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RTN3 reticulon 3 [ Homo sapiens (human) ]

Gene ID: 10313, updated on 3-Apr-2024

Summary

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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
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Genomic context

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See RTN3 in Genome Data Viewer
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_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369335 Neighboring gene phospholipase A and acyltransferase 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:63368875-63369376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63372619-63373384 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:63378198-63378707 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63379461-63379961 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3436 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3437 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:63398741-63399940 Neighboring gene inner mitochondrial membrane peptidase subunit 1 pseudogene 1 Neighboring gene atlastin GTPase 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:63438213-63438714 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:63438715-63439214 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4874 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3441 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:63529087-63529846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3442 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3443 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3445 Neighboring gene zinc finger translocation associated Neighboring gene RNA, 7SL, cytoplasmic 596, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Reticulon-3 Promotes Endosome Maturation at ER Membrane Contact Sites. Wu H, et al. Dev Cell, 2021 Jan 11. PMID 33434526, Free PMC Article
  2. Reticulon-3 modulates the incorporation of replication competent hepatitis C virus molecules for release inside infectious exosomes. Li J, et al. PLoS One, 2020. PMID 32941510, Free PMC Article
  3. Full length RTN3 regulates turnover of tubular endoplasmic reticulum via selective autophagy. Grumati P, et al. Elife, 2017 Jun 15. PMID 28617241, Free PMC Article
  4. Intrahepatic HCV RNA Level and Genotype 1 Independently Associate with Hepatic Reticulon 3 Expression. Lin CL, et al. Anticancer Res, 2017 Jun. PMID 28551625
  5. Preventing formation of reticulon 3 immunoreactive dystrophic neurites improves cognitive function in mice. Shi Q, et al. J Neurosci, 2013 Feb 13. PMID 23407961, Free PMC Article

See all (115) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. RTN3 and RTN4: Architects of SARS-CoV-2 replication organelles.
    Title: RTN3 and RTN4: Architects of SARS-CoV-2 replication organelles.
  3. 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.
  4. 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.
  5. Role of VAMP7-Dependent Secretion of Reticulon 3 in Neurite Growth.
    Title: Role of VAMP7-Dependent Secretion of Reticulon 3 in Neurite Growth.
  6. 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.
  7. 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.
  8. Reticulon-3 Promotes Endosome Maturation at ER Membrane Contact Sites.
    Title: Reticulon-3 Promotes Endosome Maturation at ER Membrane Contact Sites.
  9. 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.
  10. 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)

Genotypes

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

Pathways from PubChem

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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

Homology

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)

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  1. 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

  2. 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

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    63681450..63759891
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    B7Z8W8
    Conserved Domains (1) summary
    pfam02453
    Location:844 → 999
    Reticulon; Reticulon

  2. XM_011544731.3 → XP_011543033.1  reticulon-3 isoform X4

    Conserved Domains (1) summary
    pfam02453
    Location:67 → 222
    Reticulon; Reticulon

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

    UniProtKB/TrEMBL
    B7Z8W8

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

    UniProtKB/TrEMBL
    B7Z8W8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    63670790..63749258
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054367449.1 → XP_054223424.1  reticulon-3 isoform X1

  2. XM_054367452.1 → XP_054223427.1  reticulon-3 isoform X4

  3. XM_054367450.1 → XP_054223425.1  reticulon-3 isoform X2

  4. XM_054367451.1 → XP_054223426.1  reticulon-3 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O95197.2 GenPept UniProtKB/Swiss-Prot:O95197

Gene LinkOut

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