pcdh18b protocadherin 18b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: pcdh18bprovided by ZNC
Official Full Name: protocadherin 18bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-080804-1
See related: Ensembl:ENSDARG00000052494 AllianceGenome:ZFIN:ZDB-GENE-080804-1
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; fj19f12; wu:fj19f12
Summary: Predicted to enable calcium ion binding activity. Acts upstream of or within neuron projection morphogenesis. Predicted to be located in membrane. Predicted to be active in plasma membrane. Is expressed in several structures, including head; nervous system; neural rod; pectoral fin bud; and spinal cord neural tube. Orthologous to human PCDH18 (protocadherin 18). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 14

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	14	NC_007125.7 (42172257..42179798)
105	previous assembly	GRCz10 (GCF_000002035.5)	14	NC_007125.6 (41804953..41812540)

Chromosome 14 - NC_007125.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pcdh18b and Nap1 regulate axon arborization by affecting the density of filopodia along the shaft of the extending axon.
Title: Protocadherin-18b interacts with Nap1 to control motor axon growth and arborization in zebrafish.
These results suggest a role for Pcdh18a in cell adhesion, migration and behavior but not cell specification during gastrula and segmentation stages of development.
Title: Protocadherin-18a has a role in cell adhesion, behavior and migration in zebrafish development.

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General gene information

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Markers

G39454 (e-PCR)
- UniSTS:46859

fj19f12.x1 (e-PCR)
- UniSTS:198715

G47981 (e-PCR)
- UniSTS:108746

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
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 homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuron projection morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

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	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: protocadherin-18b

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)

NM_001115099.1 → NP_001108571.1 protocadherin-18b precursor

See identical proteins and their annotated locations for NP_001108571.1

Status: PROVISIONAL

Source sequence(s)

AB297803

UniProtKB/TrEMBL

A9CPE6

Related

ENSDARP00000068851.4, ENSDART00000074362.6

Conserved Domains (2) summary

cd11304
Location:257 → 356

Cadherin_repeat; Cadherin tandem repeat domain

cl09101
Location:35 → 117

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

NC_007125.7 Reference GRCz11 Primary Assembly

Range

42172257..42179798

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005157329.5 → XP_005157386.1 protocadherin-18b isoform X1

UniProtKB/TrEMBL

A0A8M2B3F9

Related

ENSDARP00000124086.2, ENSDART00000148544.3

Conserved Domains (2) summary

cd11304
Location:257 → 356

Cadherin_repeat; Cadherin tandem repeat domain

cl09101
Location:35 → 117

E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus