-16 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001191674.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an in-frame segment in the 3' coding region, as compared to variant 1. The resulting isoform (3) lacks an internal segment, as compared to isoform 1.
    Source sequence(s)
    AK298255, BC027912, DC361453
    Consensus CDS
    CCDS58471.1
    UniProtKB/Swiss-Prot
    O75309
    Related
    ENSP00000454784.1, ENST00000565796.5
    Conserved Domains (2) summary
    cd11304
    Location:342445
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:47124
    CA; Cadherin repeats
  3. NM_001204746.2NP_001191675.1  cadherin-16 isoform 4 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame segment in the 5' coding region, as compared to variant 1. The resulting isoform (4) lacks an internal segment, as compared to isoform 1.
    Source sequence(s)
    AK225544, DC361453
    Consensus CDS
    CCDS58472.1
    UniProtKB/Swiss-Prot
    O75309
    Related
    ENSP00000455263.1, ENST00000568632.5
    Conserved Domains (2) summary
    cd11304
    Location:245348
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:47123
    CA; Cadherin repeats
  4. NM_004062.4NP_004053.1  cadherin-16 isoform 1 precursor

    See identical proteins and their annotated locations for NP_004053.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AF016272, BC027912, DC361453
    Consensus CDS
    CCDS10823.1
    UniProtKB/Swiss-Prot
    O75309
    Related
    ENSP00000299752.4, ENST00000299752.9
    Conserved Domains (2) summary
    cd11304
    Location:342445
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:47124
    CA; Cadherin repeats

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    66908122..66918885 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522807.2XP_011521109.1  cadherin-16 isoform X1

    Conserved Domains (2) summary
    cd11304
    Location:342445
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:47124
    CA; Cadherin repeats
  2. XM_005255770.2XP_005255827.1  cadherin-16 isoform X2

    Conserved Domains (1) summary
    cd11304
    Location:164267
    Cadherin_repeat; Cadherin tandem repeat domain
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