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RTN3 reticulon 3 [ Homo sapiens (human) ]

Gene ID: 10313, updated on 29-Mar-2020

Summary

Official Symbol
RTN3provided by HGNC
Official Full Name
reticulon 3provided by HGNC
Primary source
HGNC:HGNC:10469
See related
Ensembl:ENSG00000133318 MIM:604249
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

Genomic context

See RTN3 in Genome Data Viewer
Location:
11q13.1
Exon count:
11
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (63681315..63759891)
105 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 uncharacterized LOC107984336 Neighboring gene inner mitochondrial membrane peptidase subunit 1 pseudogene 1 Neighboring gene atlastin GTPase 3 Neighboring gene chromosome 11 open reading frame 95 Neighboring gene RNA, 7SL, cytoplasmic 596, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum tubular network formation IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum tubular network organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
vesicle-mediated transport IEA
Inferred from Electronic Annotation
more info
 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 
endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
extracellular space TAS
Traceable Author Statement
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
synapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

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)

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_001265589.2NP_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
    O95197
    Related
    ENSP00000367050.5, ENST00000377819.10
    Conserved Domains (1) summary
    pfam02453
    Location:8441008
    Reticulon; Reticulon
  2. NM_001265590.2NP_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/Swiss-Prot
    O95197
    Related
    ENSP00000442733.1, ENST00000540798.5
    Conserved Domains (1) summary
    pfam02453
    Location:732896
    Reticulon; Reticulon
  3. NM_001265591.2NP_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:48107
    Reticulon; Reticulon
  4. NM_006054.4NP_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/Swiss-Prot
    O95197
    UniProtKB/TrEMBL
    A0A024R5C4
    Related
    ENSP00000440874.1, ENST00000537981.5
    Conserved Domains (1) summary
    pfam02453
    Location:48212
    Reticulon; Reticulon
  5. NM_201428.3NP_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/Swiss-Prot
    O95197
    Related
    ENSP00000344106.4, ENST00000339997.8
    Conserved Domains (1) summary
    pfam02453
    Location:825989
    Reticulon; Reticulon
  6. NM_201429.2NP_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:67231
    Reticulon; Reticulon
  7. NM_201430.3NP_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:48203
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    63681315..63759891
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (1) summary
    pfam02453
    Location:67222
    Reticulon; Reticulon
  2. XM_011544730.2XP_011543032.1  reticulon-3 isoform X1

    Conserved Domains (1) summary
    pfam02453
    Location:844999
    Reticulon; Reticulon
  3. XM_017017091.1XP_016872580.1  reticulon-3 isoform X2

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

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