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    CDH16 cadherin 16 [ Homo sapiens (human) ]

    Gene ID: 1014, updated on 3-Dec-2024

    Summary

    Official Symbol
    CDH16provided by HGNC
    Official Full Name
    cadherin 16provided by HGNC
    Primary source
    HGNC:HGNC:1755
    See related
    Ensembl:ENSG00000166589 MIM:603118; AllianceGenome:HGNC:1755
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CDH16 in Genome Data Viewer
    Location:
    16q22.1
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (66908122..66918885, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (72702422..72713185, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (66942025..66952788, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66933011-66933906 Neighboring gene uncharacterized LOC107984821 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66933907-66934800 Neighboring gene VISTA enhancer hs1760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66945849-66946350 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66955545-66956068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66956069-66956592 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7571 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7572 Neighboring gene RRAD, Ras related glycolysis inhibitor and calcium channel regulator Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:66961058-66962257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10946 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?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    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_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/TrEMBL
      B2R7S8
      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/TrEMBL
      B2R7S8
      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/TrEMBL
      B2R7S8
      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
      B4DPA8, H3BPD3, O75309, Q6UW93
      UniProtKB/TrEMBL
      B2R7S8
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_047433490.1XP_047289446.1  cadherin-16 isoform X2

      UniProtKB/TrEMBL
      H3BSG2
    2. XM_011522807.2XP_011521109.1  cadherin-16 isoform X1

      UniProtKB/TrEMBL
      B2R7S8
      Conserved Domains (2) summary
      cd11304
      Location:342445
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:47124
      CA; Cadherin repeats
    3. XM_005255770.3XP_005255827.1  cadherin-16 isoform X3

      UniProtKB/TrEMBL
      H3BSG2
      Conserved Domains (1) summary
      cd11304
      Location:164267
      Cadherin_repeat; Cadherin tandem repeat domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      72702422..72713185 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379374.1XP_054235349.1  cadherin-16 isoform X2

      UniProtKB/TrEMBL
      H3BSG2
    2. XM_054379373.1XP_054235348.1  cadherin-16 isoform X1

      UniProtKB/TrEMBL
      B2R7S8
    3. XM_054379375.1XP_054235350.1  cadherin-16 isoform X3

      UniProtKB/TrEMBL
      H3BSG2