pcdh19 protocadherin 19 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: pcdh19provided by ZNC
Official Full Name: protocadherin 19provided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-4218
See related: Ensembl:ENSDARG00000034344 AllianceGenome:ZFIN:ZDB-GENE-030131-4218
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: fc83e05; wu:fc83e05
Summary: Enables calcium ion binding activity and identical protein binding activity. Acts upstream of or within brain morphogenesis; neural tube formation; and visual perception. Is integral component of membrane. Is expressed in several structures, including brain; eye; immature eye; posterior neural keel; and spinal cord. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 9. Orthologous to human PCDH19 (protocadherin 19). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 14

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	14	NC_007125.7 (40303153..40390779, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	14	NC_007125.6 (39935160..40022788, complement)

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
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?

Study finds that the brain networks of pcdh19 mutants display enhanced clustering and an altered developmental trajectory of network assembly.
Title: Multiplane Calcium Imaging Reveals Disrupted Development of Network Topology in Zebrafish pcdh19 Mutants.
The crystal structure reveals an adhesive interface for Pcdh19, which is broadly relevant to both non-clustered delta and clustered protocadherin subfamilies.
Title: Structural determinants of adhesion by Protocadherin-19 and implications for its role in epilepsy.
pcdh19 is expressed in discrete columns of neuronsin the zebrafish optic tectum.
Title: Protocadherins control the modular assembly of neuronal columns in the zebrafish optic tectum.
Study presents a comprehensive and detailed expression of pcdh19 and pcdh17, two delta-pcdhs, and cdh6, a classical cadherin, in the entire brain of adult zebrafish
Title: Differential expression of protocadherin-19, protocadherin-17, and cadherin-6 in adult zebrafish brain.
demonstration of a novel mechanism of cell adhesion, mediated by a complex of Protocadherin-19 (Pcdh19) and N-cadherin (Ncad)
Title: A complex of Protocadherin-19 and N-cadherin mediates a novel mechanism of cell adhesion.
Protocadherin-19 and N-cadherin interact to control cell movements during anterior neurulation
Title: Protocadherin-19 and N-cadherin interact to control cell movements during anterior neurulation.
Data show that similar to its expression in the brain, Pcdh19 expression in the eye and ear was also spatially and temporally regulated.
Title: Expression of protocadherin-19 in the nervous system of the embryonic zebrafish.
We have identified the zebrafish homolog of protocadherin-19, a member of the cadherin superfamily, which is expressed in the anterior neural plate and is required for brain morphogenesis
Title: Protocadherin-19 is essential for early steps in brain morphogenesis.

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General gene information

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Markers

ha3100 (e-PCR)
- UniSTS:515646

fc83e05.x1 (e-PCR)
- UniSTS:188315

fb48g12.x1 (e-PCR)
- UniSTS:203233

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables cadherin binding	IPI Inferred from Physical Interaction more info	PubMed
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within brain morphogenesis	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
involved_in cell-cell adhesion	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within excitatory postsynaptic potential	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
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neural tube formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neural tube formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of neuronal action potential	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within visual perception	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
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-19

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_001127519.2 → NP_001120991.2 protocadherin-19 precursor

Status: PROVISIONAL

Source sequence(s)

BC129243, CF543950, EH581688

UniProtKB/Swiss-Prot

A0A140LG84, A0A8M1NJM2, A0A8M2BGV1, A0A9K3Y6L2, F8W3X3

UniProtKB/TrEMBL

A0A9U5BCE3

Related

ENSDARP00000124001.2, ENSDART00000149443.3

Conserved Domains (3) summary

cd11304
Location:243 → 343

Cadherin_repeat; Cadherin tandem repeat domain

pfam16492
Location:676 → 708

Cadherin_C_2; Cadherin cytoplasmic C-terminal

cl09101
Location:28 → 107

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...

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

40303153..40390779 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_009291121.3 → XP_009289396.1 protocadherin-19 isoform X2

UniProtKB/Swiss-Prot

A0A140LG84, A0A8M1NJM2, A0A8M2BGV1, A0A9K3Y6L2, F8W3X3

UniProtKB/TrEMBL

A0A8M3AP82

Conserved Domains (3) summary

cd11304
Location:243 → 343

Cadherin_repeat; Cadherin tandem repeat domain

pfam16492
Location:676 → 731

Cadherin_C_2; Cadherin cytoplasmic C-terminal

cl09101
Location:28 → 107

E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
XM_005169595.4 → XP_005169652.1 protocadherin-19 isoform X3

UniProtKB/Swiss-Prot

A0A140LG84, A0A8M1NJM2, A0A8M2BGV1, A0A9K3Y6L2, F8W3X3

Related

ENSDARP00000142262.1, ENSDART00000173398.2

Conserved Domains (3) summary

cd11304
Location:243 → 343

Cadherin_repeat; Cadherin tandem repeat domain

pfam16492
Location:676 → 708

Cadherin_C_2; Cadherin cytoplasmic C-terminal

cl09101
Location:28 → 107

E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
XM_009291120.3 → XP_009289395.1 protocadherin-19 isoform X1

UniProtKB/Swiss-Prot

A0A140LG84, A0A8M1NJM2, A0A8M2BGV1, A0A9K3Y6L2, F8W3X3

UniProtKB/TrEMBL

A0A2R8QME5, A0A8M3AS27

Related

ENSDARP00000155634.1, ENSDART00000181581.1

Conserved Domains (3) summary

cd11304
Location:243 → 343

Cadherin_repeat; Cadherin tandem repeat domain

pfam16492
Location:676 → 731

Cadherin_C_2; Cadherin cytoplasmic C-terminal

cl09101
Location:28 → 107

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