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    RTN3 reticulon 3 [ Homo sapiens (human) ]

    Gene ID: 10313, updated on 3-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (63681450..63759891)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (63670790..63749258)
    RS_2024_09 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 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. 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
    2. Reticulon-3 Promotes Endosome Maturation at ER Membrane Contact Sites. Wu H, et al. Dev Cell, 2021 Jan 11. PMID 33434526, Free PMC Article
    3. Co-involvement of the mitochondria and endoplasmic reticulum in cell death induced by the novel ER-targeted protein HAP. Xu H, et al. Cell Mol Biol Lett, 2006. PMID 16847569, Free PMC Article
    4. 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
    5. Reticulon 3 binds the 2C protein of enterovirus 71 and is required for viral replication. Tang WF, et al. J Biol Chem, 2007 Feb 23. PMID 17182608

    See all (129) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RTN3L and CALCOCO1 function in parallel to maintain proteostasis in the endoplasmic reticulum.
      Title: RTN3L and CALCOCO1 function in parallel to maintain proteostasis in the endoplasmic reticulum.
    2. 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.
    3. RTN3 and RTN4: Architects of SARS-CoV-2 replication organelles.
      Title: RTN3 and RTN4: Architects of SARS-CoV-2 replication organelles.
    4. 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.
    5. 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.
    6. Role of VAMP7-Dependent Secretion of Reticulon 3 in Neurite Growth.
      Title: Role of VAMP7-Dependent Secretion of Reticulon 3 in Neurite Growth.
    7. 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.
    8. 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.
    9. Reticulon-3 Promotes Endosome Maturation at ER Membrane Contact Sites.
      Title: Reticulon-3 Promotes Endosome Maturation at ER Membrane Contact Sites.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (45)

    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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    NEW Try the new Transcript table

    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_2024_08

    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

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