cdh4 cadherin 4, type 1, R-cadherin (retinal) [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: cdh4provided by ZNC
Official Full Name: cadherin 4, type 1, R-cadherin (retinal)provided by ZNC
Primary source: ZFIN:ZDB-GENE-991207-1
See related: Ensembl:ENSDARG00000015002 AllianceGenome:ZFIN:ZDB-GENE-991207-1
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: rcad; R-cadherin; zgc:136316
Summary: Predicted to enable beta-catenin binding activity and cadherin binding activity. Acts upstream of or within cranial nerve development; regulation of eye photoreceptor cell development; and sensory system development. Predicted to be located in anchoring junction and plasma membrane. Predicted to be part of catenin complex. Predicted to be active in adherens junction. Is expressed in eye and nervous system. Orthologous to human CDH4 (cadherin 4). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 11

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	11	NC_007122.7 (20371182..20827160)
105	previous assembly	GRCz10 (GCF_000002035.5)	11	NC_007122.6 (20269870..20725441)

Chromosome 11 - NC_007122.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

analyzed expression patterns of three zebrafish classical (type I) cadherins (cadherin-1, -2, and -4) in the embryonic zebrafish cranial ganglia and lateral line system
Title: Cadherin-1, -2 and -4 expression in the cranial ganglia and lateral line system of developing zebrafish.
Both Cdh2 and Cdh4 immunoreactivities were specifically up-regulated in regenerating retina and/or the optic pathway and both may be important for regeneration of injured retinal ganglion cell axons
Title: Up-regulation of cadherin-2 and cadherin-4 in regenerating visual structures of adult zebrafish.
Results indicate that Cdh4 plays a role in the normal formation of the zebrafish lateral line system and a subset of the cranial ganglia.
Title: Cadherin-4 plays a role in the development of zebrafish cranial ganglia and lateral line system.
Cadherin-4 was not detected in the embryonic Zebrafish cerebellum, but it was expressed in the Purkinje cells of the larval and adult cerebellum.
Title: Cadherin-2 and cadherin-4 in developing, adult and regenerating zebrafish cerebellum.
Cdh4 is necessary for neural retina survival and differentiation
Title: Zebrafish R-cadherin (Cdh4) controls visual system development and differentiation.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables beta-catenin binding	IBA Inferred from Biological aspect of Ancestor more info
enables cadherin binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in adherens junction organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within camera-type eye morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell-cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cell-cell adhesion mediated by cadherin	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell junction assembly	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cranial nerve development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epithelium development	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 lateral line system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of eye photoreceptor cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retina morphogenesis in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in anchoring junction	IEA Inferred from Electronic Annotation more info
part_of catenin complex	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: cadherin-4

Names: cadherin 4, retinal

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_001045273.2 → NP_001038738.2 cadherin-4 isoform 2 precursor

See identical proteins and their annotated locations for NP_001038738.2

Status: PROVISIONAL

Description

Transcript Variant: This variant (2) lacks numerous exons and transcription extends through a splice site in the 5' coding that results in a novel 3' coding region and 3' UTR, compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

BC135069

UniProtKB/TrEMBL

A4IGF0

Related

ENSDARP00000094797.3, ENSDART00000104022.4

Conserved Domains (1) summary

cl07391
Location:33 → 57

Cadherin_pro; Cadherin prodomain like
NM_131086.2 → NP_571161.2 cadherin-4 isoform 1 precursor

See identical proteins and their annotated locations for NP_571161.2

Status: PROVISIONAL

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).

Source sequence(s)

BC129136

UniProtKB/TrEMBL

A0A8M1P6X2, A1L1M6

Related

ENSDARP00000134356.1, ENSDART00000164982.2

Conserved Domains (5) summary

cd11304
Location:295 → 402

Cadherin_repeat; Cadherin tandem repeat domain

smart01055
Location:34 → 128

Cadherin_pro; Cadherin prodomain like

pfam00028
Location:632 → 726

Cadherin; Cadherin domain

pfam01049
Location:784 → 926

Cadherin_C; Cadherin cytoplasmic region

cl09101
Location:187 → 287

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