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Aliases for RTN3 Gene

Aliases for RTN3 Gene

  • Reticulon 3 2 3 5
  • Neuroendocrine-Specific Protein-Like 2 2 3 4
  • Homolog Of ASY Protein 2 3 4
  • NSP-Like Protein II 2 3 4
  • Neuroendocrine-Specific Protein-Like II 3 4
  • ASY Interacting Protein 2 3
  • NSP-Like Protein 2 3 4
  • NSPLII 3 4
  • ASYIP 3 4
  • NSPL2 3 4
  • HAP 3 4
  • Isoforme III 2
  • Reticulon-3 3
  • RTN3-A1 3

External Ids for RTN3 Gene

Previous GeneCards Identifiers for RTN3 Gene

  • GC11P065970
  • GC11P065024
  • GC11P063224
  • GC11P063205
  • GC11P063448
  • GC11P059778

Summaries for RTN3 Gene

Entrez Gene Summary for RTN3 Gene

  • 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]

GeneCards Summary for RTN3 Gene

RTN3 (Reticulon 3) is a Protein Coding gene. Diseases associated with RTN3 include Retinitis Pigmentosa 23 and Alzheimer Disease. Among its related pathways are Protein-protein interactions at synapses and SALM protein interactions at the synapses. An important paralog of this gene is RTN4.

UniProtKB/Swiss-Prot for RTN3 Gene

  • May be involved in membrane trafficking in the early secretory pathway. Inhibits BACE1 activity and amyloid precursor protein processing. May induce caspase-8 cascade and apoptosis. May favor BCL2 translocation to the mitochondria upon endoplasmic reticulum stress. In case of enteroviruses infection, RTN3 may be involved in the viral replication or pathogenesis. Induces the formation of endoplasmic reticulum tubules (PubMed:25612671).

Gene Wiki entry for RTN3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RTN3 Gene

Genomics for RTN3 Gene

Regulatory Elements for RTN3 Gene

Enhancers for RTN3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11G063718 1 dbSUPER 19.9 +39.9 39861 6.1 ATF1 FOXA2 TCF12 ZNF766 GATA2 SP5 NFIL3 SMARCA4 HMBOX1 NBN ATL3 RTN3 PLA2G16 ENSG00000256789 ENSG00000203520 C11orf84 ENSG00000271100 GC11M063761
GH11G063865 1.6 Ensembl ENCODE dbSUPER 10.2 +189.0 189015 9.8 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 YY1 SLC30A9 ZNF143 NAA40 MARK2 C11orf84 RTN3 PLA2G16 LOC105369340 GC11M063862 RNU6-1306P
GH11G063862 1.4 Ensembl ENCODE dbSUPER 10.2 +181.6 181583 1.4 ELF3 FOXA2 MLX ARID4B ZNF48 ZSCAN9 RAD21 RARA YY1 MIXL1 MARK2 NAA40 C11orf84 RTN3 ENSG00000256341 COX8A GC11M063862 RNU6-1306P
GH11G063478 1.3 Ensembl ENCODE dbSUPER 10.2 -202.3 -202305 0.3 HDGF RB1 ARNT RAD21 YY1 RFX5 GATA2 ZNF143 DEK ZNF654 ENSG00000256789 ENSG00000203520 PLA2G16 HRASLS2 RTN3 LOC100533643 HRASLS5
GH11G063713 0.6 dbSUPER 20.2 +33.9 33882 4.3 SOX5 SOX13 FOXA2 ZBTB33 CUX1 KDM1A FOXA1 ATL3 RTN3 PLA2G16 ENSG00000203520 ENSG00000256789 ENSG00000271100 GC11M063761
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RTN3 on UCSC Golden Path with GeneCards custom track

Promoters for RTN3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000040554 740 2201 PKNOX1 FOXA2 CREB3L1 ARNT WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2

Genomic Location for RTN3 Gene

Chromosome:
11
Start:
63,681,360 bp from pter
End:
63,759,891 bp from pter
Size:
78,532 bases
Orientation:
Plus strand

Genomic View for RTN3 Gene

Genes around RTN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RTN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RTN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RTN3 Gene

Proteins for RTN3 Gene

  • Protein details for RTN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95197-RTN3_HUMAN
    Recommended name:
    Reticulon-3
    Protein Accession:
    O95197
    Secondary Accessions:
    • B3KQS2
    • B7Z308
    • B7Z4M0
    • F5H774
    • Q147U9
    • Q496K2
    • Q53GN3
    • Q59EP0
    • Q5UEP2
    • Q6T930
    • Q7RTM7
    • Q7RTM8
    • Q7RTN3

    Protein attributes for RTN3 Gene

    Size:
    1032 amino acids
    Molecular mass:
    112611 Da
    Quaternary structure:
    • Homodimer. Interacts with ATL1 (By similarity). Interacts with RTN4. Isoform 3 interacts with BACE1, BACE2, BCL2 and FADD. Interacts with Coxsackievirus A16, enterovirus 71 and poliovirus P2C proteins. Interacts with ATL2. Interacts with TMEM33 (By similarity). Interacts with ZFYVE27 and with KIF5A in a ZFYVE27-dependent manner (PubMed:21976701).
    SequenceCaution:
    • Sequence=BAD93008.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for RTN3 Gene

neXtProt entry for RTN3 Gene

Post-translational modifications for RTN3 Gene

  • Ubiquitination at Lys998 and isoforms=2, 3, 4, 71018
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RTN3 Gene

Domains & Families for RTN3 Gene

Protein Domains for RTN3 Gene

InterPro:
Blocks:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RTN3: view

No data available for Gene Families and UniProtKB/Swiss-Prot for RTN3 Gene

Function for RTN3 Gene

Molecular function for RTN3 Gene

GENATLAS Biochemistry:
reticulon 3,neuroendocrine protein,associated with the endoplasmic reticulum,expressed in neural tissues,particularly in the macular region of the retina
UniProtKB/Swiss-Prot Function:
May be involved in membrane trafficking in the early secretory pathway. Inhibits BACE1 activity and amyloid precursor protein processing. May induce caspase-8 cascade and apoptosis. May favor BCL2 translocation to the mitochondria upon endoplasmic reticulum stress. In case of enteroviruses infection, RTN3 may be involved in the viral replication or pathogenesis. Induces the formation of endoplasmic reticulum tubules (PubMed:25612671).
UniProtKB/Swiss-Prot Induction:
By endoplasmic reticulum stress (at protein level).

Gene Ontology (GO) - Molecular Function for RTN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
genes like me logo Genes that share ontologies with RTN3: view
genes like me logo Genes that share phenotypes with RTN3: view

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RTN3 Gene

Localization for RTN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RTN3 Gene

Endoplasmic reticulum membrane; Multi-pass membrane protein. Golgi apparatus membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RTN3 gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 5
golgi apparatus 3
cytosol 2

Gene Ontology (GO) - Cellular Components for RTN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005615 extracellular space TAS 10331947
GO:0005783 endoplasmic reticulum IDA --
GO:0005789 endoplasmic reticulum membrane IDA,IEA 24262037
GO:0005794 Golgi apparatus IEA --
genes like me logo Genes that share ontologies with RTN3: view

Pathways & Interactions for RTN3 Gene

genes like me logo Genes that share pathways with RTN3: view

Pathways by source for RTN3 Gene

Gene Ontology (GO) - Biological Process for RTN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006915 apoptotic process IEA --
GO:0016032 viral process IEA --
GO:0016192 vesicle-mediated transport IEA --
GO:0071786 endoplasmic reticulum tubular network organization IMP 18779370
genes like me logo Genes that share ontologies with RTN3: view

No data available for SIGNOR curated interactions for RTN3 Gene

Drugs & Compounds for RTN3 Gene

No Compound Related Data Available

Transcripts for RTN3 Gene

Unigene Clusters for RTN3 Gene

Reticulon 3:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for RTN3 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d · 4e · 4f ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8a · 8b · 8c ^ 9 ^ 10 ^ 11a · 11b · 11c
SP1: - - - - - - - - - -
SP2: - - - - - - - - - - -
SP3: - - - - - - - - -
SP4: - - - - - - - - -
SP5: - - - - - - -
SP6:
SP7: - - -
SP8:
SP9: - - - -
SP10: - -
SP11: - - -

Relevant External Links for RTN3 Gene

GeneLoc Exon Structure for
RTN3
ECgene alternative splicing isoforms for
RTN3

Expression for RTN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RTN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RTN3 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x4.7) and Brain - Anterior cingulate cortex (BA24) (x4.2).

Protein differential expression in normal tissues from HIPED for RTN3 Gene

This gene is overexpressed in Nasal epithelium (20.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RTN3 Gene



Protein tissue co-expression partners for RTN3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RTN3 Gene:

RTN3

SOURCE GeneReport for Unigene cluster for RTN3 Gene:

Hs.743229

mRNA Expression by UniProt/SwissProt for RTN3 Gene:

O95197-RTN3_HUMAN
Tissue specificity: Isoform 3 is widely expressed, with highest levels in brain, where it is enriched in neuronal cell bodies from gray matter (at protein level). Three times more abundant in macula than in peripheral retina. Isoform 1 is expressed at high levels in brain and at low levels in skeletal muscle. Isoform 2 is only found in melanoma.

Evidence on tissue expression from TISSUES for RTN3 Gene

  • Nervous system(5)
  • Kidney(4.8)
  • Eye(4.7)
  • Lung(3.4)
  • Intestine(3.1)
  • Blood(3)
  • Pancreas(2.9)
  • Skin(2.8)
genes like me logo Genes that share expression patterns with RTN3: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for RTN3 Gene

Orthologs for RTN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for RTN3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RTN3 34 35
  • 99.34 (n)
mouse
(Mus musculus)
Mammalia Rtn3 34 16 35
  • 80.43 (n)
rat
(Rattus norvegicus)
Mammalia Rtn3 34
  • 78.72 (n)
cow
(Bos Taurus)
Mammalia RTN3 35
  • 75 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RTN3 35
  • 74 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RTN3 35
  • 58 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RTN3 35
  • 44 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RTN3 35
  • 39 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.1940 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.19053 34
zebrafish
(Danio rerio)
Actinopterygii rtn3 35 35
  • 65 (a)
OneToMany
zgc56439 34
fruit fly
(Drosophila melanogaster)
Insecta Rtnl2 35
  • 26 (a)
ManyToMany
Rtnl1 35
  • 24 (a)
ManyToMany
CG42853 35
  • 16 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea ret-1 35
  • 6 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10170 35
  • 29 (a)
OneToMany
Species where no ortholog for RTN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RTN3 Gene

ENSEMBL:
Gene Tree for RTN3 (if available)
TreeFam:
Gene Tree for RTN3 (if available)

Paralogs for RTN3 Gene

Paralogs for RTN3 Gene

(3) SIMAP similar genes for RTN3 Gene using alignment to 6 proteins:

Pseudogenes.org Pseudogenes for RTN3 Gene

genes like me logo Genes that share paralogs with RTN3: view

Variants for RTN3 Gene

Sequence variations from dbSNP and Humsavar for RTN3 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs1000018794 -- 63,698,501(+) TGGCA(C/T)CATTT intron-variant
rs1000029911 -- 63,705,233(+) CTGTA(A/T)TCTCA intron-variant
rs1000034711 -- 63,735,455(+) GCTAT(C/G)TTCAT intron-variant
rs1000067106 -- 63,691,965(+) ATCCT(C/T)AGAAG intron-variant
rs1000071214 -- 63,698,117(+) TCTGT(C/G)ACCCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RTN3 Gene

Variant ID Type Subtype PubMed ID
esv2673702 CNV deletion 23128226
esv3626650 CNV loss 21293372
esv3626651 CNV loss 21293372
nsv1145539 CNV deletion 24896259
nsv555180 CNV loss 21841781
nsv825940 CNV loss 20364138
nsv832183 CNV loss 17160897
nsv975941 CNV duplication 23825009

Variation tolerance for RTN3 Gene

Residual Variation Intolerance Score: 6.01% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.21; 69.87% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RTN3 Gene

Human Gene Mutation Database (HGMD)
RTN3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RTN3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RTN3 Gene

Disorders for RTN3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for RTN3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
retinitis pigmentosa 23
  • rp23
alzheimer disease
  • alzheimer disease, late-onset
- elite association - COSMIC cancer census association via MalaCards
Search RTN3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for RTN3

Genetic Association Database (GAD)
RTN3
Human Genome Epidemiology (HuGE) Navigator
RTN3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RTN3
genes like me logo Genes that share disorders with RTN3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RTN3 Gene

Publications for RTN3 Gene

  1. Cloning of a novel member of the reticulon gene family (RTN3): gene structure and chromosomal localization to 11q13. (PMID: 10331947) Moreira E.F. … Rodriguez I.R. (Genomics 1999) 2 3 4 22 64
  2. Reticulon 3 mediates Bcl-2 accumulation in mitochondria in response to endoplasmic reticulum stress. (PMID: 17191123) Wan Q. … Liu Y. (Apoptosis 2007) 3 4 22 64
  3. Tissue specificity and regulation of the N-terminal diversity of reticulon 3. (PMID: 15350194) Di Scala F. … Loeffler J.-P. (Biochem. J. 2005) 3 4 22 64
  4. Identification of a new RTN3 transcript, RTN3-A1, and its distribution in adult mouse brain. (PMID: 15946766) Cai Y. … Yu L. (Brain Res. Mol. Brain Res. 2005) 3 4 22 64
  5. Pro-apoptotic ASY/Nogo-B protein associates with ASYIP. (PMID: 12811824) Qi B. … Yutsudo M. (J. Cell. Physiol. 2003) 3 4 22 64

Products for RTN3 Gene

  • Addgene plasmids for RTN3

Sources for RTN3 Gene

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