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    pcdh18a protocadherin 18a [ Danio rerio (zebrafish) ]

    Gene ID: 572532, updated on 9-Dec-2024

    Summary

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    Official Symbol
    pcdh18aprovided by ZNC
    Official Full Name
    protocadherin 18aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-000607-1
    See related
    Ensembl:ENSDARG00000089805 AllianceGenome:ZFIN:ZDB-GENE-000607-1
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    pcdh18; id:ibd5114
    Summary
    Predicted to enable calcium ion binding activity. Acts upstream of or within calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules; cell migration involved in gastrulation; and epiboly involved in gastrulation with mouth forming second. Located in plasma membrane. Is expressed in several structures, including axis; epiblast; midbrain neural keel; nervous system; and spinal cord neural rod. Orthologous to human PCDH18 (protocadherin 18). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See pcdh18a in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 1 NC_007112.7 (13261116..13271100, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 1 NC_007112.6 (12574318..12584330, complement)

    Chromosome 1 - NC_007112.7Genomic Context describing neighboring genes Neighboring gene protocadherin 10a Neighboring gene uncharacterized LOC137495459 Neighboring gene uncharacterized LOC101886760 Neighboring gene uncharacterized LOC101886790

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Expression of protocadherin-9 and protocadherin-17 in the nervous system of the embryonic zebrafish. Liu Q, et al. Gene Expr Patterns, 2009 Oct. PMID 19616130, Free PMC Article
    2. A dual involvement of Protocadherin 18a in stromal cell development guides the formation of a functional hematopoietic niche. Touret AL, et al. Development, 2022 Oct 1. PMID 36168784
    3. Single-molecule imaging correlates decreasing nuclear volume with increasing TF-chromatin associations during zebrafish development. Reisser M, et al. Nat Commun, 2018 Dec 6. PMID 30523256, Free PMC Article
    4. Ethanol exposure disrupts extraembryonic microtubule cytoskeleton and embryonic blastomere cell adhesion, producing epiboly and gastrulation defects. Sarmah S, et al. Biol Open, 2013. PMID 24167711, Free PMC Article
    5. Pcdh18a regulates endocytosis of E-cadherin during axial mesoderm development in zebrafish. Bosze B, et al. Histochem Cell Biol, 2020 Nov. PMID 32488346, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Pcdh18a regulates endocytosis of E-cadherin during axial mesoderm development in zebrafish.
      Title: Pcdh18a regulates endocytosis of E-cadherin during axial mesoderm development in zebrafish.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables calcium 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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within cell migration involved in gastrulation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within epiboly involved in gastrulation with mouth forming second IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    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 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protocadherin-18a
    Names
    protocadherin 18

    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)

    1. NM_001115058.1 → NP_001108530.1  protocadherin-18a precursor

      See identical proteins and their annotated locations for NP_001108530.1

      Status: PROVISIONAL

      Source sequence(s)
      EU267178
      UniProtKB/TrEMBL
      A9QUV5
      Related
      ENSDARP00000148237.1, ENSDART00000193663.1
      Conserved Domains (2) summary
      cd11304
      Location:251 → 351
      Cadherin_repeat; Cadherin tandem repeat domain
      cl09101
      Location:30 → 112
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007112.7 Reference GRCz11 Primary Assembly

      Range
      13261116..13271100 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005159847.5 → XP_005159904.1  protocadherin-18a isoform X3

      UniProtKB/TrEMBL
      A0A8M2B6M3
      Conserved Domains (2) summary
      cd11304
      Location:251 → 351
      Cadherin_repeat; Cadherin tandem repeat domain
      cl09101
      Location:30 → 112
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    2. XM_005159846.5 → XP_005159903.1  protocadherin-18a isoform X2

      UniProtKB/TrEMBL
      A0A8M2B6N3
      Conserved Domains (2) summary
      cd11304
      Location:251 → 351
      Cadherin_repeat; Cadherin tandem repeat domain
      cl09101
      Location:30 → 112
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    3. XM_005159845.5 → XP_005159902.1  protocadherin-18a isoform X1

      UniProtKB/TrEMBL
      A0A8M2B6Q8, F1QRP2
      Related
      ENSDARP00000108171.2, ENSDART00000127838.4
      Conserved Domains (2) summary
      cd11304
      Location:251 → 351
      Cadherin_repeat; Cadherin tandem repeat domain
      cl09101
      Location:30 → 112
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    Nucleotide Protein Strain
    Heading Accession and Version

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