Human Gene RTN3 (ENST00000377819.10_7) from GENCODE V47lift37
  Description: reticulon 3, transcript variant 5 (from RefSeq NM_001265589.2)
Gencode Transcript: ENST00000377819.10_7
Gencode Gene: ENSG00000133318.14_15
Transcript (Including UTRs)
   Position: hg19 chr11:63,448,972-63,527,354 Size: 78,383 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr11:63,449,109-63,525,673 Size: 76,565 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:63,448,972-63,527,354)mRNA (may differ from genome)Protein (1032 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RTN3_HUMAN
DESCRIPTION: RecName: Full=Reticulon-3; AltName: Full=Neuroendocrine-specific protein-like 2; Short=NSP-like protein 2; AltName: Full=Neuroendocrine-specific protein-like II; Short=NSP-like protein II; Short=NSPLII;
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.
SUBUNIT: 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.
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein. Golgi apparatus membrane; Multi-pass membrane protein.
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.
INDUCTION: By endoplasmic reticulum stress (at protein level).
SIMILARITY: Contains 1 reticulon domain.
SEQUENCE CAUTION: Sequence=BAD93008.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 252.00 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 2623.21 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -30.30137-0.221 Picture PostScript Text
3' UTR -449.301681-0.267 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003388 - Reticulon

Pfam Domains:
PF02453 - Reticulon

ModBase Predicted Comparative 3D Structure on O95197
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0006915 apoptotic process
GO:0016032 viral process
GO:0016192 vesicle-mediated transport
GO:0071786 endoplasmic reticulum tubular network organization
GO:0071787 endoplasmic reticulum tubular network assembly

Cellular Component:
GO:0000139 Golgi membrane
GO:0005615 extracellular space
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  LF385278 - JP 2014500723-A/192781: Polycomb-Associated Non-Coding RNAs.
LP895220 - Sequence 84 from Patent EP3253886.
AY427821 - Homo sapiens reticulon 3-A (RTN3) mRNA, complete cds.
AY750848 - Homo sapiens RTN3-A1 (RTN3) mRNA, complete cds.
AK309766 - Homo sapiens cDNA, FLJ99807.
AK304100 - Homo sapiens cDNA FLJ54729 complete cds, highly similar to Homo sapiens reticulon 3 (RTN3), transcript variant 2, mRNA.
AK297533 - Homo sapiens cDNA FLJ59931 complete cds, highly similar to Reticulon-3.
AK307811 - Homo sapiens cDNA, FLJ97759.
AK075412 - Homo sapiens cDNA PSEC0103 fis, clone NT2RP2004755, highly similar to Reticulon-3.
BC011394 - Homo sapiens reticulon 3, mRNA (cDNA clone IMAGE:3873400), complete cds.
AK295534 - Homo sapiens cDNA FLJ50772 complete cds, highly similar to Reticulon-3.
AK308083 - Homo sapiens cDNA, FLJ98031.
BC022993 - Homo sapiens reticulon 3, mRNA (cDNA clone IMAGE:4940867), complete cds.
AB209771 - Homo sapiens mRNA for reticulon 3 isoform a variant protein.
AK222898 - Homo sapiens mRNA for reticulon 3 isoform a variant, clone: HRC01821.
AF059524 - Homo sapiens reticulon gene family protein (RTN3) mRNA, complete cds.
AF119297 - Homo sapiens neuroendocrine-specific protein-like protein 1 (NSPL1) mRNA, complete cds.
BC100822 - Homo sapiens reticulon 3, mRNA (cDNA clone IMAGE:40001104), complete cds.
BC100823 - Homo sapiens reticulon 3, mRNA (cDNA clone IMAGE:40001106), complete cds.
BC118550 - Homo sapiens reticulon 3, mRNA (cDNA clone IMAGE:40010300), complete cds.
BC118628 - Homo sapiens reticulon 3, mRNA (cDNA clone IMAGE:40010298), complete cds.
JD211130 - Sequence 192154 from Patent EP1572962.
AK295758 - Homo sapiens cDNA FLJ60267 complete cds, highly similar to Homo sapiens reticulon 3 (RTN3), transcript variant 2, mRNA.
BC010556 - Homo sapiens reticulon 3, mRNA (cDNA clone IMAGE:4154804), complete cds.
BC105982 - Homo sapiens reticulon 3, mRNA (cDNA clone IMAGE:6139199), complete cds.
JD204269 - Sequence 185293 from Patent EP1572962.
LF344689 - JP 2014500723-A/152192: Polycomb-Associated Non-Coding RNAs.
BC000634 - Homo sapiens reticulon 3, mRNA (cDNA clone IMAGE:3344908), complete cds.
AK295361 - Homo sapiens cDNA FLJ51855 complete cds, highly similar to Homo sapiens reticulon 3 (RTN3), transcript variant 3, mRNA.
JD183440 - Sequence 164464 from Patent EP1572962.
BC105981 - Homo sapiens reticulon 3, mRNA (cDNA clone IMAGE:6138716), complete cds.
AK297529 - Homo sapiens cDNA FLJ52565 complete cds, highly similar to Reticulon-3.
JD128793 - Sequence 109817 from Patent EP1572962.
JD394109 - Sequence 375133 from Patent EP1572962.
LF344688 - JP 2014500723-A/152191: Polycomb-Associated Non-Coding RNAs.
AB591013 - Synthetic construct DNA, clone: pFN21AE0054, Homo sapiens RTN3 gene for reticulon 3, without stop codon, in Flexi system.
BC148632 - Synthetic construct Homo sapiens clone IMAGE:100015582, MGC:183106 reticulon 3 (RTN3) mRNA, encodes complete protein.
CU679745 - Synthetic construct Homo sapiens gateway clone IMAGE:100016847 5' read RTN3 mRNA.
KJ893003 - Synthetic construct Homo sapiens clone ccsbBroadEn_02397 RTN3 gene, encodes complete protein.
AK127079 - Homo sapiens cDNA FLJ45136 fis, clone BRAWH3038324, highly similar to Reticulon protein 3.
AK094965 - Homo sapiens cDNA FLJ37646 fis, clone BRHIP2000312, highly similar to Homo sapiens reticulon gene family protein (RTN3) mRNA.
AK122727 - Homo sapiens cDNA FLJ16232 fis, clone FEBRA2027742, highly similar to Homo sapiens reticulon gene family protein (RTN3) mRNA.
LF344672 - JP 2014500723-A/152175: Polycomb-Associated Non-Coding RNAs.
LF344670 - JP 2014500723-A/152173: Polycomb-Associated Non-Coding RNAs.
LF344669 - JP 2014500723-A/152172: Polycomb-Associated Non-Coding RNAs.
LF344668 - JP 2014500723-A/152171: Polycomb-Associated Non-Coding RNAs.
JD263613 - Sequence 244637 from Patent EP1572962.
JD560258 - Sequence 541282 from Patent EP1572962.
JD331222 - Sequence 312246 from Patent EP1572962.
JD161215 - Sequence 142239 from Patent EP1572962.
LF344667 - JP 2014500723-A/152170: Polycomb-Associated Non-Coding RNAs.
JD314997 - Sequence 296021 from Patent EP1572962.
JD539074 - Sequence 520098 from Patent EP1572962.
JD215370 - Sequence 196394 from Patent EP1572962.
JD085968 - Sequence 66992 from Patent EP1572962.
JD282468 - Sequence 263492 from Patent EP1572962.
JD496307 - Sequence 477331 from Patent EP1572962.
JD490925 - Sequence 471949 from Patent EP1572962.
LF211222 - JP 2014500723-A/18725: Polycomb-Associated Non-Coding RNAs.
LF344666 - JP 2014500723-A/152169: Polycomb-Associated Non-Coding RNAs.
BC000865 - Homo sapiens, clone IMAGE:3460093, mRNA, partial cds.
JD490569 - Sequence 471593 from Patent EP1572962.
LF344665 - JP 2014500723-A/152168: Polycomb-Associated Non-Coding RNAs.
JD241496 - Sequence 222520 from Patent EP1572962.
JD269148 - Sequence 250172 from Patent EP1572962.
JD251461 - Sequence 232485 from Patent EP1572962.
LF344664 - JP 2014500723-A/152167: Polycomb-Associated Non-Coding RNAs.
JD079237 - Sequence 60261 from Patent EP1572962.
JD218638 - Sequence 199662 from Patent EP1572962.
JD203469 - Sequence 184493 from Patent EP1572962.
JD363644 - Sequence 344668 from Patent EP1572962.
LF344663 - JP 2014500723-A/152166: Polycomb-Associated Non-Coding RNAs.
MA620855 - JP 2018138019-A/192781: Polycomb-Associated Non-Coding RNAs.
MA580266 - JP 2018138019-A/152192: Polycomb-Associated Non-Coding RNAs.
MA580265 - JP 2018138019-A/152191: Polycomb-Associated Non-Coding RNAs.
MA580249 - JP 2018138019-A/152175: Polycomb-Associated Non-Coding RNAs.
MA580247 - JP 2018138019-A/152173: Polycomb-Associated Non-Coding RNAs.
MA580246 - JP 2018138019-A/152172: Polycomb-Associated Non-Coding RNAs.
MA580245 - JP 2018138019-A/152171: Polycomb-Associated Non-Coding RNAs.
MA580244 - JP 2018138019-A/152170: Polycomb-Associated Non-Coding RNAs.
MA580243 - JP 2018138019-A/152169: Polycomb-Associated Non-Coding RNAs.
MA580242 - JP 2018138019-A/152168: Polycomb-Associated Non-Coding RNAs.
MA580241 - JP 2018138019-A/152167: Polycomb-Associated Non-Coding RNAs.
MA580240 - JP 2018138019-A/152166: Polycomb-Associated Non-Coding RNAs.
MA446799 - JP 2018138019-A/18725: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O95197 (Reactome details) participates in the following event(s):

R-HSA-8849882 SALMs 1-4 bind reticulon 3
R-HSA-8849932 Synaptic adhesion-like molecules
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: ASYIP, B3KQS2, B7Z308, B7Z4M0, ENST00000377819.1, ENST00000377819.2, ENST00000377819.3, ENST00000377819.4, ENST00000377819.5, ENST00000377819.6, ENST00000377819.7, ENST00000377819.8, ENST00000377819.9, F5H774, NM_001265589, NSPL2, O95197, Q147U9, Q496K2, Q53GN3, Q59EP0, Q5UEP2, Q6T930, Q7RTM7, Q7RTM8, Q7RTN3, RTN3_HUMAN, uc318nwi.1, uc318nwi.2
UCSC ID: ENST00000377819.10_7
RefSeq Accession: NM_001265589.2
Protein: O95197 (aka RTN3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.