RTN3 reticulon 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RTN3provided by HGNC
Official Full Name: reticulon 3provided by HGNC
Primary source: HGNC:HGNC:10469
See related: Ensembl:ENSG00000133318 MIM:604249; AllianceGenome:HGNC:10469
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HAP; ASYIP; NSPL2; NSPLII; RTN3-A1
Summary: This gene belongs to the reticulon family of highly conserved genes that are preferentially expressed in neuroendocrine tissues. This family of proteins interact with, and modulate the activity of beta-amyloid converting enzyme 1 (BACE1), and the production of amyloid-beta. An increase in the expression of any reticulon protein substantially reduces the production of amyloid-beta, suggesting that reticulon proteins are negative modulators of BACE1 in cells. Alternatively spliced transcript variants encoding different isoforms have been found for this gene, and pseudogenes of this gene are located on chromosomes 4 and 12. [provided by RefSeq, May 2012]
Expression: Broad expression in brain (RPKM 157.4), fat (RPKM 54.4) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q13.1

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (63681450..63759891)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (63670790..63749258)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (63448922..63527363)

Chromosome 11 - NC_000011.10 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RTN3 deficiency exacerbates cisplatin-induced acute kidney injury through the disruption of mitochondrial stability.
Title: RTN3 deficiency exacerbates cisplatin-induced acute kidney injury through the disruption of mitochondrial stability.
RTN3 and RTN4: Architects of SARS-CoV-2 replication organelles.
Title: RTN3 and RTN4: Architects of SARS-CoV-2 replication organelles.
Loss of RTN3 phenocopies chronic kidney disease and results in activation of the IGF2-JAK2 pathway in proximal tubular epithelial cells.
Title: Loss of RTN3 phenocopies chronic kidney disease and results in activation of the IGF2-JAK2 pathway in proximal tubular epithelial cells.
LINC02288 promotes chondrocyte apoptosis and inflammation through miR-374a-3p targeting RTN3.
Title: LINC02288 promotes chondrocyte apoptosis and inflammation through miR-374a-3p targeting RTN3.
Role of VAMP7-Dependent Secretion of Reticulon 3 in Neurite Growth.
Title: Role of VAMP7-Dependent Secretion of Reticulon 3 in Neurite Growth.
RTN3 inhibits RIG-I-mediated antiviral responses by impairing TRIM25-mediated K63-linked polyubiquitination.
Title: RTN3 inhibits RIG-I-mediated antiviral responses by impairing TRIM25-mediated K63-linked polyubiquitination.
The Implication of Reticulons (RTNs) in Neurodegenerative Diseases: From Molecular Mechanisms to Potential Diagnostic and Therapeutic Approaches.
Title: The Implication of Reticulons (RTNs) in Neurodegenerative Diseases: From Molecular Mechanisms to Potential Diagnostic and Therapeutic Approaches.
Reticulon-3 Promotes Endosome Maturation at ER Membrane Contact Sites.
Title: Reticulon-3 Promotes Endosome Maturation at ER Membrane Contact Sites.
Reticulon-3 modulates the incorporation of replication competent hepatitis C virus molecules for release inside infectious exosomes.
Title: Reticulon-3 modulates the incorporation of replication competent hepatitis C virus molecules for release inside infectious exosomes.
We also find that RTN3 participates in the clearance of other mutant prohormone aggregates. Together, these results identify a series of substrates of RTN3-mediated ER-phagy, highlighting RTN3 in the disposal of pathogenic prohormone aggregates.
Title: Cells Deploy a Two-Pronged Strategy to Rectify Misfolded Proinsulin Aggregates.

Submit: New GeneRIF Correction See all GeneRIFs (44)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of reticulon 3 (RTN3) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Vpu	vpu	HIV-1 Vpu is identified to have a physical interaction with reticulon 3 (RTN3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2301E (e-PCR)
- UniSTS:58416

D11S4017 (e-PCR)
- UniSTS:63853

D7S2862 (e-PCR)
- UniSTS:72584

D3S4219 (e-PCR)
- UniSTS:51611

D11S4400 (e-PCR)
- UniSTS:83116

RH91589 (e-PCR)
- UniSTS:90037

SHGC-132011 (e-PCR)
- UniSTS:184513

Rtn3 (e-PCR), detects polymorphism
- UniSTS:547531

D11S2837 (e-PCR)
- UniSTS:152023

Gene Ontology Provided by GOA

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

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	IDA Inferred from Direct Assay more info	PubMed
involved_in endoplasmic reticulum tubular network organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of amyloid-beta formation	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular space	TAS Traceable Author Statement more info	PubMed
is_active_in neuron projection	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info
is_active_in postsynaptic density	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: reticulon-3

Names: ASY interacting protein; NSP-like protein 2; NSP-like protein II; homolog of ASY protein; neuroendocrine-specific protein-like 2; neuroendocrine-specific protein-like II

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_001265589.2 → NP_001252518.1 reticulon-3 isoform e

See identical proteins and their annotated locations for NP_001252518.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) includes two consecutive alternate exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (e) is longer than isoform a.

Source sequence(s)

AY750848

Consensus CDS

CCDS58141.1

UniProtKB/Swiss-Prot

B3KQS2, B7Z308, B7Z4M0, F5H774, O95197, Q147U9, Q496K2, Q53GN3, Q59EP0, Q5UEP2, Q6T930, Q7RTM7, Q7RTM8, Q7RTN3

UniProtKB/TrEMBL

B7Z8W8

Related

ENSP00000367050.5, ENST00000377819.10

Conserved Domains (1) summary

pfam02453
Location:844 → 1008

Reticulon; Reticulon
NM_001265590.2 → NP_001252519.1 reticulon-3 isoform f

Status: REVIEWED

Description

Transcript Variant: This variant (6) includes an alternate exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (f) is longer than isoform a.

Source sequence(s)

AK309766, AY427821, BK001681

Consensus CDS

CCDS58142.1

UniProtKB/TrEMBL

B7Z3E3

Related

ENSP00000442733.1, ENST00000540798.5

Conserved Domains (1) summary

pfam02453
Location:732 → 896

Reticulon; Reticulon
NM_001265591.2 → NP_001252520.1 reticulon-3 isoform g

See identical proteins and their annotated locations for NP_001252520.1

Status: REVIEWED

Description

Transcript Variant: This variant (7) lacks three consecutive exons in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (g) is shorter and has a distinct C-terminus, compared to isoform a.

Source sequence(s)

AK297529, AY427821, BK001681

Consensus CDS

CCDS58143.1

UniProtKB/Swiss-Prot

O95197

Related

ENSP00000346492.4, ENST00000354497.4

Conserved Domains (1) summary

pfam02453
Location:48 → 107

Reticulon; Reticulon
NM_006054.4 → NP_006045.1 reticulon-3 isoform a

See identical proteins and their annotated locations for NP_006045.1

Status: REVIEWED

Description

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

Source sequence(s)

BC011394, BK001681

Consensus CDS

CCDS8049.1

UniProtKB/TrEMBL

B7Z361

Related

ENSP00000440874.1, ENST00000537981.5

Conserved Domains (1) summary

pfam02453
Location:48 → 212

Reticulon
NM_201428.3 → NP_958831.1 reticulon-3 isoform b

See identical proteins and their annotated locations for NP_958831.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) includes an alternate exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (b) is longer than isoform a.

Source sequence(s)

AY427821

Consensus CDS

CCDS8050.1

UniProtKB/TrEMBL

B7Z8W8

Related

ENSP00000344106.4, ENST00000339997.8

Conserved Domains (1) summary

pfam02453
Location:825 → 989

Reticulon; Reticulon
NM_201429.2 → NP_958832.1 reticulon-3 isoform c

See identical proteins and their annotated locations for NP_958832.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) includes an alternate exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (c) is longer than isoform a.

Source sequence(s)

AK295361, AY427821, BC022993, BK001681

Consensus CDS

CCDS41664.1

UniProtKB/Swiss-Prot

O95197

Related

ENSP00000348279.3, ENST00000356000.7

Conserved Domains (1) summary

pfam02453
Location:67 → 231

Reticulon
NM_201430.3 → NP_958833.1 reticulon-3 isoform d

See identical proteins and their annotated locations for NP_958833.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (d) is longer and has a distinct C-terminus, compared to isoform a.

Source sequence(s)

AY427821, BK001685

Consensus CDS

CCDS8048.1

UniProtKB/Swiss-Prot

O95197

Related

ENSP00000340903.2, ENST00000341307.6

Conserved Domains (1) summary

pfam02453
Location:48 → 203

Reticulon; Reticulon

RNA

NR_049750.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (8) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AY427821, BK001682
NR_049751.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (9) lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK297533, AY427821

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

63681450..63759891

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011544730.3 → XP_011543032.1 reticulon-3 isoform X1

UniProtKB/TrEMBL

B7Z8W8

Conserved Domains (1) summary

pfam02453
Location:844 → 999

Reticulon; Reticulon
XM_011544731.3 → XP_011543033.1 reticulon-3 isoform X4

Conserved Domains (1) summary

pfam02453
Location:67 → 222

Reticulon; Reticulon
XM_017017091.2 → XP_016872580.1 reticulon-3 isoform X2

UniProtKB/TrEMBL

B7Z8W8
XM_017017092.2 → XP_016872581.1 reticulon-3 isoform X3

UniProtKB/TrEMBL

B7Z8W8