Rtn3 reticulon 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Rtn3provided by RGD
Official Full Name: reticulon 3provided by RGD
Primary source: RGD:620988
See related: Ensembl:ENSRNOG00000021202 AllianceGenome:RGD:620988
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: This gene encodes a member of the reticulon family, a large group of membrane-bound proteins that primarily localize to the endoplasmic reticulum with a small subpopulation at the cell surface. These proteins play roles in endocytosis, exocytosis, trafficking and neuronal outgrowth. Proteins belonging to this family are characterized by a carboxy-terminal reticulon homology domain that consists of a small hydrophilic loop flanked by hydrophobic regions. In rat, this protein has been shown to interact with two members of the synaptic adhesion-like molecule family, suggesting that it may function in trafficking of these proteins. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2015]
Expression: Biased expression in Brain (RPKM 712.6), Kidney (RPKM 196.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q43

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (214041838..214098644, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (204612675..204669212, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (222677359..222734307, complement)

Chromosome 1 - NC_086019.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Overexpression of Reticulon 3 Enhances CNS Axon Regeneration and Functional Recovery after Traumatic Injury.
Title: Overexpression of Reticulon 3 Enhances CNS Axon Regeneration and Functional Recovery after Traumatic Injury.
PGRMC1 acts as a size-selective cargo receptor to drive ER-phagic clearance of mutant prohormones.
Title: PGRMC1 acts as a size-selective cargo receptor to drive ER-phagic clearance of mutant prohormones.
RTN3 regulates very low density lipoprotein (VLDL) secretion by controlling VLDL transport vesicle-mediated endoplasmic reticulum-to-Golgi transport of nascent VLDL.
Title: Reticulon 3 regulates very low density lipoprotein secretion by controlling very low density lipoprotein transport vesicle biogenesis.
oxidative damage caused the formation of toxic RTN3 aggregates, which participated in the pathogenesis of central neuritic dystrophy in diabetic brain.
Title: Diabetes-induced central neuritic dystrophy and cognitive deficits are associated with the formation of oligomeric reticulon-3 via oxidative stress.
results show that reticulon 3 may play a role in the trafficking of the synaptic adhesion-like molecules family of adhesion molecules
Title: Reticulon 3 is an interacting partner of the SALM family of adhesion molecules.
RTN3 may play an important role in developing axons and also in some glial cells such as Muller cells.
Title: Reticulon3 expression in rat optic and olfactory systems.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BF398783 (e-PCR)
- UniSTS:246911

RH139483 (e-PCR)
- UniSTS:221569

RH140316 (e-PCR)
- UniSTS:222393

AW558451 (e-PCR)
- UniSTS:181189

RH129377 (e-PCR)
- UniSTS:212684

BF387073 (e-PCR)
- UniSTS:244177

BF404310 (e-PCR)
- UniSTS:247036

Gene Ontology Provided by RGD

Process	Evidence Code	Pubs
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
involved_in endoplasmic reticulum tubular network formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in endoplasmic reticulum tubular network formation	IEA Inferred from Electronic Annotation more info
involved_in endoplasmic reticulum tubular network formation	ISO Inferred from Sequence Orthology more info
involved_in endoplasmic reticulum tubular network organization	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of amyloid-beta formation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of amyloid-beta formation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of amyloid-beta formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle-mediated transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in neuron projection	IBA Inferred from Biological aspect of Ancestor more info
is_active_in postsynaptic density	IBA Inferred from Biological aspect of Ancestor more info
is_active_in presynapse	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IEA Inferred from Electronic Annotation more info
is_active_in synapse	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: reticulon-3

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_001009953.3 → NP_001009953.2 reticulon-3 isoform A1

See identical proteins and their annotated locations for NP_001009953.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an internal in-frame exon compared to variant 1. It encodes isoform A1, which is shorter than isoform A.

Source sequence(s)

BC107448, JAXUCZ010000001

UniProtKB/TrEMBL

A1L1I6, A6HZP8

Related

ENSRNOP00000091327.1, ENSRNOT00000099817.1

Conserved Domains (1) summary

pfam02453
Location:49 → 213

Reticulon; Reticulon
NM_080909.3 → NP_543185.2 reticulon-3 isoform A

See identical proteins and their annotated locations for NP_543185.2

Status: REVIEWED

Description

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

Source sequence(s)

AY496443, JAXUCZ010000001

UniProtKB/Swiss-Prot

Q6P6R3, Q6RJR6, Q8VBU0

Related

ENSRNOP00000028785.5, ENSRNOT00000028785.8

Conserved Domains (1) summary

pfam02453
Location:752 → 916

Reticulon; Reticulon

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

214041838..214098644 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063271575.1 → XP_063127645.1 reticulon-3 isoform X2

UniProtKB/TrEMBL

A0A8I6AFX0, A6HZP9
XM_006230649.5 → XP_006230711.1 reticulon-3 isoform X1

UniProtKB/TrEMBL

A0A8I6ASN6

Related

ENSRNOP00000096049.1

Conserved Domains (1) summary

pfam02453
Location:771 → 935

Reticulon; Reticulon
XM_006230650.5 → XP_006230712.1 reticulon-3 isoform X3

UniProtKB/TrEMBL

A0A8I6G4J6

Related

ENSRNOP00000080451.1

Conserved Domains (1) summary

pfam02453
Location:48 → 212

Reticulon; Reticulon