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RTN4 reticulon 4 [ Homo sapiens (human) ]

Gene ID: 57142, updated on 1-Jun-2020

Summary

Official Symbol
RTN4provided by HGNC
Official Full Name
reticulon 4provided by HGNC
Primary source
HGNC:HGNC:14085
See related
Ensembl:ENSG00000115310 MIM:604475
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
ASY; NSP; NOGO; RTN-X; NSP-CL; RTN4-A; RTN4-C; RTN4-B1; RTN4-B2; NI220/250; Nbla00271; Nbla10545
Summary
This gene belongs to the family of reticulon encoding genes. Reticulons are associated with the endoplasmic reticulum, and are involved in neuroendocrine secretion or in membrane trafficking in neuroendocrine cells. The product of this gene is a potent neurite outgrowth inhibitor which may also help block the regeneration of the central nervous system in higher vertebrates. Alternatively spliced transcript variants derived both from differential splicing and differential promoter usage and encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in fat (RPKM 122.1), brain (RPKM 104.7) and 24 other tissues See more
Orthologs

Genomic context

See RTN4 in Genome Data Viewer
Location:
2p16.1
Exon count:
17
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (54972189..55137831, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (55199325..55307770, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene EML6 antisense RNA 1 Neighboring gene EMAP like 6 Neighboring gene RNA, U7 small nuclear 81 pseudogene Neighboring gene RNA, U6 small nuclear 433, pseudogene Neighboring gene uncharacterized LOC105374662 Neighboring gene Sharpr-MPRA regulatory region 4359 Neighboring gene Sharpr-MPRA regulatory region 647 Neighboring gene CRISPRi-validated cis-regulatory element chr2.2087 Neighboring gene uncharacterized LOC105374674

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

Protein interactions

Protein Gene Interaction Pubs
Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of reticulon 4 (RTN4) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed
Vpu vpu HIV-1 Vpu is identified to have a physical interaction with reticulon 4 (RTN4) 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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: CLHC1

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
cadherin binding HDA PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
apoptotic process NAS
Non-traceable Author Statement
more info
PubMed 
axonal fasciculation ISS
Inferred from Sequence or Structural Similarity
more info
 
blastocyst formation IEA
Inferred from Electronic Annotation
more info
 
cardiac epithelial to mesenchymal transition IEA
Inferred from Electronic Annotation
more info
 
cellular sphingolipid homeostasis IEA
Inferred from Electronic Annotation
more info
 
cerebral cortex radial glia guided migration ISS
Inferred from Sequence or Structural Similarity
more info
 
endoplasmic reticulum tubular network formation IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum tubular network membrane organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
endoplasmic reticulum tubular network organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of axon extension IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of axonogenesis TAS
Traceable Author Statement
more info
 
negative regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
PubMed 
nuclear pore complex assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of ERBB3 signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of epithelial cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of mammary gland epithelial cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of protein kinase B signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of protein localization to endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of toll-like receptor 9 signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
protein localization to lysosome ISS
Inferred from Sequence or Structural Similarity
more info
 
protein stabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of apoptotic process NAS
Non-traceable Author Statement
more info
PubMed 
regulation of branching morphogenesis of a nerve ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cell IEA
Inferred from Electronic Annotation
more info
 
cell projection IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum HDA PubMed 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 
endoplasmic reticulum NAS
Non-traceable Author Statement
more info
PubMed 
endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum tubular network IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum tubular network membrane IDA
Inferred from Direct Assay
more info
PubMed 
integral component of endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
nuclear envelope IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
postsynaptic density IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
reticulon-4
Names
Human NogoA
My043 protein
foocen
neurite growth inhibitor 220
neurite outgrowth inhibitor
neuroendocrine-specific protein C homolog
reticulon 5

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.

Genomic

  1. NG_029037.2 RefSeqGene

    Range
    92381..170643
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001321859.2NP_001308788.1  reticulon-4 isoform E

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6), along with variants 5, 7, 8, 9, 10, and 11, encodes isoform E.
    Source sequence(s)
    AC093165, AY123245, BC150182
    Consensus CDS
    CCDS1852.1
    UniProtKB/Swiss-Prot
    Q9NQC3
    Related
    ENSP00000385650.1, ENST00000404909.5
    Conserved Domains (1) summary
    pfam02453
    Location:799963
    Reticulon; Reticulon
  2. NM_001321860.1NP_001308789.1  reticulon-4 isoform E

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7), along with variants 5, 6, 8, 9, 10, and 11, encodes isoform E.
    Source sequence(s)
    AY123246, BC150182
    Consensus CDS
    CCDS1852.1
    UniProtKB/Swiss-Prot
    Q9NQC3
    Related
    ENSP00000378109.2, ENST00000394611.6
    Conserved Domains (1) summary
    pfam02453
    Location:799963
    Reticulon; Reticulon
  3. NM_001321861.1NP_001308790.1  reticulon-4 isoform E

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8), along with variants 5, 6, 7, 9, 10, and 11, encodes isoform E.
    Source sequence(s)
    AY123247, BC150182
    Consensus CDS
    CCDS1852.1
    UniProtKB/Swiss-Prot
    Q9NQC3
    Conserved Domains (1) summary
    pfam02453
    Location:799963
    Reticulon; Reticulon
  4. NM_001321862.1NP_001308791.1  reticulon-4 isoform E

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9), along with variants 5, 6, 7, 8, and 10, encodes isoform E.
    Source sequence(s)
    AY123249, BC150182, DB094021
    Consensus CDS
    CCDS1852.1
    UniProtKB/Swiss-Prot
    Q9NQC3
    Conserved Domains (1) summary
    pfam02453
    Location:799963
    Reticulon; Reticulon
  5. NM_001321863.2NP_001308792.1  reticulon-4 isoform E

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10), along with variants 5, 6, 7, 8, 9, and 11, encodes isoform E.
    Source sequence(s)
    AC093165, AY123250, BC150182
    Consensus CDS
    CCDS1852.1
    UniProtKB/Swiss-Prot
    Q9NQC3
    Related
    ENSP00000384471.1, ENST00000405240.5
    Conserved Domains (1) summary
    pfam02453
    Location:799963
    Reticulon; Reticulon
  6. NM_001321904.2NP_001308833.1  reticulon-4 isoform E

    Status: REVIEWED

    Description
    Transcript Variant: This variant (11), along with variants 5, 6, 7, 8, 9, and 10, encodes isoform E.
    Source sequence(s)
    AC013414, AC092461, AC093165, BC150182
    Consensus CDS
    CCDS1852.1
    UniProtKB/Swiss-Prot
    Q9NQC3
    Conserved Domains (1) summary
    pfam02453
    Location:799963
    Reticulon; Reticulon
  7. NM_007008.3NP_008939.1  reticulon-4 isoform C

    See identical proteins and their annotated locations for NP_008939.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3), also known as Foocen-S and Nogo-C, differs in the 5' UTR and the 5' coding region, compared to variant 1. The resulting isoform (C) contains a distinct N-terminus, compared to isoform A.
    Source sequence(s)
    AF125103, AF132048, AI671568, AY102276
    Consensus CDS
    CCDS42685.1
    UniProtKB/Swiss-Prot
    Q9NQC3
    Related
    ENSP00000378107.2, ENST00000394609.6
    Conserved Domains (1) summary
    pfam02453
    Location:12176
    Reticulon; Reticulon
  8. NM_020532.5NP_065393.1  reticulon-4 isoform A

    See identical proteins and their annotated locations for NP_065393.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), also known as Nogo-A and RTN-XL, represents the longest transcript, and encodes the longest isoform (A).
    Source sequence(s)
    AF125103, AF132048, AY123250, BC016165
    Consensus CDS
    CCDS42684.1
    UniProtKB/Swiss-Prot
    Q9NQC3
    Related
    ENSP00000337838.6, ENST00000337526.11
    Conserved Domains (1) summary
    pfam02453
    Location:10051169
    Reticulon; Reticulon
  9. NM_153828.3NP_722550.1  reticulon-4 isoform B

    See identical proteins and their annotated locations for NP_722550.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), also known as Foocen-M, Nogo-B, RTN-XS and RTN4-B1, lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (B), that is missing an internal segment, compared to isoform A.
    Source sequence(s)
    AF125103, AF132048, AY123250, BC016165
    Consensus CDS
    CCDS1851.1
    UniProtKB/Swiss-Prot
    Q9NQC3
    Related
    ENSP00000322147.7, ENST00000317610.11
    Conserved Domains (1) summary
    pfam02453
    Location:186350
    Reticulon; Reticulon
  10. NM_207520.2NP_997403.1  reticulon-4 isoform D

    See identical proteins and their annotated locations for NP_997403.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), also known as Foocen-m2 and RTN4-B2, lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (D), that is missing an internal segment, compared to isoform A.
    Source sequence(s)
    AF125103, AF132048, AY123250, BC016165
    Consensus CDS
    CCDS42683.1
    UniProtKB/Swiss-Prot
    Q9NQC3
    Related
    ENSP00000350365.4, ENST00000357732.8
    Conserved Domains (1) summary
    pfam02453
    Location:205369
    Reticulon; Reticulon
  11. NM_207521.2NP_997404.1  reticulon-4 isoform E

    See identical proteins and their annotated locations for NP_997404.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5), also known as hRTN4-E, differs in the 5' UTR and the 5' coding region, compared to variant 1. The resulting isoform (E) has a shorter N-terminus, compared to isoform A. This variant (5), along with variants 6, 7, 8, 9, 10, and 11, encodes isoform E.
    Source sequence(s)
    AF125103, AF132048, AF333336, AY123250, BC016165
    Consensus CDS
    CCDS1852.1
    UniProtKB/Swiss-Prot
    Q9NQC3
    Related
    ENSP00000349944.3, ENST00000357376.7
    Conserved Domains (1) summary
    pfam02453
    Location:799963
    Reticulon; Reticulon

RNA

  1. NR_135829.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AY123247, BC150182, CN429712
  2. NR_135830.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AF333336, BC150182

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_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    54972189..55137831 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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