rtn4a reticulon 4a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: rtn4aprovided by ZNC
Official Full Name: reticulon 4aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030710-1
See related: Ensembl:ENSDARG00000044601 AllianceGenome:ZFIN:ZDB-GENE-030710-1
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: nogo; rtn4; Nogo-B; zgc:92163; wu:fb17a02; wu:fb22f12; wu:fd61a07
Summary: Acts upstream of or within several processes, including mesenchymal to epithelial transition; nervous system development; and sensory system development. Predicted to be located in endoplasmic reticulum membrane. Is expressed in several structures, including heart; liver; muscle; nervous system; and pectoral fin. Orthologous to human RTN4 (reticulon 4). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 6

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	6	NC_007117.7 (6231382..6258524, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	6	NC_007117.6 (6074213..6101355, complement)

Chromosome 6 - NC_007117.7 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?

Conditional overexpression of rtn4a in muscle of adult zebrafish displays defects similar to human amyotrophic lateral sclerosis.
Title: Conditional Overexpression of rtn4al in Muscle of Adult Zebrafish Displays Defects Similar to Human Amyotrophic Lateral Sclerosis.
rtn4a is essential for embryonic development and patterning of the nervous system.
Title: Essential roles of zebrafish rtn4/Nogo paralogues in embryonic development.
data demonstrates that zebrafish Rtn4/Nogo transcripts might be generated by coupling mechanisms of alternative first exons and alternative promoter usage.
Title: Identification and characterization of alternative promoters of zebrafish Rtn-4/Nogo genes in cultured cells and zebrafish embryos.
The present results have uncovered new factors underlying successful axon regeneration in the fish CNS: Binding of Nogo-66 of fish RTN-4 to NgR is growth promoting on fish retinal ganglion cell axon growth
Title: No Nogo66- and NgR-mediated inhibition of regenerating axons in the zebrafish optic nerve.
Data suggest that localized Nogo/Nogo66 expression defines inhibitory territories that through repulsion restrict axon growth to permissive regions.
Title: Nogo-Nogo receptor signalling in PNS axon outgrowth and pathfinding.

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General gene information

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Markers

AI397219 (e-PCR)
- UniSTS:206668

fk18f10.y1 (e-PCR)
- UniSTS:200617

fb17a02.x1 (e-PCR)
- UniSTS:202979

fd61a07.x1 (e-PCR)
- UniSTS:195819

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within axon guidance	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within axonogenesis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within brain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within camera-type eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mesenchymal to epithelial transition	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within neuromast development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within optic nerve development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within peripheral nervous system neuron axonogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within posterior lateral line development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within posterior lateral line neuromast deposition	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within somite development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within sprouting angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: reticulon-4a

Names: reticulon 4

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_001004555.2 → NP_001004555.2 reticulon-4a isoform 1

See identical proteins and their annotated locations for NP_001004555.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

BX324134

UniProtKB/TrEMBL

A0A8M1N243, Q4G5V9

Related

ENSDARP00000076390.4, ENSDART00000081952.6

Conserved Domains (1) summary

pfam02453
Location:25 → 189

Reticulon; Reticulon
NM_001079912.2 → NP_001073381.1 reticulon-4a isoform 4-l

See identical proteins and their annotated locations for NP_001073381.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate 5' most exon which results in a distinct 5' UTR and the use of an alternate start codon compared to variant 1. The encoded isoform (4-I) is longer an has a distinct N-terminus compared to isoform 1.

Source sequence(s)

BX324134

UniProtKB/TrEMBL

A0A8M1NCF0, Q4G5W2

Related

ENSDARP00000076404.3, ENSDART00000081966.5

Conserved Domains (1) summary

pfam02453
Location:137 → 299

Reticulon; Reticulon
NM_001201446.1 → NP_001188375.1 reticulon-4a isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate 5' most exon which results in a distinct 5' UTR and the use of an alternate start codon compared to variant 1. The encoded isoform (3) is shorter an has a distinct N-terminus compared to isoform 1.

Source sequence(s)

BX324134

UniProtKB/TrEMBL

A0A8M1P2F7, F1QT89

Related

ENSDARP00000108083.2, ENSDART00000124662.4

Conserved Domains (1) summary

pfam02453
Location:9 → 173

Reticulon; Reticulon