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pcdh18a protocadherin 18a [ Danio rerio (zebrafish) ]

Gene ID: 572532, updated on 11-Apr-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, Apr 2022]
Orthologs
human mouse 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
106 current GRCz11 (GCF_000002035.6) 1 NC_007112.7 (13261115..13271156, 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 si:dkeyp-7b3.2 Neighboring gene si:dkey-5n7.2 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. 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
  3. 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
  4. 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
  5. Protocadherin-18a has a role in cell adhesion, behavior and migration in zebrafish development. Aamar E, et al. Dev Biol, 2008 Jun 15. PMID 18468594

See all (11) 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-18; 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: Danio rerio Annotation Release 106 details...Open this link in a new tab

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
    13261115..13271156 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005159846.4 → XP_005159903.1  protocadherin-18 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

  2. XM_005159847.4 → XP_005159904.1  protocadherin-18 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

  3. XM_005159845.4 → XP_005159902.1  protocadherin-18 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

RNA

  1. XR_222598.4 RNA Sequence

  2. XR_222599.4 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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